From 776984b7488efcfd7cea7649db2e4f2683c7896e Mon Sep 17 00:00:00 2001 From: Niklas Schandry Date: Fri, 28 Aug 2026 08:59:35 +0200 Subject: [PATCH 01/17] lift annotations if use_ref is true and annotations are provided --- .../local/utils_nfcore_genomeassembler_pipeline/main.nf | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/subworkflows/local/utils_nfcore_genomeassembler_pipeline/main.nf b/subworkflows/local/utils_nfcore_genomeassembler_pipeline/main.nf index c50c171d..d8c47e1c 100644 --- a/subworkflows/local/utils_nfcore_genomeassembler_pipeline/main.nf +++ b/subworkflows/local/utils_nfcore_genomeassembler_pipeline/main.nf @@ -132,6 +132,7 @@ workflow PIPELINE_INITIALISATION { def merqury = it.merqury && !it.shortread_F ? false : it.merqury def group = it.group ?: null def use_short_reads = it.shortread_F && !params.use_short_reads ? true : it.use_short_reads + def lift_annotations= it.use_ref && it.ref_gff ? true : false it + [ group: group, assembler_ont: assembler_ont, @@ -139,7 +140,8 @@ workflow PIPELINE_INITIALISATION { polish: polish, merqury: merqury, use_short_reads: use_short_reads, - paired: it.shortread_F && it.shortread_R ? true : false + paired: it.shortread_F && it.shortread_R ? true : false, + lift_annotations: lift_annotations ] } From 58b6763d3d771abba75d8631569f42821580a7b6 Mon Sep 17 00:00:00 2001 From: Niklas Schandry Date: Fri, 28 Aug 2026 09:30:13 +0200 Subject: [PATCH 02/17] fix emit of ragtag scaffolding subworkflow --- subworkflows/local/scaffold/ragtag/main.nf | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/subworkflows/local/scaffold/ragtag/main.nf b/subworkflows/local/scaffold/ragtag/main.nf index d84b398f..f4d3e6f8 100644 --- a/subworkflows/local/scaffold/ragtag/main.nf +++ b/subworkflows/local/scaffold/ragtag/main.nf @@ -67,7 +67,7 @@ workflow RUN_RAGTAG { meryl_kmers) emit: - ch_main + ch_main = ch_main_scaffolded quast_out = QC.out.quast_out busco_out = QC.out.busco_out merqury_report_files = QC.out.merqury_report_files From 910878faced4d70faf9869e899fe81483d8e5ec8 Mon Sep 17 00:00:00 2001 From: Niklas Schandry Date: Fri, 28 Aug 2026 10:57:54 +0200 Subject: [PATCH 03/17] update usage to include information on samplesheet --- docs/usage.md | 3 +++ 1 file changed, 3 insertions(+) diff --git a/docs/usage.md b/docs/usage.md index 6f6e8869..245878f2 100644 --- a/docs/usage.md +++ b/docs/usage.md @@ -20,6 +20,9 @@ This pipeline can perform assembly, polishing, scaffolding using long-reads, HiC Since it is often difficult to know which tool, or assembly strategy will perform best on a dataset, `nf-core/genomeassembler` can also be used to compare outcomes of different approaches in one run. To compare different samples, a column named `group` is required, which should contain the same value for all samples that should be compared to each other. +`nf-core/genomeassembler` performs genome qc and summarizes the results in a report. +For more in-depth qc, `nf-core/genomeassembler` generates samplesheets that can be used as inputs for [`nf-core/genomeqc`](https://nf-co.re/genomeqc) in `genomeqc_samplesheet/`. There are two samplesheets, one containing only samplename and fasta, the other also containing paths to annotation files (only for samples where annotation liftover was performed). + ## Parameterization Parameters for this pipeline can either be supplied **globally**, e.g: From f181bdf94e7c97b572568bc41d05b6059a9c2997 Mon Sep 17 00:00:00 2001 From: Niklas Schandry Date: Fri, 28 Aug 2026 10:58:29 +0200 Subject: [PATCH 04/17] fix channel structure of (unused) scaffold output channel --- subworkflows/local/scaffold/main.nf | 32 ++++++++++++++--------------- 1 file changed, 15 insertions(+), 17 deletions(-) diff --git a/subworkflows/local/scaffold/main.nf b/subworkflows/local/scaffold/main.nf index bfe33b96..c7989c09 100644 --- a/subworkflows/local/scaffold/main.nf +++ b/subworkflows/local/scaffold/main.nf @@ -62,20 +62,20 @@ workflow SCAFFOLD { // Deal with cases that are single scaffold ch_main = links_out .filter {it -> !it.meta.scaffold_longstitch && !it.meta.scaffold_ragtag } - .map { meta -> [ meta: meta - meta.subMap("links_scaffold") + [ scaffolds: [ links: meta.scaffolds_links ] ] ]} + .map { meta -> meta - meta.subMap("links_scaffold") + [ scaffolds: [ links: meta.scaffolds_links ] ] } .mix( longstitch_out .filter {it -> !it.meta.scaffold_links && !it.meta.scaffold_ragtag } - .map { meta -> [ meta: meta - meta.subMap("scaffolds_longstitch") + [ scaffolds: [ longstitch: meta.scaffolds_longstitch ] ] ]} + .map { meta -> meta - meta.subMap("scaffolds_longstitch") + [ scaffolds: [ longstitch: meta.scaffolds_longstitch ] ] } ) .mix( ragtag_out .filter {it -> !it.meta.scaffold_links && !it.meta.scaffold_longstitch } - .map { meta -> [ meta: meta - meta.subMap("scaffolds_ragtag") + [ scaffolds: [ ragtag: meta.scaffolds_ragtag ] ] ]} + .map { meta -> meta - meta.subMap("scaffolds_ragtag") + [ scaffolds: [ ragtag: meta.scaffolds_ragtag ] ] } ) .mix( hic_out - .map { meta -> [ meta: meta - meta.subMap("scaffolds_hic") + [ scaffolds: [ hic: meta.scaffolds_hic ] ] ]} + .map { meta -> meta - meta.subMap("scaffolds_hic") + [ scaffolds: [ hic: meta.scaffolds_hic ] ] } ) // mix in those that are double scaffolded: , links-ragtag, longstitch-ragtag @@ -90,10 +90,10 @@ workflow SCAFFOLD { .map {meta -> [meta.id, meta]} ) .map { - _id, meta_links, meta_longstitch -> [ - meta: meta_links - + _id, meta_links, meta_longstitch -> + meta_links - meta_links.subMap("scaffolds_links") + - [scaffolds: [links: meta_links.scaffolds_links, longstitch: meta_longstitch.scaffolds_longstitch]] ] + [scaffolds: [links: meta_links.scaffolds_links, longstitch: meta_longstitch.scaffolds_longstitch]] } ) //links-ragtag @@ -107,10 +107,10 @@ workflow SCAFFOLD { .map {meta -> [meta.id, meta]} ) .map { - _id, meta_links, meta_ragtag -> [ - meta: meta_links - + _id, meta_links, meta_ragtag -> + meta_links - meta_links.subMap("scaffolds_links") + - [scaffolds: [links: meta_links.scaffolds_links, ragtag: meta_ragtag.scaffolds_ragtag]] ] + [ scaffolds: [ links: meta_links.scaffolds_links, ragtag: meta_ragtag.scaffolds_ragtag ] ] } ) //longstitch-ragtag @@ -124,10 +124,10 @@ workflow SCAFFOLD { .map {meta -> [meta.id, meta]} ) .map { - _id, meta_longstitch, meta_ragtag -> [ - meta: meta_longstitch - + _id, meta_longstitch, meta_ragtag -> + meta_longstitch - meta_longstitch.subMap("scaffolds_longstitch") + - [scaffolds: [longstitch: meta_longstitch.scaffolds_longstitch, ragtag: meta_ragtag.scaffolds_ragtag]] ] + [scaffolds: [ longstitch: meta_longstitch.scaffolds_longstitch, ragtag: meta_ragtag.scaffolds_ragtag ] ] } ) // mix in triple-scaffolded @@ -145,8 +145,8 @@ workflow SCAFFOLD { .map {meta -> [meta.id, meta]} ) .map { - _id, meta_links, meta_longstitch, meta_ragtag -> [ - meta: meta_links - + _id, meta_links, meta_longstitch, meta_ragtag -> + meta_links - meta_links.subMap("scaffolds_links") + [ scaffolds: [ @@ -155,11 +155,9 @@ workflow SCAFFOLD { ragtag: meta_ragtag.scaffolds_ragtag ] ] - ] } ) - links_busco = RUN_LINKS.out.busco_out links_quast = RUN_LINKS.out.quast_out links_merqury = RUN_LINKS.out.merqury_report_files From d8a4c9500b51838da6e3cd91643f7b8beb3cdeb2 Mon Sep 17 00:00:00 2001 From: Niklas Schandry Date: Fri, 28 Aug 2026 10:59:01 +0200 Subject: [PATCH 05/17] WIP commit of manifest writer --- workflows/genomeassembler.nf | 110 +++++++++++++++++++++++++++++++++++ 1 file changed, 110 insertions(+) diff --git a/workflows/genomeassembler.nf b/workflows/genomeassembler.nf index 89ad8a45..2dfb7047 100644 --- a/workflows/genomeassembler.nf +++ b/workflows/genomeassembler.nf @@ -228,6 +228,116 @@ workflow GENOMEASSEMBLER { _report = REPORT.out.report_html.toList() + /* + Prepare a samplesheet that is ready to use with nf-core/genomeqc. + This uses the published output paths, not the workdir files. + */ + /* + def ch_assembly_manifest = ch_main_scaffolded + .map { it -> + def meta = it.meta + def candidates = [ + // A list of filenames, corresponding and the candidate output folder + [ meta.scaffolds ? meta.scaffolds.ragtag ?: null : null, 'scaffold/ragtag' ], + [ meta.scaffolds ? meta.scaffolds.hic ?: null : null, 'scaffold/hic/yahs' ], + [ meta.scaffolds ? meta.scaffolds.longstitch ?: null : null, 'scaffold/longstitch' ], + [ meta.scaffolds ? meta.scaffolds.links ?: null : null, 'scaffold/links' ], + [ meta.polished ? meta.polished.pilon ?: null : null, 'polish/pilon' ], + [ meta.polished ? meta.polished.medaka ?: null : null, 'polish/medaka' ], + [ meta.polished ? meta.polished.dorado ?: null : null, 'polish/dorado' ], + [ meta.assembly, { + // Assembly publishdirs are a bit more specific + meta.strategy == "single" ? ( + meta.assembler_ont == "flye" || meta.assembler_hifi == "flye" + ? 'assembly/flye' + : 'assembly/hifiasm' + ) : + meta.strategy == "hybrid" + ? 'assembly/hifiasm' + : 'assembly/ragtag' + } + ], + ] + def chosen = candidates.find { entry -> entry[0] } + if( !chosen ) + return null + def assembly_file = chosen[0] + def subdir = chosen[1] + def fasta = "${params.outdir}/${meta.id}/${subdir}/${file(assembly_file).name}" + def subdir_gff = candidates[1] ==~ "assembly" ? "assembly" : candidates[1] + def gff = "${params.outdir}/${meta.id}/${subdir_gff}/*.gff3" + def annotation = files(gff) ? files(gff).first() : null + [ meta.id, fasta ] + } + .filter { row -> row != null } + ch_assembly_manifest.view {it -> "MANIFEST: $it"} + ch_assembly_manifest + .filter( { it -> it[2] != null} ) + .map {sample, fasta, annotation -> [sample,fasta,annotation].join(",")} + .map { rows -> "species,fasta,gff\n" + rows + "\n" } + .collectFile( + name: "nf-core-genomeqc-in-gff.csv", + storeDir: "${params.outdir}/genomeqc_samplesheet", + keepHeader: true, + skip: 1 + ) + + + */ + def outdir_uri = file(params.outdir).toUriString() + + def ch_assembly_manifest = ch_main_scaffolded + .map { it -> + def meta = it.meta + // A list of filenames, corresponding and the candidate output folder + [ + [ meta.id, meta.scaffolds ? meta.scaffolds.ragtag ?: null : null, 'scaffold/ragtag' ], + [ meta.id, meta.scaffolds ? meta.scaffolds.hic ?: null : null, 'scaffold/hic/yahs' ], + [ meta.id, meta.scaffolds ? meta.scaffolds.longstitch ?: null : null, 'scaffold/longstitch' ], + [ meta.id, meta.scaffolds ? meta.scaffolds.links ?: null : null, 'scaffold/links' ], + [ meta.id, meta.polished ? meta.polished.pilon ?: null : null, 'polish/pilon' ], + [ meta.id, meta.polished ? meta.polished.medaka ?: null : null, 'polish/medaka' ], + [ meta.id, meta.polished ? meta.polished.dorado ?: null : null, 'polish/dorado' ], + [ meta.id, meta.assembly, { + // Assembly publishdirs are a bit more specific + meta.strategy == "single" ? ( + meta.assembler_ont == "flye" || meta.assembler_hifi == "flye" + ? 'assembly/flye' + : 'assembly/hifiasm' + ) : + meta.strategy == "hybrid" + ? 'assembly/hifiasm' + : 'assembly/ragtag' + } + ] + ] + } + .view( {it -> "Manifest channel: $it"}) + /* + .filter { + _id, file, _subdir -> file != null + } + .map { + id, assembly_file, subdir -> + [ + file(assembly_file).name.baseName(), + {"${outdir_uri}/${id}/${subdir}/${file(assembly_file).name}"} + ] + } + + + ch_assembly_manifest + .map {sample, fasta -> [sample,fasta].join(",")} + .map { rows -> "species,fasta\n" + rows + "\n" } + .collectFile( + name: "nf-core-genomeqc-in-no-gff.csv", + storeDir: "${params.outdir}/genomeqc_samplesheet", + keepHeader: true, + skip: 1 + ) + */ + + emit: _report } From a6179fa8e3a5a9a7eccda9e50549708142654cb7 Mon Sep 17 00:00:00 2001 From: Niklas Schandry Date: Fri, 28 Aug 2026 14:51:25 +0200 Subject: [PATCH 06/17] fix scaffolding output channel --- subworkflows/local/scaffold/main.nf | 27 ++++++++++++++------------- 1 file changed, 14 insertions(+), 13 deletions(-) diff --git a/subworkflows/local/scaffold/main.nf b/subworkflows/local/scaffold/main.nf index c7989c09..0d54f8d9 100644 --- a/subworkflows/local/scaffold/main.nf +++ b/subworkflows/local/scaffold/main.nf @@ -60,22 +60,23 @@ workflow SCAFFOLD { ragtag_out = RUN_RAGTAG.out.ch_main // Deal with cases that are single scaffold + // !!! The individual sswfs return map-channels, this means that it -> it.meta needs to be used, otherwise there is a nesting ch_main = links_out .filter {it -> !it.meta.scaffold_longstitch && !it.meta.scaffold_ragtag } - .map { meta -> meta - meta.subMap("links_scaffold") + [ scaffolds: [ links: meta.scaffolds_links ] ] } + .map { it -> [meta: it.meta - it.meta.subMap("links_scaffold") + [ scaffolds: [ links: it.meta.scaffolds_links ] ] ] } .mix( longstitch_out .filter {it -> !it.meta.scaffold_links && !it.meta.scaffold_ragtag } - .map { meta -> meta - meta.subMap("scaffolds_longstitch") + [ scaffolds: [ longstitch: meta.scaffolds_longstitch ] ] } + .map { it -> [meta: it.meta - it.meta.subMap("scaffolds_longstitch") + [ scaffolds: [ longstitch: it.meta.scaffolds_longstitch ] ]] } ) .mix( ragtag_out .filter {it -> !it.meta.scaffold_links && !it.meta.scaffold_longstitch } - .map { meta -> meta - meta.subMap("scaffolds_ragtag") + [ scaffolds: [ ragtag: meta.scaffolds_ragtag ] ] } + .map { it -> [meta: it.meta - it.meta.subMap("scaffolds_ragtag") + [ scaffolds: [ ragtag: it.meta.scaffolds_ragtag ] ] ] } ) .mix( hic_out - .map { meta -> meta - meta.subMap("scaffolds_hic") + [ scaffolds: [ hic: meta.scaffolds_hic ] ] } + .map { it -> [meta: it.meta - it.meta.subMap("scaffolds_hic") + [ scaffolds: [ hic: it.meta.scaffolds_hic ] ] ]} ) // mix in those that are double scaffolded: , links-ragtag, longstitch-ragtag @@ -83,11 +84,11 @@ workflow SCAFFOLD { .mix( links_out .filter {it -> it.meta.scaffold_longstitch && !it.meta.scaffold_ragtag } - .map {meta -> [meta.id, meta]} + .map {it -> [it.meta.id, it.meta]} // Join without filtering, inner-join .join( longstitch_out - .map {meta -> [meta.id, meta]} + .map {it -> [it.meta.id, it.meta]} ) .map { _id, meta_links, meta_longstitch -> @@ -100,11 +101,11 @@ workflow SCAFFOLD { .mix( links_out .filter {it -> !it.meta.scaffold_longstitch && it.meta.scaffold_ragtag } - .map {meta -> [meta.id, meta]} + .map {it -> [it.meta.id, it.meta]} // Join without filtering, inner-join .join( ragtag_out - .map {meta -> [meta.id, meta]} + .map {it -> [it.meta.id, it.meta]} ) .map { _id, meta_links, meta_ragtag -> @@ -117,11 +118,11 @@ workflow SCAFFOLD { .mix( longstitch_out .filter {it -> !it.meta.scaffold_links && it.meta.scaffold_ragtag } - .map {meta -> [meta.id, meta]} + .map {it -> [it.meta.id, it.meta]} // Join without filtering, inner-join .join( ragtag_out - .map {meta -> [meta.id, meta]} + .map {it -> [it.meta.id, it.meta]} ) .map { _id, meta_longstitch, meta_ragtag -> @@ -134,15 +135,15 @@ workflow SCAFFOLD { .mix( links_out .filter {it -> it.meta.scaffold_longstitch && it.meta.scaffold_ragtag } - .map {meta -> [meta.id, meta]} + .map {it -> [it.meta.id, it.meta]} // Join without filtering, inner-join .join( longstitch_out - .map {meta -> [meta.id, meta]} + .map {it -> [it.meta.id, it.meta]} ) .join( ragtag_out - .map {meta -> [meta.id, meta]} + .map {it -> [it.meta.id, it.meta]} ) .map { _id, meta_links, meta_longstitch, meta_ragtag -> From 5e06e18d47cca6645390e530e4fbbfbb5789c1d3 Mon Sep 17 00:00:00 2001 From: Niklas Schandry Date: Fri, 28 Aug 2026 14:51:53 +0200 Subject: [PATCH 07/17] improve publishing of bgzipped files --- conf/modules/assembly.config | 14 +++++++++----- conf/modules/polishing.config | 6 ++++-- conf/modules/scaffolding.config | 12 ++++++++---- 3 files changed, 21 insertions(+), 11 deletions(-) diff --git a/conf/modules/assembly.config b/conf/modules/assembly.config index f33f81a1..17d9e119 100644 --- a/conf/modules/assembly.config +++ b/conf/modules/assembly.config @@ -26,7 +26,8 @@ process { withName: '.*BGZIP_FLYE.*' { publishDir = [ path: { "${params.outdir}/${meta.id}/assembly/flye/" }, - mode: params.publish_dir_mode + mode: params.publish_dir_mode, + saveAs: { filename -> filename.tokenize("/")[1]} ] } withName: HIFIASM { @@ -64,20 +65,23 @@ process { withName: BGZIP_HIFI { publishDir = [ path: { "${params.outdir}/${meta.id}/assembly/hifiasm/fasta" }, - mode: params.publish_dir_mode + mode: params.publish_dir_mode, + saveAs: { filename -> filename.tokenize("/")[1]} ] } withName: BGZIP_ONT { publishDir = [ path: { "${params.outdir}/${meta.id}/assembly/hifiasm_ont/fasta" }, - mode: params.publish_dir_mode + mode: params.publish_dir_mode, + saveAs: { filename -> filename.tokenize("/")[1]} ] } - withName: '.*ASSEMBLE:.*BZIP_RAGTAG.*' { + withName: '.*ASSEMBLE:.*BGZIP_RAGTAG.*' { publishDir = [ path: { "${params.outdir}/${meta.id}/assembly/ragtag/" }, - mode: params.publish_dir_mode + mode: params.publish_dir_mode, + saveAs: { filename -> filename.tokenize("/")[1]} ] } diff --git a/conf/modules/polishing.config b/conf/modules/polishing.config index c600e4f3..66a87f62 100644 --- a/conf/modules/polishing.config +++ b/conf/modules/polishing.config @@ -13,7 +13,8 @@ process { withName: '.*MEDAKA:BGZIP.*' { publishDir = [ path: { "${params.outdir}/${meta.id}/polish/medaka" }, - mode: params.publish_dir_mode + mode: params.publish_dir_mode, + saveAs: { filename -> filename.tokenize("/")[1]} ] } withName: '.*MEDAKA:UNZIP.*' { @@ -62,7 +63,8 @@ process { withName: '.*:POLISH_PILON:BGZIP:.*' { publishDir = [ path: { "${params.outdir}/${meta.id}/polish/pilon" }, - mode: params.publish_dir_mode + mode: params.publish_dir_mode, + saveAs: { filename -> filename.tokenize("/")[1]} ] } } diff --git a/conf/modules/scaffolding.config b/conf/modules/scaffolding.config index d7981830..dbc0ce1f 100644 --- a/conf/modules/scaffolding.config +++ b/conf/modules/scaffolding.config @@ -15,7 +15,8 @@ process { withName: '.*:RUN_RAGTAG:BGZIP.*' { publishDir = [ path: { "${params.outdir}/${meta.id}/scaffold/ragtag/" }, - mode: params.publish_dir_mode + mode: params.publish_dir_mode, + saveAs: { filename -> filename.tokenize("/")[1]} ] } withName: LINKS { @@ -29,7 +30,8 @@ process { withName: '.*:RUN_LINKS:BGZIP.*' { publishDir = [ path: { "${params.outdir}/${meta.id}/scaffold/links/" }, - mode: params.publish_dir_mode + mode: params.publish_dir_mode, + saveAs: { filename -> filename.tokenize("/")[1]} ] } withName: LONGSTITCH { @@ -42,7 +44,8 @@ process { withName: '.*:RUN_LONGSTITCH:BGZIP.*' { publishDir = [ path: { "${params.outdir}/${meta.id}/scaffold/longstitch/" }, - mode: params.publish_dir_mode + mode: params.publish_dir_mode, + saveAs: { filename -> filename.tokenize("/")[1]} ] } withName: BWAMEM2_INDEX { @@ -94,7 +97,8 @@ process { withName: '.*:HIC:BGZIP.*' { publishDir = [ path: { "${params.outdir}/${meta.id}/scaffold/hic/yahs/" }, - mode: params.publish_dir_mode + mode: params.publish_dir_mode, + saveAs: { filename -> filename.tokenize("/")[1]} ] } withName: '.*HIC:SAMTOOLS_FAIDX.*' { From 4dd9020643d1faf998041c207200a967d29c49b5 Mon Sep 17 00:00:00 2001 From: Niklas Schandry Date: Fri, 28 Aug 2026 14:54:33 +0200 Subject: [PATCH 08/17] publish hifiasm fasta output file into hifiasm --- conf/modules/assembly.config | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/conf/modules/assembly.config b/conf/modules/assembly.config index 17d9e119..9700587a 100644 --- a/conf/modules/assembly.config +++ b/conf/modules/assembly.config @@ -50,28 +50,28 @@ process { } withName: GFA_2_FA { publishDir = [ - path: { "${params.outdir}/${meta.id}/assembly/hifiasm/fasta" }, + path: { "${params.outdir}/${meta.id}/assembly/hifiasm/" }, mode: params.publish_dir_mode, saveAs: null ] } withName: GFA_2_FA_HIFI { publishDir = [ - path: { "${params.outdir}/${meta.id}/assembly/hifiasm/fasta" }, + path: { "${params.outdir}/${meta.id}/assembly/hifiasm/" }, mode: params.publish_dir_mode, saveAs: null ] } withName: BGZIP_HIFI { publishDir = [ - path: { "${params.outdir}/${meta.id}/assembly/hifiasm/fasta" }, + path: { "${params.outdir}/${meta.id}/assembly/hifiasm/" }, mode: params.publish_dir_mode, saveAs: { filename -> filename.tokenize("/")[1]} ] } withName: BGZIP_ONT { publishDir = [ - path: { "${params.outdir}/${meta.id}/assembly/hifiasm_ont/fasta" }, + path: { "${params.outdir}/${meta.id}/assembly/hifiasm_ont/" }, mode: params.publish_dir_mode, saveAs: { filename -> filename.tokenize("/")[1]} ] From cba85c3f5efa61326f740caff202743e2693b487 Mon Sep 17 00:00:00 2001 From: Niklas Schandry Date: Fri, 28 Aug 2026 15:10:23 +0200 Subject: [PATCH 09/17] prepare genomeqc input samplesheet output --- docs/usage.md | 2 +- workflows/genomeassembler.nf | 44 ++++++++++++++++++------------------ 2 files changed, 23 insertions(+), 23 deletions(-) diff --git a/docs/usage.md b/docs/usage.md index 245878f2..792f3fdc 100644 --- a/docs/usage.md +++ b/docs/usage.md @@ -21,7 +21,7 @@ Since it is often difficult to know which tool, or assembly strategy will perfor To compare different samples, a column named `group` is required, which should contain the same value for all samples that should be compared to each other. `nf-core/genomeassembler` performs genome qc and summarizes the results in a report. -For more in-depth qc, `nf-core/genomeassembler` generates samplesheets that can be used as inputs for [`nf-core/genomeqc`](https://nf-co.re/genomeqc) in `genomeqc_samplesheet/`. There are two samplesheets, one containing only samplename and fasta, the other also containing paths to annotation files (only for samples where annotation liftover was performed). +For more in-depth qc, `nf-core/genomeassembler` generates a samplesheet that can be used as inputs for [`nf-core/genomeqc`](https://nf-co.re/genomeqc) which can be found in `/genomeqc_samplesheet/nf-core-genomeqc-in.csv`. ## Parameterization diff --git a/workflows/genomeassembler.nf b/workflows/genomeassembler.nf index 2dfb7047..f42e8b72 100644 --- a/workflows/genomeassembler.nf +++ b/workflows/genomeassembler.nf @@ -289,53 +289,53 @@ workflow GENOMEASSEMBLER { def ch_assembly_manifest = ch_main_scaffolded .map { it -> def meta = it.meta - // A list of filenames, corresponding and the candidate output folder - [ - [ meta.id, meta.scaffolds ? meta.scaffolds.ragtag ?: null : null, 'scaffold/ragtag' ], - [ meta.id, meta.scaffolds ? meta.scaffolds.hic ?: null : null, 'scaffold/hic/yahs' ], - [ meta.id, meta.scaffolds ? meta.scaffolds.longstitch ?: null : null, 'scaffold/longstitch' ], - [ meta.id, meta.scaffolds ? meta.scaffolds.links ?: null : null, 'scaffold/links' ], - [ meta.id, meta.polished ? meta.polished.pilon ?: null : null, 'polish/pilon' ], - [ meta.id, meta.polished ? meta.polished.medaka ?: null : null, 'polish/medaka' ], - [ meta.id, meta.polished ? meta.polished.dorado ?: null : null, 'polish/dorado' ], - [ meta.id, meta.assembly, { + def subout = // Assembly publishdirs are a bit more specific meta.strategy == "single" ? ( meta.assembler_ont == "flye" || meta.assembler_hifi == "flye" ? 'assembly/flye' - : 'assembly/hifiasm' + : meta.assembler_ont == 'hifiasm' + ? 'assembly/hifiasm_ont' + : 'assembly/hifiasm' ) : meta.strategy == "hybrid" ? 'assembly/hifiasm' : 'assembly/ragtag' - } + + // A list of ids, stage, files (in work), the candidate output folder + [ + [ meta.id, 'scaffold_ragtag', meta.scaffolds ? meta.scaffolds.ragtag ?: null : null, 'scaffold/ragtag' ], + [ meta.id, 'scaffold_hic' , meta.scaffolds ? meta.scaffolds.hic ?: null : null, 'scaffold/hic/yahs' ], + [ meta.id, 'scaffold_longstitch', meta.scaffolds ? meta.scaffolds.longstitch ?: null : null, 'scaffold/longstitch' ], + [ meta.id, 'scaffold_links', meta.scaffolds ? meta.scaffolds.links ?: null : null, 'scaffold/links' ], + [ meta.id, 'polish_pilon', meta.polished ? meta.polished.pilon ?: null : null, 'polish/pilon' ], + [ meta.id, 'polish_medaka', meta.polished ? meta.polished.medaka ?: null : null, 'polish/medaka' ], + [ meta.id, 'polish_dorado', meta.polished ? meta.polished.dorado ?: null : null, 'polish/dorado' ], + [ meta.id, 'initial_assembly', meta.assembly, subout ] ] } - .view( {it -> "Manifest channel: $it"}) - /* + .flatMap( { it -> it } ) .filter { - _id, file, _subdir -> file != null + _id, _stage, file, _subdir -> file != null } .map { - id, assembly_file, subdir -> + id, stage ,assembly_file, subdir -> [ - file(assembly_file).name.baseName(), - {"${outdir_uri}/${id}/${subdir}/${file(assembly_file).name}"} + "${id}-${stage}", + "${outdir_uri}/${id}/${subdir}/${file(assembly_file).name}" ] } - ch_assembly_manifest .map {sample, fasta -> [sample,fasta].join(",")} - .map { rows -> "species,fasta\n" + rows + "\n" } + .map { rows -> "assembly,fasta\n" + rows + "\n" } .collectFile( - name: "nf-core-genomeqc-in-no-gff.csv", + name: "nf-core-genomeqc-in.csv", storeDir: "${params.outdir}/genomeqc_samplesheet", keepHeader: true, skip: 1 ) - */ emit: From 927cb827e1e2d202541aa024a6d07d15cb856281 Mon Sep 17 00:00:00 2001 From: Niklas Schandry Date: Fri, 28 Aug 2026 15:32:47 +0200 Subject: [PATCH 10/17] update changelog --- CHANGELOG.md | 6 +++++- 1 file changed, 5 insertions(+), 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 6c1d6bc2..46d8e6ad 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -19,6 +19,10 @@ In addition, v2.0.0 contains these changes: Pull requests in reverse chronological order since v1.1.0 +[#215](https://github.com/nf-core/genomeassembler/pull/215) + +- Prepare samplesheet for downstream QC with [nf-core/genomeqc](https://nf-co.re/genomeqc) + [#207](https://github.com/nf-core/genomeassembler/pull/207) - additional tests for QC modules @@ -29,7 +33,7 @@ Pull requests in reverse chronological order since v1.1.0 - Switched to nf-schema for input parsing -- Added test with HiC dataset. +- Added test with HiC dataset (kindly prepared by @OlivierCoen). [#198](https://github.com/nf-core/genomeassembler/pull/198) From e2890b6dcd8a6fe42bdd840a1af269ab5ccbd0f0 Mon Sep 17 00:00:00 2001 From: Niklas Schandry Date: Fri, 28 Aug 2026 15:32:59 +0200 Subject: [PATCH 11/17] update test --- tests/default.nf.test.snap | 472 +++++++++++++++++-------------------- 1 file changed, 216 insertions(+), 256 deletions(-) diff --git a/tests/default.nf.test.snap b/tests/default.nf.test.snap index 3e69ac09..c032d040 100644 --- a/tests/default.nf.test.snap +++ b/tests/default.nf.test.snap @@ -1,7 +1,7 @@ { "-profile test_busco_quast": { "content": [ - 80, + 88, { "ADD_RG": { "picard": "3.4.0" @@ -63,6 +63,9 @@ "HIFIASM_ONT": { "hifasm": "0.25.0-r726" }, + "LIFTOFF": { + "liftoff": "1.6.3" + }, "MARKDUP": { "picard": "3.4.0" }, @@ -80,6 +83,8 @@ } }, [ + "genomeqc_samplesheet", + "genomeqc_samplesheet/nf-core-genomeqc-in.csv", "pipeline_info", "pipeline_info/nf_core_pipeline_software_versions.yml", "report", @@ -87,23 +92,20 @@ "test_flye_hifiasm", "test_flye_hifiasm/assembly", "test_flye_hifiasm/assembly/flye", - "test_flye_hifiasm/assembly/flye/out", - "test_flye_hifiasm/assembly/flye/out/test_flye_hifiasm.assembly.fa.gz", + "test_flye_hifiasm/assembly/flye/test_flye_hifiasm.assembly.fa.gz", "test_flye_hifiasm/assembly/flye/test_flye_hifiasm.assembly_graph.gfa.gz", "test_flye_hifiasm/assembly/flye/test_flye_hifiasm.assembly_graph.gv.gz", "test_flye_hifiasm/assembly/flye/test_flye_hifiasm.assembly_info.txt", "test_flye_hifiasm/assembly/flye/test_flye_hifiasm.flye.log", "test_flye_hifiasm/assembly/flye/test_flye_hifiasm.params.json", "test_flye_hifiasm/assembly/hifiasm", - "test_flye_hifiasm/assembly/hifiasm/fasta", - "test_flye_hifiasm/assembly/hifiasm/fasta/out", - "test_flye_hifiasm/assembly/hifiasm/fasta/out/test_flye_hifiasm.fa.gz", "test_flye_hifiasm/assembly/hifiasm/test_flye_hifiasm.bp.hap1.p_ctg.gfa", "test_flye_hifiasm/assembly/hifiasm/test_flye_hifiasm.bp.hap2.p_ctg.gfa", "test_flye_hifiasm/assembly/hifiasm/test_flye_hifiasm.bp.p_ctg.gfa", "test_flye_hifiasm/assembly/hifiasm/test_flye_hifiasm.bp.p_utg.gfa", "test_flye_hifiasm/assembly/hifiasm/test_flye_hifiasm.bp.r_utg.gfa", "test_flye_hifiasm/assembly/hifiasm/test_flye_hifiasm.ec.bin", + "test_flye_hifiasm/assembly/hifiasm/test_flye_hifiasm.fa.gz", "test_flye_hifiasm/assembly/hifiasm/test_flye_hifiasm.ovlp.reverse.bin", "test_flye_hifiasm/assembly/hifiasm/test_flye_hifiasm.ovlp.source.bin", "test_flye_hifiasm/assembly/hifiasm/test_flye_hifiasm.stderr.log", @@ -114,11 +116,9 @@ "test_flye_hifiasm/assembly/ragtag/test_flye_hifiasm_assembly_patch.patch.agp", "test_flye_hifiasm/assembly/ragtag/test_flye_hifiasm_assembly_patch.patch.err", "test_flye_hifiasm/assembly/ragtag/test_flye_hifiasm_assembly_patch.patch.fa", + "test_flye_hifiasm/assembly/ragtag/test_flye_hifiasm_assembly_patch.patch.fa.gz", "test_flye_hifiasm/assembly/ragtag/test_flye_hifiasm_assembly_patch.rename.agp", "test_flye_hifiasm/assembly/ragtag/test_flye_hifiasm_assembly_patch.rename.fa", - "test_flye_hifiasm/bgzip", - "test_flye_hifiasm/bgzip/out", - "test_flye_hifiasm/bgzip/out/test_flye_hifiasm_assembly_patch.patch.fa.gz", "test_flye_hifiasm/gfa2fa", "test_flye_hifiasm/gfa2fa/test_flye_hifiasm.fa", "test_flye_hifiasm/reads", @@ -135,21 +135,21 @@ "test_flye_hifiasm/reads/fastplong/ont/test_flye_hifiasm_ont.fastplong.log", "test_flye_hifiasm/scaffold", "test_flye_hifiasm/scaffold/ragtag", - "test_flye_hifiasm/scaffold/ragtag/out", - "test_flye_hifiasm/scaffold/ragtag/out/test_flye_hifiasm_ragtag.fa.gz", "test_flye_hifiasm/scaffold/ragtag/test_flye_hifiasm_ragtag.agp", "test_flye_hifiasm/scaffold/ragtag/test_flye_hifiasm_ragtag.fa", + "test_flye_hifiasm/scaffold/ragtag/test_flye_hifiasm_ragtag.fa.gz", "test_flye_hifiasm/scaffold/ragtag/test_flye_hifiasm_ragtag.stats", "test_hifi_flye", "test_hifi_flye/assembly", "test_hifi_flye/assembly/flye", - "test_hifi_flye/assembly/flye/out", - "test_hifi_flye/assembly/flye/out/test_hifi_flye.assembly.fa.gz", + "test_hifi_flye/assembly/flye/test_hifi_flye.assembly.fa.gz", "test_hifi_flye/assembly/flye/test_hifi_flye.assembly_graph.gfa.gz", "test_hifi_flye/assembly/flye/test_hifi_flye.assembly_graph.gv.gz", "test_hifi_flye/assembly/flye/test_hifi_flye.assembly_info.txt", "test_hifi_flye/assembly/flye/test_hifi_flye.flye.log", "test_hifi_flye/assembly/flye/test_hifi_flye.params.json", + "test_hifi_flye/assembly/test_hifi_flye_assembly.gff3", + "test_hifi_flye/assembly/test_hifi_flye_assembly.unmapped.txt", "test_hifi_flye/reads", "test_hifi_flye/reads/fastplong", "test_hifi_flye/reads/fastplong/hifi", @@ -164,23 +164,22 @@ "test_hifi_flye/reads/fastplong/ont/test_hifi_flye_ont.fastplong.log", "test_hifi_flye/scaffold", "test_hifi_flye/scaffold/ragtag", - "test_hifi_flye/scaffold/ragtag/out", - "test_hifi_flye/scaffold/ragtag/out/test_hifi_flye_ragtag.fa.gz", "test_hifi_flye/scaffold/ragtag/test_hifi_flye_ragtag.agp", "test_hifi_flye/scaffold/ragtag/test_hifi_flye_ragtag.fa", + "test_hifi_flye/scaffold/ragtag/test_hifi_flye_ragtag.fa.gz", + "test_hifi_flye/scaffold/ragtag/test_hifi_flye_ragtag.gff3", "test_hifi_flye/scaffold/ragtag/test_hifi_flye_ragtag.stats", + "test_hifi_flye/scaffold/ragtag/test_hifi_flye_ragtag.unmapped.txt", "test_hifi_hifiasm", "test_hifi_hifiasm/assembly", "test_hifi_hifiasm/assembly/hifiasm", - "test_hifi_hifiasm/assembly/hifiasm/fasta", - "test_hifi_hifiasm/assembly/hifiasm/fasta/out", - "test_hifi_hifiasm/assembly/hifiasm/fasta/out/test_hifi_hifiasm.fa.gz", "test_hifi_hifiasm/assembly/hifiasm/test_hifi_hifiasm.bp.hap1.p_ctg.gfa", "test_hifi_hifiasm/assembly/hifiasm/test_hifi_hifiasm.bp.hap2.p_ctg.gfa", "test_hifi_hifiasm/assembly/hifiasm/test_hifi_hifiasm.bp.p_ctg.gfa", "test_hifi_hifiasm/assembly/hifiasm/test_hifi_hifiasm.bp.p_utg.gfa", "test_hifi_hifiasm/assembly/hifiasm/test_hifi_hifiasm.bp.r_utg.gfa", "test_hifi_hifiasm/assembly/hifiasm/test_hifi_hifiasm.ec.bin", + "test_hifi_hifiasm/assembly/hifiasm/test_hifi_hifiasm.fa.gz", "test_hifi_hifiasm/assembly/hifiasm/test_hifi_hifiasm.ovlp.reverse.bin", "test_hifi_hifiasm/assembly/hifiasm/test_hifi_hifiasm.ovlp.source.bin", "test_hifi_hifiasm/assembly/hifiasm/test_hifi_hifiasm.stderr.log", @@ -201,23 +200,20 @@ "test_hifiasm_flye", "test_hifiasm_flye/assembly", "test_hifiasm_flye/assembly/flye", - "test_hifiasm_flye/assembly/flye/out", - "test_hifiasm_flye/assembly/flye/out/test_hifiasm_flye.assembly.fa.gz", + "test_hifiasm_flye/assembly/flye/test_hifiasm_flye.assembly.fa.gz", "test_hifiasm_flye/assembly/flye/test_hifiasm_flye.assembly_graph.gfa.gz", "test_hifiasm_flye/assembly/flye/test_hifiasm_flye.assembly_graph.gv.gz", "test_hifiasm_flye/assembly/flye/test_hifiasm_flye.assembly_info.txt", "test_hifiasm_flye/assembly/flye/test_hifiasm_flye.flye.log", "test_hifiasm_flye/assembly/flye/test_hifiasm_flye.params.json", "test_hifiasm_flye/assembly/hifiasm_ont", - "test_hifiasm_flye/assembly/hifiasm_ont/fasta", - "test_hifiasm_flye/assembly/hifiasm_ont/fasta/out", - "test_hifiasm_flye/assembly/hifiasm_ont/fasta/out/test_hifiasm_flye.fa.gz", "test_hifiasm_flye/assembly/hifiasm_ont/test_hifiasm_flye.bp.hap1.p_ctg.gfa", "test_hifiasm_flye/assembly/hifiasm_ont/test_hifiasm_flye.bp.hap2.p_ctg.gfa", "test_hifiasm_flye/assembly/hifiasm_ont/test_hifiasm_flye.bp.p_ctg.gfa", "test_hifiasm_flye/assembly/hifiasm_ont/test_hifiasm_flye.bp.p_utg.gfa", "test_hifiasm_flye/assembly/hifiasm_ont/test_hifiasm_flye.bp.r_utg.gfa", "test_hifiasm_flye/assembly/hifiasm_ont/test_hifiasm_flye.ec.bin", + "test_hifiasm_flye/assembly/hifiasm_ont/test_hifiasm_flye.fa.gz", "test_hifiasm_flye/assembly/hifiasm_ont/test_hifiasm_flye.ovlp.reverse.bin", "test_hifiasm_flye/assembly/hifiasm_ont/test_hifiasm_flye.ovlp.source.bin", "test_hifiasm_flye/assembly/hifiasm_ont/test_hifiasm_flye.stderr.log", @@ -228,11 +224,11 @@ "test_hifiasm_flye/assembly/ragtag/test_hifiasm_flye_assembly_patch.patch.agp", "test_hifiasm_flye/assembly/ragtag/test_hifiasm_flye_assembly_patch.patch.err", "test_hifiasm_flye/assembly/ragtag/test_hifiasm_flye_assembly_patch.patch.fa", + "test_hifiasm_flye/assembly/ragtag/test_hifiasm_flye_assembly_patch.patch.fa.gz", "test_hifiasm_flye/assembly/ragtag/test_hifiasm_flye_assembly_patch.rename.agp", "test_hifiasm_flye/assembly/ragtag/test_hifiasm_flye_assembly_patch.rename.fa", - "test_hifiasm_flye/bgzip", - "test_hifiasm_flye/bgzip/out", - "test_hifiasm_flye/bgzip/out/test_hifiasm_flye_assembly_patch.patch.fa.gz", + "test_hifiasm_flye/assembly/test_hifiasm_flye_assembly.gff3", + "test_hifiasm_flye/assembly/test_hifiasm_flye_assembly.unmapped.txt", "test_hifiasm_flye/gfa2fa", "test_hifiasm_flye/gfa2fa/test_hifiasm_flye.fa", "test_hifiasm_flye/reads", @@ -250,23 +246,20 @@ "test_hifiasm_flye_hic", "test_hifiasm_flye_hic/assembly", "test_hifiasm_flye_hic/assembly/flye", - "test_hifiasm_flye_hic/assembly/flye/out", - "test_hifiasm_flye_hic/assembly/flye/out/test_hifiasm_flye_hic.assembly.fa.gz", + "test_hifiasm_flye_hic/assembly/flye/test_hifiasm_flye_hic.assembly.fa.gz", "test_hifiasm_flye_hic/assembly/flye/test_hifiasm_flye_hic.assembly_graph.gfa.gz", "test_hifiasm_flye_hic/assembly/flye/test_hifiasm_flye_hic.assembly_graph.gv.gz", "test_hifiasm_flye_hic/assembly/flye/test_hifiasm_flye_hic.assembly_info.txt", "test_hifiasm_flye_hic/assembly/flye/test_hifiasm_flye_hic.flye.log", "test_hifiasm_flye_hic/assembly/flye/test_hifiasm_flye_hic.params.json", "test_hifiasm_flye_hic/assembly/hifiasm_ont", - "test_hifiasm_flye_hic/assembly/hifiasm_ont/fasta", - "test_hifiasm_flye_hic/assembly/hifiasm_ont/fasta/out", - "test_hifiasm_flye_hic/assembly/hifiasm_ont/fasta/out/test_hifiasm_flye_hic.fa.gz", "test_hifiasm_flye_hic/assembly/hifiasm_ont/test_hifiasm_flye_hic.bp.hap1.p_ctg.gfa", "test_hifiasm_flye_hic/assembly/hifiasm_ont/test_hifiasm_flye_hic.bp.hap2.p_ctg.gfa", "test_hifiasm_flye_hic/assembly/hifiasm_ont/test_hifiasm_flye_hic.bp.p_ctg.gfa", "test_hifiasm_flye_hic/assembly/hifiasm_ont/test_hifiasm_flye_hic.bp.p_utg.gfa", "test_hifiasm_flye_hic/assembly/hifiasm_ont/test_hifiasm_flye_hic.bp.r_utg.gfa", "test_hifiasm_flye_hic/assembly/hifiasm_ont/test_hifiasm_flye_hic.ec.bin", + "test_hifiasm_flye_hic/assembly/hifiasm_ont/test_hifiasm_flye_hic.fa.gz", "test_hifiasm_flye_hic/assembly/hifiasm_ont/test_hifiasm_flye_hic.ovlp.reverse.bin", "test_hifiasm_flye_hic/assembly/hifiasm_ont/test_hifiasm_flye_hic.ovlp.source.bin", "test_hifiasm_flye_hic/assembly/hifiasm_ont/test_hifiasm_flye_hic.stderr.log", @@ -277,11 +270,11 @@ "test_hifiasm_flye_hic/assembly/ragtag/test_hifiasm_flye_hic_assembly_patch.patch.agp", "test_hifiasm_flye_hic/assembly/ragtag/test_hifiasm_flye_hic_assembly_patch.patch.err", "test_hifiasm_flye_hic/assembly/ragtag/test_hifiasm_flye_hic_assembly_patch.patch.fa", + "test_hifiasm_flye_hic/assembly/ragtag/test_hifiasm_flye_hic_assembly_patch.patch.fa.gz", "test_hifiasm_flye_hic/assembly/ragtag/test_hifiasm_flye_hic_assembly_patch.rename.agp", "test_hifiasm_flye_hic/assembly/ragtag/test_hifiasm_flye_hic_assembly_patch.rename.fa", - "test_hifiasm_flye_hic/bgzip", - "test_hifiasm_flye_hic/bgzip/out", - "test_hifiasm_flye_hic/bgzip/out/test_hifiasm_flye_hic_assembly_patch.patch.fa.gz", + "test_hifiasm_flye_hic/assembly/test_hifiasm_flye_hic_assembly.gff3", + "test_hifiasm_flye_hic/assembly/test_hifiasm_flye_hic_assembly.unmapped.txt", "test_hifiasm_flye_hic/gfa2fa", "test_hifiasm_flye_hic/gfa2fa/test_hifiasm_flye_hic.fa", "test_hifiasm_flye_hic/hic_reads", @@ -321,12 +314,12 @@ "test_hifiasm_flye_hic/scaffold/hic/markdup/test_hifiasm_flye_hic_hic_dedup.MarkDuplicates.metrics.txt", "test_hifiasm_flye_hic/scaffold/hic/markdup/test_hifiasm_flye_hic_hic_dedup.bai", "test_hifiasm_flye_hic/scaffold/hic/markdup/test_hifiasm_flye_hic_hic_dedup.bam", + "test_hifiasm_flye_hic/scaffold/hic/test_hifiasm_flye_hic_links.gff3", + "test_hifiasm_flye_hic/scaffold/hic/test_hifiasm_flye_hic_links.unmapped.txt", "test_hifiasm_flye_hic/scaffold/hic/yahs", "test_hifiasm_flye_hic/scaffold/hic/yahs/index", "test_hifiasm_flye_hic/scaffold/hic/yahs/index/test_hifiasm_flye_hic_assembly_patch.patch.fa.gz.fai", "test_hifiasm_flye_hic/scaffold/hic/yahs/index/test_hifiasm_flye_hic_assembly_patch.patch.fa.gz.gzi", - "test_hifiasm_flye_hic/scaffold/hic/yahs/out", - "test_hifiasm_flye_hic/scaffold/hic/yahs/out/test_hifiasm_flye_hic_hic_scaffolds_final.fa.gz", "test_hifiasm_flye_hic/scaffold/hic/yahs/test_hifiasm_flye_hic_hic.bin", "test_hifiasm_flye_hic/scaffold/hic/yahs/test_hifiasm_flye_hic_hic.log", "test_hifiasm_flye_hic/scaffold/hic/yahs/test_hifiasm_flye_hic_hic_inital_break_01.agp", @@ -334,18 +327,17 @@ "test_hifiasm_flye_hic/scaffold/hic/yahs/test_hifiasm_flye_hic_hic_r02_break.agp", "test_hifiasm_flye_hic/scaffold/hic/yahs/test_hifiasm_flye_hic_hic_scaffolds_final.agp", "test_hifiasm_flye_hic/scaffold/hic/yahs/test_hifiasm_flye_hic_hic_scaffolds_final.fa", + "test_hifiasm_flye_hic/scaffold/hic/yahs/test_hifiasm_flye_hic_hic_scaffolds_final.fa.gz", "test_hifiasm_ul", "test_hifiasm_ul/assembly", "test_hifiasm_ul/assembly/hifiasm", - "test_hifiasm_ul/assembly/hifiasm/fasta", - "test_hifiasm_ul/assembly/hifiasm/fasta/out", - "test_hifiasm_ul/assembly/hifiasm/fasta/out/test_hifiasm_ul.fa.gz", "test_hifiasm_ul/assembly/hifiasm/test_hifiasm_ul.bp.hap1.p_ctg.gfa", "test_hifiasm_ul/assembly/hifiasm/test_hifiasm_ul.bp.hap2.p_ctg.gfa", "test_hifiasm_ul/assembly/hifiasm/test_hifiasm_ul.bp.p_ctg.gfa", "test_hifiasm_ul/assembly/hifiasm/test_hifiasm_ul.bp.p_utg.gfa", "test_hifiasm_ul/assembly/hifiasm/test_hifiasm_ul.bp.r_utg.gfa", "test_hifiasm_ul/assembly/hifiasm/test_hifiasm_ul.ec.bin", + "test_hifiasm_ul/assembly/hifiasm/test_hifiasm_ul.fa.gz", "test_hifiasm_ul/assembly/hifiasm/test_hifiasm_ul.ovlp.reverse.bin", "test_hifiasm_ul/assembly/hifiasm/test_hifiasm_ul.ovlp.source.bin", "test_hifiasm_ul/assembly/hifiasm/test_hifiasm_ul.re.uidx.bin", @@ -392,20 +384,20 @@ "test_hifiasm_ul/scaffold/longstitch/assembly.cut250.tigmint.fa.k32.w100.z1000.trimmed_scafs.path", "test_hifiasm_ul/scaffold/longstitch/assembly.cut250.tigmint.fa.k32.w100.z1000.trimmed_scafs.tsv", "test_hifiasm_ul/scaffold/longstitch/assembly.cut250.tigmint.fa.k32.w100.z1000.verbose_mapping.tsv", - "test_hifiasm_ul/scaffold/longstitch/out", - "test_hifiasm_ul/scaffold/longstitch/out/test_hifiasm_ul_longstitch.tigmint-ntLink-arks.fa.gz", "test_hifiasm_ul/scaffold/longstitch/test_hifiasm_ul_longstitch.tigmint-ntLink-arks.fa", + "test_hifiasm_ul/scaffold/longstitch/test_hifiasm_ul_longstitch.tigmint-ntLink-arks.fa.gz", "test_hifiasm_ul/scaffold/longstitch/versions.yml", "test_ont_flye", "test_ont_flye/assembly", "test_ont_flye/assembly/flye", - "test_ont_flye/assembly/flye/out", - "test_ont_flye/assembly/flye/out/test_ont_flye.assembly.fa.gz", + "test_ont_flye/assembly/flye/test_ont_flye.assembly.fa.gz", "test_ont_flye/assembly/flye/test_ont_flye.assembly_graph.gfa.gz", "test_ont_flye/assembly/flye/test_ont_flye.assembly_graph.gv.gz", "test_ont_flye/assembly/flye/test_ont_flye.assembly_info.txt", "test_ont_flye/assembly/flye/test_ont_flye.flye.log", "test_ont_flye/assembly/flye/test_ont_flye.params.json", + "test_ont_flye/assembly/test_ont_flye_assembly.gff3", + "test_ont_flye/assembly/test_ont_flye_assembly.unmapped.txt", "test_ont_flye/reads", "test_ont_flye/reads/fastplong", "test_ont_flye/reads/fastplong/hifi", @@ -421,18 +413,18 @@ "test_ont_hifiasm", "test_ont_hifiasm/assembly", "test_ont_hifiasm/assembly/hifiasm_ont", - "test_ont_hifiasm/assembly/hifiasm_ont/fasta", - "test_ont_hifiasm/assembly/hifiasm_ont/fasta/out", - "test_ont_hifiasm/assembly/hifiasm_ont/fasta/out/test_ont_hifiasm.fa.gz", "test_ont_hifiasm/assembly/hifiasm_ont/test_ont_hifiasm.bp.hap1.p_ctg.gfa", "test_ont_hifiasm/assembly/hifiasm_ont/test_ont_hifiasm.bp.hap2.p_ctg.gfa", "test_ont_hifiasm/assembly/hifiasm_ont/test_ont_hifiasm.bp.p_ctg.gfa", "test_ont_hifiasm/assembly/hifiasm_ont/test_ont_hifiasm.bp.p_utg.gfa", "test_ont_hifiasm/assembly/hifiasm_ont/test_ont_hifiasm.bp.r_utg.gfa", "test_ont_hifiasm/assembly/hifiasm_ont/test_ont_hifiasm.ec.bin", + "test_ont_hifiasm/assembly/hifiasm_ont/test_ont_hifiasm.fa.gz", "test_ont_hifiasm/assembly/hifiasm_ont/test_ont_hifiasm.ovlp.reverse.bin", "test_ont_hifiasm/assembly/hifiasm_ont/test_ont_hifiasm.ovlp.source.bin", "test_ont_hifiasm/assembly/hifiasm_ont/test_ont_hifiasm.stderr.log", + "test_ont_hifiasm/assembly/test_ont_hifiasm_assembly.gff3", + "test_ont_hifiasm/assembly/test_ont_hifiasm_assembly.unmapped.txt", "test_ont_hifiasm/gfa2fa", "test_ont_hifiasm/gfa2fa/test_ont_hifiasm.fa", "test_ont_hifiasm/reads", @@ -449,23 +441,22 @@ "test_ont_hifiasm/reads/fastplong/ont/test_ont_hifiasm_ont.fastplong.log", "test_ont_hifiasm/scaffold", "test_ont_hifiasm/scaffold/ragtag", - "test_ont_hifiasm/scaffold/ragtag/out", - "test_ont_hifiasm/scaffold/ragtag/out/test_ont_hifiasm_ragtag.fa.gz", "test_ont_hifiasm/scaffold/ragtag/test_ont_hifiasm_ragtag.agp", "test_ont_hifiasm/scaffold/ragtag/test_ont_hifiasm_ragtag.fa", + "test_ont_hifiasm/scaffold/ragtag/test_ont_hifiasm_ragtag.fa.gz", + "test_ont_hifiasm/scaffold/ragtag/test_ont_hifiasm_ragtag.gff3", "test_ont_hifiasm/scaffold/ragtag/test_ont_hifiasm_ragtag.stats", + "test_ont_hifiasm/scaffold/ragtag/test_ont_hifiasm_ragtag.unmapped.txt", "test_ont_hifiasm_hic", "test_ont_hifiasm_hic/assembly", "test_ont_hifiasm_hic/assembly/hifiasm_ont", - "test_ont_hifiasm_hic/assembly/hifiasm_ont/fasta", - "test_ont_hifiasm_hic/assembly/hifiasm_ont/fasta/out", - "test_ont_hifiasm_hic/assembly/hifiasm_ont/fasta/out/test_ont_hifiasm_hic.fa.gz", "test_ont_hifiasm_hic/assembly/hifiasm_ont/test_ont_hifiasm_hic.bp.hap1.p_ctg.gfa", "test_ont_hifiasm_hic/assembly/hifiasm_ont/test_ont_hifiasm_hic.bp.hap2.p_ctg.gfa", "test_ont_hifiasm_hic/assembly/hifiasm_ont/test_ont_hifiasm_hic.bp.p_ctg.gfa", "test_ont_hifiasm_hic/assembly/hifiasm_ont/test_ont_hifiasm_hic.bp.p_utg.gfa", "test_ont_hifiasm_hic/assembly/hifiasm_ont/test_ont_hifiasm_hic.bp.r_utg.gfa", "test_ont_hifiasm_hic/assembly/hifiasm_ont/test_ont_hifiasm_hic.ec.bin", + "test_ont_hifiasm_hic/assembly/hifiasm_ont/test_ont_hifiasm_hic.fa.gz", "test_ont_hifiasm_hic/assembly/hifiasm_ont/test_ont_hifiasm_hic.ovlp.reverse.bin", "test_ont_hifiasm_hic/assembly/hifiasm_ont/test_ont_hifiasm_hic.ovlp.source.bin", "test_ont_hifiasm_hic/assembly/hifiasm_ont/test_ont_hifiasm_hic.stderr.log", @@ -512,19 +503,18 @@ "test_ont_hifiasm_hic/scaffold/hic/yahs/index", "test_ont_hifiasm_hic/scaffold/hic/yahs/index/test_ont_hifiasm_hic.fa.gz.fai", "test_ont_hifiasm_hic/scaffold/hic/yahs/index/test_ont_hifiasm_hic.fa.gz.gzi", - "test_ont_hifiasm_hic/scaffold/hic/yahs/out", - "test_ont_hifiasm_hic/scaffold/hic/yahs/out/test_ont_hifiasm_hic_hic_scaffolds_final.fa.gz", "test_ont_hifiasm_hic/scaffold/hic/yahs/test_ont_hifiasm_hic_hic.bin", "test_ont_hifiasm_hic/scaffold/hic/yahs/test_ont_hifiasm_hic_hic.log", "test_ont_hifiasm_hic/scaffold/hic/yahs/test_ont_hifiasm_hic_hic_inital_break_01.agp", "test_ont_hifiasm_hic/scaffold/hic/yahs/test_ont_hifiasm_hic_hic_r01_break.agp", "test_ont_hifiasm_hic/scaffold/hic/yahs/test_ont_hifiasm_hic_hic_r02_break.agp", "test_ont_hifiasm_hic/scaffold/hic/yahs/test_ont_hifiasm_hic_hic_scaffolds_final.agp", - "test_ont_hifiasm_hic/scaffold/hic/yahs/test_ont_hifiasm_hic_hic_scaffolds_final.fa" + "test_ont_hifiasm_hic/scaffold/hic/yahs/test_ont_hifiasm_hic_hic_scaffolds_final.fa", + "test_ont_hifiasm_hic/scaffold/hic/yahs/test_ont_hifiasm_hic_hic_scaffolds_final.fa.gz" ], [ + "nf-core-genomeqc-in.csv:md5,ee60673c5c108c08220d3e7a9ad2926c", "test_flye_hifiasm.params.json:md5,afa91c041bce5e190f4a699d11b69db6", - "test_flye_hifiasm.fa.gz:md5,77e3d5af48175c784bfd217048fe271b", "test_flye_hifiasm.bp.hap1.p_ctg.gfa:md5,46ee70869884ad585165bd48081414e9", "test_flye_hifiasm.bp.hap2.p_ctg.gfa:md5,7792865547989d6d284f640425c4e36c", "test_flye_hifiasm.bp.p_ctg.gfa:md5,8fe65466d76815ffe1663ff6d8f2e8d1", @@ -536,11 +526,12 @@ "test_flye_hifiasm_hifi.fastplong.json:md5,0e20fedb8dfe0646232060da502883ee", "test_flye_hifiasm_ont.fastplong.json:md5,826cc5a321dd130a2f2c53cdb1a345b2", "test_hifi_flye.params.json:md5,54b576cb6d4d27656878a7fd3657bde9", + "test_hifi_flye_assembly.unmapped.txt:md5,d41d8cd98f00b204e9800998ecf8427e", "test_hifi_flye_hifi.fastplong.json:md5,daad59b32b84b79c29c274ed20f03cce", "test_hifi_flye_ont.fastplong.json:md5,198eb762846548340557f5f861f10c11", "test_hifi_flye_ragtag.fa:md5,79d2708ebfdbd7b766b9e7c6ee795d5b", "test_hifi_flye_ragtag.stats:md5,25325bb3c27246be0934f38f291b57b2", - "test_hifi_hifiasm.fa.gz:md5,77e3d5af48175c784bfd217048fe271b", + "test_hifi_flye_ragtag.unmapped.txt:md5,d41d8cd98f00b204e9800998ecf8427e", "test_hifi_hifiasm.bp.hap1.p_ctg.gfa:md5,46ee70869884ad585165bd48081414e9", "test_hifi_hifiasm.bp.hap2.p_ctg.gfa:md5,7792865547989d6d284f640425c4e36c", "test_hifi_hifiasm.bp.p_ctg.gfa:md5,8fe65466d76815ffe1663ff6d8f2e8d1", @@ -550,7 +541,6 @@ "test_hifi_hifiasm_hifi.fastplong.json:md5,e58f896e9b70344ae4e607324c2c6742", "test_hifi_hifiasm_ont.fastplong.json:md5,eedbb98c4d3870f38320d75b21c86604", "test_hifiasm_flye.params.json:md5,54b576cb6d4d27656878a7fd3657bde9", - "test_hifiasm_flye.fa.gz:md5,35d9e542fb372022a36ecf4854467e80", "test_hifiasm_flye.bp.hap1.p_ctg.gfa:md5,c9a084903ea872a7ac28f3bbd5eee8f3", "test_hifiasm_flye.bp.hap2.p_ctg.gfa:md5,d41d8cd98f00b204e9800998ecf8427e", "test_hifiasm_flye.bp.p_ctg.gfa:md5,d78f7a647429b254d9d46aab4d1306a0", @@ -561,11 +551,11 @@ "test_hifiasm_flye_assembly_patch.patch.err:md5,d41d8cd98f00b204e9800998ecf8427e", "test_hifiasm_flye_assembly_patch.patch.fa:md5,6ff15d809eaa0ecf6381400cdd7f0770", "test_hifiasm_flye_assembly_patch.rename.fa:md5,48208c6df370a225c6f54f378d7a8e39", + "test_hifiasm_flye_assembly.unmapped.txt:md5,e99c39c4afff7b433fb3973359dae6a4", "test_hifiasm_flye.fa:md5,35d9e542fb372022a36ecf4854467e80", "test_hifiasm_flye_hifi.fastplong.json:md5,2671b946d2bf533341b86a9f2424e5c3", "test_hifiasm_flye_ont.fastplong.json:md5,924d11a05764994135ff5de294052a02", "test_hifiasm_flye_hic.params.json:md5,54b576cb6d4d27656878a7fd3657bde9", - "test_hifiasm_flye_hic.fa.gz:md5,35d9e542fb372022a36ecf4854467e80", "test_hifiasm_flye_hic.bp.hap1.p_ctg.gfa:md5,c9a084903ea872a7ac28f3bbd5eee8f3", "test_hifiasm_flye_hic.bp.hap2.p_ctg.gfa:md5,d41d8cd98f00b204e9800998ecf8427e", "test_hifiasm_flye_hic.bp.p_ctg.gfa:md5,d78f7a647429b254d9d46aab4d1306a0", @@ -576,6 +566,7 @@ "test_hifiasm_flye_hic_assembly_patch.patch.err:md5,d41d8cd98f00b204e9800998ecf8427e", "test_hifiasm_flye_hic_assembly_patch.patch.fa:md5,6ff15d809eaa0ecf6381400cdd7f0770", "test_hifiasm_flye_hic_assembly_patch.rename.fa:md5,48208c6df370a225c6f54f378d7a8e39", + "test_hifiasm_flye_hic_assembly.unmapped.txt:md5,e99c39c4afff7b433fb3973359dae6a4", "test_hifiasm_flye_hic.fa:md5,35d9e542fb372022a36ecf4854467e80", "test_hifiasm_flye_hic_hicreads.fastp.json:md5,639daa4b554b8562208d2f7dff3a118f", "test_hifiasm_flye_hic_hifi.fastplong.json:md5,1c4764224854af4537899de86c8e2e56", @@ -589,11 +580,10 @@ "test_hifiasm_flye_hic_bwamem.bam:md5,837f8fbfbaf79b1049093e62a23a02b2", "test_hifiasm_flye_hic_hic_dedup.bai:md5,aeda4dd1092e5ae65a44c90faa2a4e86", "test_hifiasm_flye_hic_hic_dedup.bam:md5,d93aabe7dbda135b1562eeef7808d347", + "test_hifiasm_flye_hic_links.unmapped.txt:md5,e99c39c4afff7b433fb3973359dae6a4", "test_hifiasm_flye_hic_assembly_patch.patch.fa.gz.fai:md5,06f2947d7897ca8a7c6f30a81bd6bdcc", "test_hifiasm_flye_hic_assembly_patch.patch.fa.gz.gzi:md5,251cd3924556d6f48e9d5127bdd15ee2", - "test_hifiasm_flye_hic_hic_scaffolds_final.fa.gz:md5,3ac2a0232e899bcb28b72e3c4f1c2d79", "test_hifiasm_flye_hic_hic_scaffolds_final.fa:md5,3ac2a0232e899bcb28b72e3c4f1c2d79", - "test_hifiasm_ul.fa.gz:md5,77e3d5af48175c784bfd217048fe271b", "test_hifiasm_ul.bp.hap1.p_ctg.gfa:md5,46ee70869884ad585165bd48081414e9", "test_hifiasm_ul.bp.hap2.p_ctg.gfa:md5,7792865547989d6d284f640425c4e36c", "test_hifiasm_ul.bp.p_ctg.gfa:md5,8fe65466d76815ffe1663ff6d8f2e8d1", @@ -604,20 +594,21 @@ "test_hifiasm_ul_ont.fastplong.json:md5,86da6d58ac4630bfeae3ee08014ecb0b", "versions.yml:md5,c6c0c66defcf12c9bd29c649fbef58af", "test_ont_flye.params.json:md5,afa91c041bce5e190f4a699d11b69db6", + "test_ont_flye_assembly.unmapped.txt:md5,d41d8cd98f00b204e9800998ecf8427e", "test_ont_flye_hifi.fastplong.json:md5,9205a4cf65cce249429badc208348349", "test_ont_flye_ont.fastplong.json:md5,e418b2481ade21bc45e77d1437bad913", - "test_ont_hifiasm.fa.gz:md5,35d9e542fb372022a36ecf4854467e80", "test_ont_hifiasm.bp.hap1.p_ctg.gfa:md5,c9a084903ea872a7ac28f3bbd5eee8f3", "test_ont_hifiasm.bp.hap2.p_ctg.gfa:md5,d41d8cd98f00b204e9800998ecf8427e", "test_ont_hifiasm.bp.p_ctg.gfa:md5,d78f7a647429b254d9d46aab4d1306a0", "test_ont_hifiasm.bp.p_utg.gfa:md5,e2b6621386edda1636dfb84ddd676ea8", "test_ont_hifiasm.bp.r_utg.gfa:md5,e2b6621386edda1636dfb84ddd676ea8", + "test_ont_hifiasm_assembly.unmapped.txt:md5,e99c39c4afff7b433fb3973359dae6a4", "test_ont_hifiasm.fa:md5,35d9e542fb372022a36ecf4854467e80", "test_ont_hifiasm_hifi.fastplong.json:md5,91878df7edc2b07a885c103f260fc70e", "test_ont_hifiasm_ont.fastplong.json:md5,e97714274268b5a30be4d9851f2b61b3", "test_ont_hifiasm_ragtag.fa:md5,51f2975257b49657716d2ca7cc6d5fe2", "test_ont_hifiasm_ragtag.stats:md5,466273b499384b2c781c83dc583b8c99", - "test_ont_hifiasm_hic.fa.gz:md5,35d9e542fb372022a36ecf4854467e80", + "test_ont_hifiasm_ragtag.unmapped.txt:md5,e99c39c4afff7b433fb3973359dae6a4", "test_ont_hifiasm_hic.bp.hap1.p_ctg.gfa:md5,c9a084903ea872a7ac28f3bbd5eee8f3", "test_ont_hifiasm_hic.bp.hap2.p_ctg.gfa:md5,d41d8cd98f00b204e9800998ecf8427e", "test_ont_hifiasm_hic.bp.p_ctg.gfa:md5,d78f7a647429b254d9d46aab4d1306a0", @@ -638,11 +629,10 @@ "test_ont_hifiasm_hic_hic_dedup.bam:md5,9246dec2c1b6d6f4fd37383ddda244cb", "test_ont_hifiasm_hic.fa.gz.fai:md5,3f23b28c147c40cb4f1d6571cf2dc045", "test_ont_hifiasm_hic.fa.gz.gzi:md5,a5721349018bd8e33902a3e18ef9f530", - "test_ont_hifiasm_hic_hic_scaffolds_final.fa.gz:md5,3ac2a0232e899bcb28b72e3c4f1c2d79", "test_ont_hifiasm_hic_hic_scaffolds_final.fa:md5,3ac2a0232e899bcb28b72e3c4f1c2d79" ] ], - "timestamp": "2026-07-21T11:22:02.206144024", + "timestamp": "2026-08-28T15:31:58.143500933", "meta": { "nf-test": "0.9.5", "nextflow": "25.10.4" @@ -650,7 +640,7 @@ }, "-profile test": { "content": [ - 80, + 88, { "ADD_RG": { "picard": "3.4.0" @@ -712,6 +702,9 @@ "HIFIASM_ONT": { "hifasm": "0.25.0-r726" }, + "LIFTOFF": { + "liftoff": "1.6.3" + }, "MARKDUP": { "picard": "3.4.0" }, @@ -729,6 +722,8 @@ } }, [ + "genomeqc_samplesheet", + "genomeqc_samplesheet/nf-core-genomeqc-in.csv", "pipeline_info", "pipeline_info/nf_core_pipeline_software_versions.yml", "report", @@ -736,23 +731,20 @@ "test_flye_hifiasm", "test_flye_hifiasm/assembly", "test_flye_hifiasm/assembly/flye", - "test_flye_hifiasm/assembly/flye/out", - "test_flye_hifiasm/assembly/flye/out/test_flye_hifiasm.assembly.fa.gz", + "test_flye_hifiasm/assembly/flye/test_flye_hifiasm.assembly.fa.gz", "test_flye_hifiasm/assembly/flye/test_flye_hifiasm.assembly_graph.gfa.gz", "test_flye_hifiasm/assembly/flye/test_flye_hifiasm.assembly_graph.gv.gz", "test_flye_hifiasm/assembly/flye/test_flye_hifiasm.assembly_info.txt", "test_flye_hifiasm/assembly/flye/test_flye_hifiasm.flye.log", "test_flye_hifiasm/assembly/flye/test_flye_hifiasm.params.json", "test_flye_hifiasm/assembly/hifiasm", - "test_flye_hifiasm/assembly/hifiasm/fasta", - "test_flye_hifiasm/assembly/hifiasm/fasta/out", - "test_flye_hifiasm/assembly/hifiasm/fasta/out/test_flye_hifiasm.fa.gz", "test_flye_hifiasm/assembly/hifiasm/test_flye_hifiasm.bp.hap1.p_ctg.gfa", "test_flye_hifiasm/assembly/hifiasm/test_flye_hifiasm.bp.hap2.p_ctg.gfa", "test_flye_hifiasm/assembly/hifiasm/test_flye_hifiasm.bp.p_ctg.gfa", "test_flye_hifiasm/assembly/hifiasm/test_flye_hifiasm.bp.p_utg.gfa", "test_flye_hifiasm/assembly/hifiasm/test_flye_hifiasm.bp.r_utg.gfa", "test_flye_hifiasm/assembly/hifiasm/test_flye_hifiasm.ec.bin", + "test_flye_hifiasm/assembly/hifiasm/test_flye_hifiasm.fa.gz", "test_flye_hifiasm/assembly/hifiasm/test_flye_hifiasm.ovlp.reverse.bin", "test_flye_hifiasm/assembly/hifiasm/test_flye_hifiasm.ovlp.source.bin", "test_flye_hifiasm/assembly/hifiasm/test_flye_hifiasm.stderr.log", @@ -763,11 +755,9 @@ "test_flye_hifiasm/assembly/ragtag/test_flye_hifiasm_assembly_patch.patch.agp", "test_flye_hifiasm/assembly/ragtag/test_flye_hifiasm_assembly_patch.patch.err", "test_flye_hifiasm/assembly/ragtag/test_flye_hifiasm_assembly_patch.patch.fa", + "test_flye_hifiasm/assembly/ragtag/test_flye_hifiasm_assembly_patch.patch.fa.gz", "test_flye_hifiasm/assembly/ragtag/test_flye_hifiasm_assembly_patch.rename.agp", "test_flye_hifiasm/assembly/ragtag/test_flye_hifiasm_assembly_patch.rename.fa", - "test_flye_hifiasm/bgzip", - "test_flye_hifiasm/bgzip/out", - "test_flye_hifiasm/bgzip/out/test_flye_hifiasm_assembly_patch.patch.fa.gz", "test_flye_hifiasm/gfa2fa", "test_flye_hifiasm/gfa2fa/test_flye_hifiasm.fa", "test_flye_hifiasm/reads", @@ -784,21 +774,21 @@ "test_flye_hifiasm/reads/fastplong/ont/test_flye_hifiasm_ont.fastplong.log", "test_flye_hifiasm/scaffold", "test_flye_hifiasm/scaffold/ragtag", - "test_flye_hifiasm/scaffold/ragtag/out", - "test_flye_hifiasm/scaffold/ragtag/out/test_flye_hifiasm_ragtag.fa.gz", "test_flye_hifiasm/scaffold/ragtag/test_flye_hifiasm_ragtag.agp", "test_flye_hifiasm/scaffold/ragtag/test_flye_hifiasm_ragtag.fa", + "test_flye_hifiasm/scaffold/ragtag/test_flye_hifiasm_ragtag.fa.gz", "test_flye_hifiasm/scaffold/ragtag/test_flye_hifiasm_ragtag.stats", "test_hifi_flye", "test_hifi_flye/assembly", "test_hifi_flye/assembly/flye", - "test_hifi_flye/assembly/flye/out", - "test_hifi_flye/assembly/flye/out/test_hifi_flye.assembly.fa.gz", + "test_hifi_flye/assembly/flye/test_hifi_flye.assembly.fa.gz", "test_hifi_flye/assembly/flye/test_hifi_flye.assembly_graph.gfa.gz", "test_hifi_flye/assembly/flye/test_hifi_flye.assembly_graph.gv.gz", "test_hifi_flye/assembly/flye/test_hifi_flye.assembly_info.txt", "test_hifi_flye/assembly/flye/test_hifi_flye.flye.log", "test_hifi_flye/assembly/flye/test_hifi_flye.params.json", + "test_hifi_flye/assembly/test_hifi_flye_assembly.gff3", + "test_hifi_flye/assembly/test_hifi_flye_assembly.unmapped.txt", "test_hifi_flye/reads", "test_hifi_flye/reads/fastplong", "test_hifi_flye/reads/fastplong/hifi", @@ -813,23 +803,22 @@ "test_hifi_flye/reads/fastplong/ont/test_hifi_flye_ont.fastplong.log", "test_hifi_flye/scaffold", "test_hifi_flye/scaffold/ragtag", - "test_hifi_flye/scaffold/ragtag/out", - "test_hifi_flye/scaffold/ragtag/out/test_hifi_flye_ragtag.fa.gz", "test_hifi_flye/scaffold/ragtag/test_hifi_flye_ragtag.agp", "test_hifi_flye/scaffold/ragtag/test_hifi_flye_ragtag.fa", + "test_hifi_flye/scaffold/ragtag/test_hifi_flye_ragtag.fa.gz", + "test_hifi_flye/scaffold/ragtag/test_hifi_flye_ragtag.gff3", "test_hifi_flye/scaffold/ragtag/test_hifi_flye_ragtag.stats", + "test_hifi_flye/scaffold/ragtag/test_hifi_flye_ragtag.unmapped.txt", "test_hifi_hifiasm", "test_hifi_hifiasm/assembly", "test_hifi_hifiasm/assembly/hifiasm", - "test_hifi_hifiasm/assembly/hifiasm/fasta", - "test_hifi_hifiasm/assembly/hifiasm/fasta/out", - "test_hifi_hifiasm/assembly/hifiasm/fasta/out/test_hifi_hifiasm.fa.gz", "test_hifi_hifiasm/assembly/hifiasm/test_hifi_hifiasm.bp.hap1.p_ctg.gfa", "test_hifi_hifiasm/assembly/hifiasm/test_hifi_hifiasm.bp.hap2.p_ctg.gfa", "test_hifi_hifiasm/assembly/hifiasm/test_hifi_hifiasm.bp.p_ctg.gfa", "test_hifi_hifiasm/assembly/hifiasm/test_hifi_hifiasm.bp.p_utg.gfa", "test_hifi_hifiasm/assembly/hifiasm/test_hifi_hifiasm.bp.r_utg.gfa", "test_hifi_hifiasm/assembly/hifiasm/test_hifi_hifiasm.ec.bin", + "test_hifi_hifiasm/assembly/hifiasm/test_hifi_hifiasm.fa.gz", "test_hifi_hifiasm/assembly/hifiasm/test_hifi_hifiasm.ovlp.reverse.bin", "test_hifi_hifiasm/assembly/hifiasm/test_hifi_hifiasm.ovlp.source.bin", "test_hifi_hifiasm/assembly/hifiasm/test_hifi_hifiasm.stderr.log", @@ -850,23 +839,20 @@ "test_hifiasm_flye", "test_hifiasm_flye/assembly", "test_hifiasm_flye/assembly/flye", - "test_hifiasm_flye/assembly/flye/out", - "test_hifiasm_flye/assembly/flye/out/test_hifiasm_flye.assembly.fa.gz", + "test_hifiasm_flye/assembly/flye/test_hifiasm_flye.assembly.fa.gz", "test_hifiasm_flye/assembly/flye/test_hifiasm_flye.assembly_graph.gfa.gz", "test_hifiasm_flye/assembly/flye/test_hifiasm_flye.assembly_graph.gv.gz", "test_hifiasm_flye/assembly/flye/test_hifiasm_flye.assembly_info.txt", "test_hifiasm_flye/assembly/flye/test_hifiasm_flye.flye.log", "test_hifiasm_flye/assembly/flye/test_hifiasm_flye.params.json", "test_hifiasm_flye/assembly/hifiasm_ont", - "test_hifiasm_flye/assembly/hifiasm_ont/fasta", - "test_hifiasm_flye/assembly/hifiasm_ont/fasta/out", - "test_hifiasm_flye/assembly/hifiasm_ont/fasta/out/test_hifiasm_flye.fa.gz", "test_hifiasm_flye/assembly/hifiasm_ont/test_hifiasm_flye.bp.hap1.p_ctg.gfa", "test_hifiasm_flye/assembly/hifiasm_ont/test_hifiasm_flye.bp.hap2.p_ctg.gfa", "test_hifiasm_flye/assembly/hifiasm_ont/test_hifiasm_flye.bp.p_ctg.gfa", "test_hifiasm_flye/assembly/hifiasm_ont/test_hifiasm_flye.bp.p_utg.gfa", "test_hifiasm_flye/assembly/hifiasm_ont/test_hifiasm_flye.bp.r_utg.gfa", "test_hifiasm_flye/assembly/hifiasm_ont/test_hifiasm_flye.ec.bin", + "test_hifiasm_flye/assembly/hifiasm_ont/test_hifiasm_flye.fa.gz", "test_hifiasm_flye/assembly/hifiasm_ont/test_hifiasm_flye.ovlp.reverse.bin", "test_hifiasm_flye/assembly/hifiasm_ont/test_hifiasm_flye.ovlp.source.bin", "test_hifiasm_flye/assembly/hifiasm_ont/test_hifiasm_flye.stderr.log", @@ -877,11 +863,11 @@ "test_hifiasm_flye/assembly/ragtag/test_hifiasm_flye_assembly_patch.patch.agp", "test_hifiasm_flye/assembly/ragtag/test_hifiasm_flye_assembly_patch.patch.err", "test_hifiasm_flye/assembly/ragtag/test_hifiasm_flye_assembly_patch.patch.fa", + "test_hifiasm_flye/assembly/ragtag/test_hifiasm_flye_assembly_patch.patch.fa.gz", "test_hifiasm_flye/assembly/ragtag/test_hifiasm_flye_assembly_patch.rename.agp", "test_hifiasm_flye/assembly/ragtag/test_hifiasm_flye_assembly_patch.rename.fa", - "test_hifiasm_flye/bgzip", - "test_hifiasm_flye/bgzip/out", - "test_hifiasm_flye/bgzip/out/test_hifiasm_flye_assembly_patch.patch.fa.gz", + "test_hifiasm_flye/assembly/test_hifiasm_flye_assembly.gff3", + "test_hifiasm_flye/assembly/test_hifiasm_flye_assembly.unmapped.txt", "test_hifiasm_flye/gfa2fa", "test_hifiasm_flye/gfa2fa/test_hifiasm_flye.fa", "test_hifiasm_flye/reads", @@ -899,23 +885,20 @@ "test_hifiasm_flye_hic", "test_hifiasm_flye_hic/assembly", "test_hifiasm_flye_hic/assembly/flye", - "test_hifiasm_flye_hic/assembly/flye/out", - "test_hifiasm_flye_hic/assembly/flye/out/test_hifiasm_flye_hic.assembly.fa.gz", + "test_hifiasm_flye_hic/assembly/flye/test_hifiasm_flye_hic.assembly.fa.gz", "test_hifiasm_flye_hic/assembly/flye/test_hifiasm_flye_hic.assembly_graph.gfa.gz", "test_hifiasm_flye_hic/assembly/flye/test_hifiasm_flye_hic.assembly_graph.gv.gz", "test_hifiasm_flye_hic/assembly/flye/test_hifiasm_flye_hic.assembly_info.txt", "test_hifiasm_flye_hic/assembly/flye/test_hifiasm_flye_hic.flye.log", "test_hifiasm_flye_hic/assembly/flye/test_hifiasm_flye_hic.params.json", "test_hifiasm_flye_hic/assembly/hifiasm_ont", - "test_hifiasm_flye_hic/assembly/hifiasm_ont/fasta", - "test_hifiasm_flye_hic/assembly/hifiasm_ont/fasta/out", - "test_hifiasm_flye_hic/assembly/hifiasm_ont/fasta/out/test_hifiasm_flye_hic.fa.gz", "test_hifiasm_flye_hic/assembly/hifiasm_ont/test_hifiasm_flye_hic.bp.hap1.p_ctg.gfa", "test_hifiasm_flye_hic/assembly/hifiasm_ont/test_hifiasm_flye_hic.bp.hap2.p_ctg.gfa", "test_hifiasm_flye_hic/assembly/hifiasm_ont/test_hifiasm_flye_hic.bp.p_ctg.gfa", "test_hifiasm_flye_hic/assembly/hifiasm_ont/test_hifiasm_flye_hic.bp.p_utg.gfa", "test_hifiasm_flye_hic/assembly/hifiasm_ont/test_hifiasm_flye_hic.bp.r_utg.gfa", "test_hifiasm_flye_hic/assembly/hifiasm_ont/test_hifiasm_flye_hic.ec.bin", + "test_hifiasm_flye_hic/assembly/hifiasm_ont/test_hifiasm_flye_hic.fa.gz", "test_hifiasm_flye_hic/assembly/hifiasm_ont/test_hifiasm_flye_hic.ovlp.reverse.bin", "test_hifiasm_flye_hic/assembly/hifiasm_ont/test_hifiasm_flye_hic.ovlp.source.bin", "test_hifiasm_flye_hic/assembly/hifiasm_ont/test_hifiasm_flye_hic.stderr.log", @@ -926,11 +909,11 @@ "test_hifiasm_flye_hic/assembly/ragtag/test_hifiasm_flye_hic_assembly_patch.patch.agp", "test_hifiasm_flye_hic/assembly/ragtag/test_hifiasm_flye_hic_assembly_patch.patch.err", "test_hifiasm_flye_hic/assembly/ragtag/test_hifiasm_flye_hic_assembly_patch.patch.fa", + "test_hifiasm_flye_hic/assembly/ragtag/test_hifiasm_flye_hic_assembly_patch.patch.fa.gz", "test_hifiasm_flye_hic/assembly/ragtag/test_hifiasm_flye_hic_assembly_patch.rename.agp", "test_hifiasm_flye_hic/assembly/ragtag/test_hifiasm_flye_hic_assembly_patch.rename.fa", - "test_hifiasm_flye_hic/bgzip", - "test_hifiasm_flye_hic/bgzip/out", - "test_hifiasm_flye_hic/bgzip/out/test_hifiasm_flye_hic_assembly_patch.patch.fa.gz", + "test_hifiasm_flye_hic/assembly/test_hifiasm_flye_hic_assembly.gff3", + "test_hifiasm_flye_hic/assembly/test_hifiasm_flye_hic_assembly.unmapped.txt", "test_hifiasm_flye_hic/gfa2fa", "test_hifiasm_flye_hic/gfa2fa/test_hifiasm_flye_hic.fa", "test_hifiasm_flye_hic/hic_reads", @@ -970,12 +953,12 @@ "test_hifiasm_flye_hic/scaffold/hic/markdup/test_hifiasm_flye_hic_hic_dedup.MarkDuplicates.metrics.txt", "test_hifiasm_flye_hic/scaffold/hic/markdup/test_hifiasm_flye_hic_hic_dedup.bai", "test_hifiasm_flye_hic/scaffold/hic/markdup/test_hifiasm_flye_hic_hic_dedup.bam", + "test_hifiasm_flye_hic/scaffold/hic/test_hifiasm_flye_hic_links.gff3", + "test_hifiasm_flye_hic/scaffold/hic/test_hifiasm_flye_hic_links.unmapped.txt", "test_hifiasm_flye_hic/scaffold/hic/yahs", "test_hifiasm_flye_hic/scaffold/hic/yahs/index", "test_hifiasm_flye_hic/scaffold/hic/yahs/index/test_hifiasm_flye_hic_assembly_patch.patch.fa.gz.fai", "test_hifiasm_flye_hic/scaffold/hic/yahs/index/test_hifiasm_flye_hic_assembly_patch.patch.fa.gz.gzi", - "test_hifiasm_flye_hic/scaffold/hic/yahs/out", - "test_hifiasm_flye_hic/scaffold/hic/yahs/out/test_hifiasm_flye_hic_hic_scaffolds_final.fa.gz", "test_hifiasm_flye_hic/scaffold/hic/yahs/test_hifiasm_flye_hic_hic.bin", "test_hifiasm_flye_hic/scaffold/hic/yahs/test_hifiasm_flye_hic_hic.log", "test_hifiasm_flye_hic/scaffold/hic/yahs/test_hifiasm_flye_hic_hic_inital_break_01.agp", @@ -983,18 +966,17 @@ "test_hifiasm_flye_hic/scaffold/hic/yahs/test_hifiasm_flye_hic_hic_r02_break.agp", "test_hifiasm_flye_hic/scaffold/hic/yahs/test_hifiasm_flye_hic_hic_scaffolds_final.agp", "test_hifiasm_flye_hic/scaffold/hic/yahs/test_hifiasm_flye_hic_hic_scaffolds_final.fa", + "test_hifiasm_flye_hic/scaffold/hic/yahs/test_hifiasm_flye_hic_hic_scaffolds_final.fa.gz", "test_hifiasm_ul", "test_hifiasm_ul/assembly", "test_hifiasm_ul/assembly/hifiasm", - "test_hifiasm_ul/assembly/hifiasm/fasta", - "test_hifiasm_ul/assembly/hifiasm/fasta/out", - "test_hifiasm_ul/assembly/hifiasm/fasta/out/test_hifiasm_ul.fa.gz", "test_hifiasm_ul/assembly/hifiasm/test_hifiasm_ul.bp.hap1.p_ctg.gfa", "test_hifiasm_ul/assembly/hifiasm/test_hifiasm_ul.bp.hap2.p_ctg.gfa", "test_hifiasm_ul/assembly/hifiasm/test_hifiasm_ul.bp.p_ctg.gfa", "test_hifiasm_ul/assembly/hifiasm/test_hifiasm_ul.bp.p_utg.gfa", "test_hifiasm_ul/assembly/hifiasm/test_hifiasm_ul.bp.r_utg.gfa", "test_hifiasm_ul/assembly/hifiasm/test_hifiasm_ul.ec.bin", + "test_hifiasm_ul/assembly/hifiasm/test_hifiasm_ul.fa.gz", "test_hifiasm_ul/assembly/hifiasm/test_hifiasm_ul.ovlp.reverse.bin", "test_hifiasm_ul/assembly/hifiasm/test_hifiasm_ul.ovlp.source.bin", "test_hifiasm_ul/assembly/hifiasm/test_hifiasm_ul.re.uidx.bin", @@ -1041,20 +1023,20 @@ "test_hifiasm_ul/scaffold/longstitch/assembly.cut250.tigmint.fa.k32.w100.z1000.trimmed_scafs.path", "test_hifiasm_ul/scaffold/longstitch/assembly.cut250.tigmint.fa.k32.w100.z1000.trimmed_scafs.tsv", "test_hifiasm_ul/scaffold/longstitch/assembly.cut250.tigmint.fa.k32.w100.z1000.verbose_mapping.tsv", - "test_hifiasm_ul/scaffold/longstitch/out", - "test_hifiasm_ul/scaffold/longstitch/out/test_hifiasm_ul_longstitch.tigmint-ntLink-arks.fa.gz", "test_hifiasm_ul/scaffold/longstitch/test_hifiasm_ul_longstitch.tigmint-ntLink-arks.fa", + "test_hifiasm_ul/scaffold/longstitch/test_hifiasm_ul_longstitch.tigmint-ntLink-arks.fa.gz", "test_hifiasm_ul/scaffold/longstitch/versions.yml", "test_ont_flye", "test_ont_flye/assembly", "test_ont_flye/assembly/flye", - "test_ont_flye/assembly/flye/out", - "test_ont_flye/assembly/flye/out/test_ont_flye.assembly.fa.gz", + "test_ont_flye/assembly/flye/test_ont_flye.assembly.fa.gz", "test_ont_flye/assembly/flye/test_ont_flye.assembly_graph.gfa.gz", "test_ont_flye/assembly/flye/test_ont_flye.assembly_graph.gv.gz", "test_ont_flye/assembly/flye/test_ont_flye.assembly_info.txt", "test_ont_flye/assembly/flye/test_ont_flye.flye.log", "test_ont_flye/assembly/flye/test_ont_flye.params.json", + "test_ont_flye/assembly/test_ont_flye_assembly.gff3", + "test_ont_flye/assembly/test_ont_flye_assembly.unmapped.txt", "test_ont_flye/reads", "test_ont_flye/reads/fastplong", "test_ont_flye/reads/fastplong/hifi", @@ -1070,18 +1052,18 @@ "test_ont_hifiasm", "test_ont_hifiasm/assembly", "test_ont_hifiasm/assembly/hifiasm_ont", - "test_ont_hifiasm/assembly/hifiasm_ont/fasta", - "test_ont_hifiasm/assembly/hifiasm_ont/fasta/out", - "test_ont_hifiasm/assembly/hifiasm_ont/fasta/out/test_ont_hifiasm.fa.gz", "test_ont_hifiasm/assembly/hifiasm_ont/test_ont_hifiasm.bp.hap1.p_ctg.gfa", "test_ont_hifiasm/assembly/hifiasm_ont/test_ont_hifiasm.bp.hap2.p_ctg.gfa", "test_ont_hifiasm/assembly/hifiasm_ont/test_ont_hifiasm.bp.p_ctg.gfa", "test_ont_hifiasm/assembly/hifiasm_ont/test_ont_hifiasm.bp.p_utg.gfa", "test_ont_hifiasm/assembly/hifiasm_ont/test_ont_hifiasm.bp.r_utg.gfa", "test_ont_hifiasm/assembly/hifiasm_ont/test_ont_hifiasm.ec.bin", + "test_ont_hifiasm/assembly/hifiasm_ont/test_ont_hifiasm.fa.gz", "test_ont_hifiasm/assembly/hifiasm_ont/test_ont_hifiasm.ovlp.reverse.bin", "test_ont_hifiasm/assembly/hifiasm_ont/test_ont_hifiasm.ovlp.source.bin", "test_ont_hifiasm/assembly/hifiasm_ont/test_ont_hifiasm.stderr.log", + "test_ont_hifiasm/assembly/test_ont_hifiasm_assembly.gff3", + "test_ont_hifiasm/assembly/test_ont_hifiasm_assembly.unmapped.txt", "test_ont_hifiasm/gfa2fa", "test_ont_hifiasm/gfa2fa/test_ont_hifiasm.fa", "test_ont_hifiasm/reads", @@ -1098,23 +1080,22 @@ "test_ont_hifiasm/reads/fastplong/ont/test_ont_hifiasm_ont.fastplong.log", "test_ont_hifiasm/scaffold", "test_ont_hifiasm/scaffold/ragtag", - "test_ont_hifiasm/scaffold/ragtag/out", - "test_ont_hifiasm/scaffold/ragtag/out/test_ont_hifiasm_ragtag.fa.gz", "test_ont_hifiasm/scaffold/ragtag/test_ont_hifiasm_ragtag.agp", "test_ont_hifiasm/scaffold/ragtag/test_ont_hifiasm_ragtag.fa", + "test_ont_hifiasm/scaffold/ragtag/test_ont_hifiasm_ragtag.fa.gz", + "test_ont_hifiasm/scaffold/ragtag/test_ont_hifiasm_ragtag.gff3", "test_ont_hifiasm/scaffold/ragtag/test_ont_hifiasm_ragtag.stats", + "test_ont_hifiasm/scaffold/ragtag/test_ont_hifiasm_ragtag.unmapped.txt", "test_ont_hifiasm_hic", "test_ont_hifiasm_hic/assembly", "test_ont_hifiasm_hic/assembly/hifiasm_ont", - "test_ont_hifiasm_hic/assembly/hifiasm_ont/fasta", - "test_ont_hifiasm_hic/assembly/hifiasm_ont/fasta/out", - "test_ont_hifiasm_hic/assembly/hifiasm_ont/fasta/out/test_ont_hifiasm_hic.fa.gz", "test_ont_hifiasm_hic/assembly/hifiasm_ont/test_ont_hifiasm_hic.bp.hap1.p_ctg.gfa", "test_ont_hifiasm_hic/assembly/hifiasm_ont/test_ont_hifiasm_hic.bp.hap2.p_ctg.gfa", "test_ont_hifiasm_hic/assembly/hifiasm_ont/test_ont_hifiasm_hic.bp.p_ctg.gfa", "test_ont_hifiasm_hic/assembly/hifiasm_ont/test_ont_hifiasm_hic.bp.p_utg.gfa", "test_ont_hifiasm_hic/assembly/hifiasm_ont/test_ont_hifiasm_hic.bp.r_utg.gfa", "test_ont_hifiasm_hic/assembly/hifiasm_ont/test_ont_hifiasm_hic.ec.bin", + "test_ont_hifiasm_hic/assembly/hifiasm_ont/test_ont_hifiasm_hic.fa.gz", "test_ont_hifiasm_hic/assembly/hifiasm_ont/test_ont_hifiasm_hic.ovlp.reverse.bin", "test_ont_hifiasm_hic/assembly/hifiasm_ont/test_ont_hifiasm_hic.ovlp.source.bin", "test_ont_hifiasm_hic/assembly/hifiasm_ont/test_ont_hifiasm_hic.stderr.log", @@ -1161,19 +1142,18 @@ "test_ont_hifiasm_hic/scaffold/hic/yahs/index", "test_ont_hifiasm_hic/scaffold/hic/yahs/index/test_ont_hifiasm_hic.fa.gz.fai", "test_ont_hifiasm_hic/scaffold/hic/yahs/index/test_ont_hifiasm_hic.fa.gz.gzi", - "test_ont_hifiasm_hic/scaffold/hic/yahs/out", - "test_ont_hifiasm_hic/scaffold/hic/yahs/out/test_ont_hifiasm_hic_hic_scaffolds_final.fa.gz", "test_ont_hifiasm_hic/scaffold/hic/yahs/test_ont_hifiasm_hic_hic.bin", "test_ont_hifiasm_hic/scaffold/hic/yahs/test_ont_hifiasm_hic_hic.log", "test_ont_hifiasm_hic/scaffold/hic/yahs/test_ont_hifiasm_hic_hic_inital_break_01.agp", "test_ont_hifiasm_hic/scaffold/hic/yahs/test_ont_hifiasm_hic_hic_r01_break.agp", "test_ont_hifiasm_hic/scaffold/hic/yahs/test_ont_hifiasm_hic_hic_r02_break.agp", "test_ont_hifiasm_hic/scaffold/hic/yahs/test_ont_hifiasm_hic_hic_scaffolds_final.agp", - "test_ont_hifiasm_hic/scaffold/hic/yahs/test_ont_hifiasm_hic_hic_scaffolds_final.fa" + "test_ont_hifiasm_hic/scaffold/hic/yahs/test_ont_hifiasm_hic_hic_scaffolds_final.fa", + "test_ont_hifiasm_hic/scaffold/hic/yahs/test_ont_hifiasm_hic_hic_scaffolds_final.fa.gz" ], [ + "nf-core-genomeqc-in.csv:md5,dfd339a042d4be575d4d61924100de3e", "test_flye_hifiasm.params.json:md5,afa91c041bce5e190f4a699d11b69db6", - "test_flye_hifiasm.fa.gz:md5,77e3d5af48175c784bfd217048fe271b", "test_flye_hifiasm.bp.hap1.p_ctg.gfa:md5,46ee70869884ad585165bd48081414e9", "test_flye_hifiasm.bp.hap2.p_ctg.gfa:md5,7792865547989d6d284f640425c4e36c", "test_flye_hifiasm.bp.p_ctg.gfa:md5,8fe65466d76815ffe1663ff6d8f2e8d1", @@ -1185,11 +1165,12 @@ "test_flye_hifiasm_hifi.fastplong.json:md5,0e20fedb8dfe0646232060da502883ee", "test_flye_hifiasm_ont.fastplong.json:md5,826cc5a321dd130a2f2c53cdb1a345b2", "test_hifi_flye.params.json:md5,54b576cb6d4d27656878a7fd3657bde9", + "test_hifi_flye_assembly.unmapped.txt:md5,d41d8cd98f00b204e9800998ecf8427e", "test_hifi_flye_hifi.fastplong.json:md5,daad59b32b84b79c29c274ed20f03cce", "test_hifi_flye_ont.fastplong.json:md5,198eb762846548340557f5f861f10c11", "test_hifi_flye_ragtag.fa:md5,79d2708ebfdbd7b766b9e7c6ee795d5b", "test_hifi_flye_ragtag.stats:md5,25325bb3c27246be0934f38f291b57b2", - "test_hifi_hifiasm.fa.gz:md5,77e3d5af48175c784bfd217048fe271b", + "test_hifi_flye_ragtag.unmapped.txt:md5,d41d8cd98f00b204e9800998ecf8427e", "test_hifi_hifiasm.bp.hap1.p_ctg.gfa:md5,46ee70869884ad585165bd48081414e9", "test_hifi_hifiasm.bp.hap2.p_ctg.gfa:md5,7792865547989d6d284f640425c4e36c", "test_hifi_hifiasm.bp.p_ctg.gfa:md5,8fe65466d76815ffe1663ff6d8f2e8d1", @@ -1199,7 +1180,6 @@ "test_hifi_hifiasm_hifi.fastplong.json:md5,e58f896e9b70344ae4e607324c2c6742", "test_hifi_hifiasm_ont.fastplong.json:md5,eedbb98c4d3870f38320d75b21c86604", "test_hifiasm_flye.params.json:md5,54b576cb6d4d27656878a7fd3657bde9", - "test_hifiasm_flye.fa.gz:md5,35d9e542fb372022a36ecf4854467e80", "test_hifiasm_flye.bp.hap1.p_ctg.gfa:md5,c9a084903ea872a7ac28f3bbd5eee8f3", "test_hifiasm_flye.bp.hap2.p_ctg.gfa:md5,d41d8cd98f00b204e9800998ecf8427e", "test_hifiasm_flye.bp.p_ctg.gfa:md5,d78f7a647429b254d9d46aab4d1306a0", @@ -1210,11 +1190,11 @@ "test_hifiasm_flye_assembly_patch.patch.err:md5,d41d8cd98f00b204e9800998ecf8427e", "test_hifiasm_flye_assembly_patch.patch.fa:md5,6ff15d809eaa0ecf6381400cdd7f0770", "test_hifiasm_flye_assembly_patch.rename.fa:md5,48208c6df370a225c6f54f378d7a8e39", + "test_hifiasm_flye_assembly.unmapped.txt:md5,e99c39c4afff7b433fb3973359dae6a4", "test_hifiasm_flye.fa:md5,35d9e542fb372022a36ecf4854467e80", "test_hifiasm_flye_hifi.fastplong.json:md5,2671b946d2bf533341b86a9f2424e5c3", "test_hifiasm_flye_ont.fastplong.json:md5,924d11a05764994135ff5de294052a02", "test_hifiasm_flye_hic.params.json:md5,54b576cb6d4d27656878a7fd3657bde9", - "test_hifiasm_flye_hic.fa.gz:md5,35d9e542fb372022a36ecf4854467e80", "test_hifiasm_flye_hic.bp.hap1.p_ctg.gfa:md5,c9a084903ea872a7ac28f3bbd5eee8f3", "test_hifiasm_flye_hic.bp.hap2.p_ctg.gfa:md5,d41d8cd98f00b204e9800998ecf8427e", "test_hifiasm_flye_hic.bp.p_ctg.gfa:md5,d78f7a647429b254d9d46aab4d1306a0", @@ -1225,6 +1205,7 @@ "test_hifiasm_flye_hic_assembly_patch.patch.err:md5,d41d8cd98f00b204e9800998ecf8427e", "test_hifiasm_flye_hic_assembly_patch.patch.fa:md5,6ff15d809eaa0ecf6381400cdd7f0770", "test_hifiasm_flye_hic_assembly_patch.rename.fa:md5,48208c6df370a225c6f54f378d7a8e39", + "test_hifiasm_flye_hic_assembly.unmapped.txt:md5,e99c39c4afff7b433fb3973359dae6a4", "test_hifiasm_flye_hic.fa:md5,35d9e542fb372022a36ecf4854467e80", "test_hifiasm_flye_hic_hicreads.fastp.json:md5,639daa4b554b8562208d2f7dff3a118f", "test_hifiasm_flye_hic_hifi.fastplong.json:md5,1c4764224854af4537899de86c8e2e56", @@ -1238,11 +1219,10 @@ "test_hifiasm_flye_hic_bwamem.bam:md5,837f8fbfbaf79b1049093e62a23a02b2", "test_hifiasm_flye_hic_hic_dedup.bai:md5,aeda4dd1092e5ae65a44c90faa2a4e86", "test_hifiasm_flye_hic_hic_dedup.bam:md5,d93aabe7dbda135b1562eeef7808d347", + "test_hifiasm_flye_hic_links.unmapped.txt:md5,e99c39c4afff7b433fb3973359dae6a4", "test_hifiasm_flye_hic_assembly_patch.patch.fa.gz.fai:md5,06f2947d7897ca8a7c6f30a81bd6bdcc", "test_hifiasm_flye_hic_assembly_patch.patch.fa.gz.gzi:md5,251cd3924556d6f48e9d5127bdd15ee2", - "test_hifiasm_flye_hic_hic_scaffolds_final.fa.gz:md5,3ac2a0232e899bcb28b72e3c4f1c2d79", "test_hifiasm_flye_hic_hic_scaffolds_final.fa:md5,3ac2a0232e899bcb28b72e3c4f1c2d79", - "test_hifiasm_ul.fa.gz:md5,77e3d5af48175c784bfd217048fe271b", "test_hifiasm_ul.bp.hap1.p_ctg.gfa:md5,46ee70869884ad585165bd48081414e9", "test_hifiasm_ul.bp.hap2.p_ctg.gfa:md5,7792865547989d6d284f640425c4e36c", "test_hifiasm_ul.bp.p_ctg.gfa:md5,8fe65466d76815ffe1663ff6d8f2e8d1", @@ -1253,20 +1233,21 @@ "test_hifiasm_ul_ont.fastplong.json:md5,86da6d58ac4630bfeae3ee08014ecb0b", "versions.yml:md5,c6c0c66defcf12c9bd29c649fbef58af", "test_ont_flye.params.json:md5,afa91c041bce5e190f4a699d11b69db6", + "test_ont_flye_assembly.unmapped.txt:md5,d41d8cd98f00b204e9800998ecf8427e", "test_ont_flye_hifi.fastplong.json:md5,9205a4cf65cce249429badc208348349", "test_ont_flye_ont.fastplong.json:md5,e418b2481ade21bc45e77d1437bad913", - "test_ont_hifiasm.fa.gz:md5,35d9e542fb372022a36ecf4854467e80", "test_ont_hifiasm.bp.hap1.p_ctg.gfa:md5,c9a084903ea872a7ac28f3bbd5eee8f3", "test_ont_hifiasm.bp.hap2.p_ctg.gfa:md5,d41d8cd98f00b204e9800998ecf8427e", "test_ont_hifiasm.bp.p_ctg.gfa:md5,d78f7a647429b254d9d46aab4d1306a0", "test_ont_hifiasm.bp.p_utg.gfa:md5,e2b6621386edda1636dfb84ddd676ea8", "test_ont_hifiasm.bp.r_utg.gfa:md5,e2b6621386edda1636dfb84ddd676ea8", + "test_ont_hifiasm_assembly.unmapped.txt:md5,e99c39c4afff7b433fb3973359dae6a4", "test_ont_hifiasm.fa:md5,35d9e542fb372022a36ecf4854467e80", "test_ont_hifiasm_hifi.fastplong.json:md5,91878df7edc2b07a885c103f260fc70e", "test_ont_hifiasm_ont.fastplong.json:md5,e97714274268b5a30be4d9851f2b61b3", "test_ont_hifiasm_ragtag.fa:md5,51f2975257b49657716d2ca7cc6d5fe2", "test_ont_hifiasm_ragtag.stats:md5,466273b499384b2c781c83dc583b8c99", - "test_ont_hifiasm_hic.fa.gz:md5,35d9e542fb372022a36ecf4854467e80", + "test_ont_hifiasm_ragtag.unmapped.txt:md5,e99c39c4afff7b433fb3973359dae6a4", "test_ont_hifiasm_hic.bp.hap1.p_ctg.gfa:md5,c9a084903ea872a7ac28f3bbd5eee8f3", "test_ont_hifiasm_hic.bp.hap2.p_ctg.gfa:md5,d41d8cd98f00b204e9800998ecf8427e", "test_ont_hifiasm_hic.bp.p_ctg.gfa:md5,d78f7a647429b254d9d46aab4d1306a0", @@ -1287,11 +1268,10 @@ "test_ont_hifiasm_hic_hic_dedup.bam:md5,9246dec2c1b6d6f4fd37383ddda244cb", "test_ont_hifiasm_hic.fa.gz.fai:md5,3f23b28c147c40cb4f1d6571cf2dc045", "test_ont_hifiasm_hic.fa.gz.gzi:md5,a5721349018bd8e33902a3e18ef9f530", - "test_ont_hifiasm_hic_hic_scaffolds_final.fa.gz:md5,3ac2a0232e899bcb28b72e3c4f1c2d79", "test_ont_hifiasm_hic_hic_scaffolds_final.fa:md5,3ac2a0232e899bcb28b72e3c4f1c2d79" ] ], - "timestamp": "2026-07-21T11:06:30.037902788", + "timestamp": "2026-08-28T15:16:42.348431261", "meta": { "nf-test": "0.9.5", "nextflow": "25.10.4" @@ -1299,7 +1279,7 @@ }, "-profile test_busco": { "content": [ - 80, + 88, { "ADD_RG": { "picard": "3.4.0" @@ -1361,6 +1341,9 @@ "HIFIASM_ONT": { "hifasm": "0.25.0-r726" }, + "LIFTOFF": { + "liftoff": "1.6.3" + }, "MARKDUP": { "picard": "3.4.0" }, @@ -1378,6 +1361,8 @@ } }, [ + "genomeqc_samplesheet", + "genomeqc_samplesheet/nf-core-genomeqc-in.csv", "pipeline_info", "pipeline_info/nf_core_pipeline_software_versions.yml", "report", @@ -1385,23 +1370,20 @@ "test_flye_hifiasm", "test_flye_hifiasm/assembly", "test_flye_hifiasm/assembly/flye", - "test_flye_hifiasm/assembly/flye/out", - "test_flye_hifiasm/assembly/flye/out/test_flye_hifiasm.assembly.fa.gz", + "test_flye_hifiasm/assembly/flye/test_flye_hifiasm.assembly.fa.gz", "test_flye_hifiasm/assembly/flye/test_flye_hifiasm.assembly_graph.gfa.gz", "test_flye_hifiasm/assembly/flye/test_flye_hifiasm.assembly_graph.gv.gz", "test_flye_hifiasm/assembly/flye/test_flye_hifiasm.assembly_info.txt", "test_flye_hifiasm/assembly/flye/test_flye_hifiasm.flye.log", "test_flye_hifiasm/assembly/flye/test_flye_hifiasm.params.json", "test_flye_hifiasm/assembly/hifiasm", - "test_flye_hifiasm/assembly/hifiasm/fasta", - "test_flye_hifiasm/assembly/hifiasm/fasta/out", - "test_flye_hifiasm/assembly/hifiasm/fasta/out/test_flye_hifiasm.fa.gz", "test_flye_hifiasm/assembly/hifiasm/test_flye_hifiasm.bp.hap1.p_ctg.gfa", "test_flye_hifiasm/assembly/hifiasm/test_flye_hifiasm.bp.hap2.p_ctg.gfa", "test_flye_hifiasm/assembly/hifiasm/test_flye_hifiasm.bp.p_ctg.gfa", "test_flye_hifiasm/assembly/hifiasm/test_flye_hifiasm.bp.p_utg.gfa", "test_flye_hifiasm/assembly/hifiasm/test_flye_hifiasm.bp.r_utg.gfa", "test_flye_hifiasm/assembly/hifiasm/test_flye_hifiasm.ec.bin", + "test_flye_hifiasm/assembly/hifiasm/test_flye_hifiasm.fa.gz", "test_flye_hifiasm/assembly/hifiasm/test_flye_hifiasm.ovlp.reverse.bin", "test_flye_hifiasm/assembly/hifiasm/test_flye_hifiasm.ovlp.source.bin", "test_flye_hifiasm/assembly/hifiasm/test_flye_hifiasm.stderr.log", @@ -1412,11 +1394,9 @@ "test_flye_hifiasm/assembly/ragtag/test_flye_hifiasm_assembly_patch.patch.agp", "test_flye_hifiasm/assembly/ragtag/test_flye_hifiasm_assembly_patch.patch.err", "test_flye_hifiasm/assembly/ragtag/test_flye_hifiasm_assembly_patch.patch.fa", + "test_flye_hifiasm/assembly/ragtag/test_flye_hifiasm_assembly_patch.patch.fa.gz", "test_flye_hifiasm/assembly/ragtag/test_flye_hifiasm_assembly_patch.rename.agp", "test_flye_hifiasm/assembly/ragtag/test_flye_hifiasm_assembly_patch.rename.fa", - "test_flye_hifiasm/bgzip", - "test_flye_hifiasm/bgzip/out", - "test_flye_hifiasm/bgzip/out/test_flye_hifiasm_assembly_patch.patch.fa.gz", "test_flye_hifiasm/gfa2fa", "test_flye_hifiasm/gfa2fa/test_flye_hifiasm.fa", "test_flye_hifiasm/reads", @@ -1433,21 +1413,21 @@ "test_flye_hifiasm/reads/fastplong/ont/test_flye_hifiasm_ont.fastplong.log", "test_flye_hifiasm/scaffold", "test_flye_hifiasm/scaffold/ragtag", - "test_flye_hifiasm/scaffold/ragtag/out", - "test_flye_hifiasm/scaffold/ragtag/out/test_flye_hifiasm_ragtag.fa.gz", "test_flye_hifiasm/scaffold/ragtag/test_flye_hifiasm_ragtag.agp", "test_flye_hifiasm/scaffold/ragtag/test_flye_hifiasm_ragtag.fa", + "test_flye_hifiasm/scaffold/ragtag/test_flye_hifiasm_ragtag.fa.gz", "test_flye_hifiasm/scaffold/ragtag/test_flye_hifiasm_ragtag.stats", "test_hifi_flye", "test_hifi_flye/assembly", "test_hifi_flye/assembly/flye", - "test_hifi_flye/assembly/flye/out", - "test_hifi_flye/assembly/flye/out/test_hifi_flye.assembly.fa.gz", + "test_hifi_flye/assembly/flye/test_hifi_flye.assembly.fa.gz", "test_hifi_flye/assembly/flye/test_hifi_flye.assembly_graph.gfa.gz", "test_hifi_flye/assembly/flye/test_hifi_flye.assembly_graph.gv.gz", "test_hifi_flye/assembly/flye/test_hifi_flye.assembly_info.txt", "test_hifi_flye/assembly/flye/test_hifi_flye.flye.log", "test_hifi_flye/assembly/flye/test_hifi_flye.params.json", + "test_hifi_flye/assembly/test_hifi_flye_assembly.gff3", + "test_hifi_flye/assembly/test_hifi_flye_assembly.unmapped.txt", "test_hifi_flye/reads", "test_hifi_flye/reads/fastplong", "test_hifi_flye/reads/fastplong/hifi", @@ -1462,23 +1442,22 @@ "test_hifi_flye/reads/fastplong/ont/test_hifi_flye_ont.fastplong.log", "test_hifi_flye/scaffold", "test_hifi_flye/scaffold/ragtag", - "test_hifi_flye/scaffold/ragtag/out", - "test_hifi_flye/scaffold/ragtag/out/test_hifi_flye_ragtag.fa.gz", "test_hifi_flye/scaffold/ragtag/test_hifi_flye_ragtag.agp", "test_hifi_flye/scaffold/ragtag/test_hifi_flye_ragtag.fa", + "test_hifi_flye/scaffold/ragtag/test_hifi_flye_ragtag.fa.gz", + "test_hifi_flye/scaffold/ragtag/test_hifi_flye_ragtag.gff3", "test_hifi_flye/scaffold/ragtag/test_hifi_flye_ragtag.stats", + "test_hifi_flye/scaffold/ragtag/test_hifi_flye_ragtag.unmapped.txt", "test_hifi_hifiasm", "test_hifi_hifiasm/assembly", "test_hifi_hifiasm/assembly/hifiasm", - "test_hifi_hifiasm/assembly/hifiasm/fasta", - "test_hifi_hifiasm/assembly/hifiasm/fasta/out", - "test_hifi_hifiasm/assembly/hifiasm/fasta/out/test_hifi_hifiasm.fa.gz", "test_hifi_hifiasm/assembly/hifiasm/test_hifi_hifiasm.bp.hap1.p_ctg.gfa", "test_hifi_hifiasm/assembly/hifiasm/test_hifi_hifiasm.bp.hap2.p_ctg.gfa", "test_hifi_hifiasm/assembly/hifiasm/test_hifi_hifiasm.bp.p_ctg.gfa", "test_hifi_hifiasm/assembly/hifiasm/test_hifi_hifiasm.bp.p_utg.gfa", "test_hifi_hifiasm/assembly/hifiasm/test_hifi_hifiasm.bp.r_utg.gfa", "test_hifi_hifiasm/assembly/hifiasm/test_hifi_hifiasm.ec.bin", + "test_hifi_hifiasm/assembly/hifiasm/test_hifi_hifiasm.fa.gz", "test_hifi_hifiasm/assembly/hifiasm/test_hifi_hifiasm.ovlp.reverse.bin", "test_hifi_hifiasm/assembly/hifiasm/test_hifi_hifiasm.ovlp.source.bin", "test_hifi_hifiasm/assembly/hifiasm/test_hifi_hifiasm.stderr.log", @@ -1499,23 +1478,20 @@ "test_hifiasm_flye", "test_hifiasm_flye/assembly", "test_hifiasm_flye/assembly/flye", - "test_hifiasm_flye/assembly/flye/out", - "test_hifiasm_flye/assembly/flye/out/test_hifiasm_flye.assembly.fa.gz", + "test_hifiasm_flye/assembly/flye/test_hifiasm_flye.assembly.fa.gz", "test_hifiasm_flye/assembly/flye/test_hifiasm_flye.assembly_graph.gfa.gz", "test_hifiasm_flye/assembly/flye/test_hifiasm_flye.assembly_graph.gv.gz", "test_hifiasm_flye/assembly/flye/test_hifiasm_flye.assembly_info.txt", "test_hifiasm_flye/assembly/flye/test_hifiasm_flye.flye.log", "test_hifiasm_flye/assembly/flye/test_hifiasm_flye.params.json", "test_hifiasm_flye/assembly/hifiasm_ont", - "test_hifiasm_flye/assembly/hifiasm_ont/fasta", - "test_hifiasm_flye/assembly/hifiasm_ont/fasta/out", - "test_hifiasm_flye/assembly/hifiasm_ont/fasta/out/test_hifiasm_flye.fa.gz", "test_hifiasm_flye/assembly/hifiasm_ont/test_hifiasm_flye.bp.hap1.p_ctg.gfa", "test_hifiasm_flye/assembly/hifiasm_ont/test_hifiasm_flye.bp.hap2.p_ctg.gfa", "test_hifiasm_flye/assembly/hifiasm_ont/test_hifiasm_flye.bp.p_ctg.gfa", "test_hifiasm_flye/assembly/hifiasm_ont/test_hifiasm_flye.bp.p_utg.gfa", "test_hifiasm_flye/assembly/hifiasm_ont/test_hifiasm_flye.bp.r_utg.gfa", "test_hifiasm_flye/assembly/hifiasm_ont/test_hifiasm_flye.ec.bin", + "test_hifiasm_flye/assembly/hifiasm_ont/test_hifiasm_flye.fa.gz", "test_hifiasm_flye/assembly/hifiasm_ont/test_hifiasm_flye.ovlp.reverse.bin", "test_hifiasm_flye/assembly/hifiasm_ont/test_hifiasm_flye.ovlp.source.bin", "test_hifiasm_flye/assembly/hifiasm_ont/test_hifiasm_flye.stderr.log", @@ -1526,11 +1502,11 @@ "test_hifiasm_flye/assembly/ragtag/test_hifiasm_flye_assembly_patch.patch.agp", "test_hifiasm_flye/assembly/ragtag/test_hifiasm_flye_assembly_patch.patch.err", "test_hifiasm_flye/assembly/ragtag/test_hifiasm_flye_assembly_patch.patch.fa", + "test_hifiasm_flye/assembly/ragtag/test_hifiasm_flye_assembly_patch.patch.fa.gz", "test_hifiasm_flye/assembly/ragtag/test_hifiasm_flye_assembly_patch.rename.agp", "test_hifiasm_flye/assembly/ragtag/test_hifiasm_flye_assembly_patch.rename.fa", - "test_hifiasm_flye/bgzip", - "test_hifiasm_flye/bgzip/out", - "test_hifiasm_flye/bgzip/out/test_hifiasm_flye_assembly_patch.patch.fa.gz", + "test_hifiasm_flye/assembly/test_hifiasm_flye_assembly.gff3", + "test_hifiasm_flye/assembly/test_hifiasm_flye_assembly.unmapped.txt", "test_hifiasm_flye/gfa2fa", "test_hifiasm_flye/gfa2fa/test_hifiasm_flye.fa", "test_hifiasm_flye/reads", @@ -1548,23 +1524,20 @@ "test_hifiasm_flye_hic", "test_hifiasm_flye_hic/assembly", "test_hifiasm_flye_hic/assembly/flye", - "test_hifiasm_flye_hic/assembly/flye/out", - "test_hifiasm_flye_hic/assembly/flye/out/test_hifiasm_flye_hic.assembly.fa.gz", + "test_hifiasm_flye_hic/assembly/flye/test_hifiasm_flye_hic.assembly.fa.gz", "test_hifiasm_flye_hic/assembly/flye/test_hifiasm_flye_hic.assembly_graph.gfa.gz", "test_hifiasm_flye_hic/assembly/flye/test_hifiasm_flye_hic.assembly_graph.gv.gz", "test_hifiasm_flye_hic/assembly/flye/test_hifiasm_flye_hic.assembly_info.txt", "test_hifiasm_flye_hic/assembly/flye/test_hifiasm_flye_hic.flye.log", "test_hifiasm_flye_hic/assembly/flye/test_hifiasm_flye_hic.params.json", "test_hifiasm_flye_hic/assembly/hifiasm_ont", - "test_hifiasm_flye_hic/assembly/hifiasm_ont/fasta", - "test_hifiasm_flye_hic/assembly/hifiasm_ont/fasta/out", - "test_hifiasm_flye_hic/assembly/hifiasm_ont/fasta/out/test_hifiasm_flye_hic.fa.gz", "test_hifiasm_flye_hic/assembly/hifiasm_ont/test_hifiasm_flye_hic.bp.hap1.p_ctg.gfa", "test_hifiasm_flye_hic/assembly/hifiasm_ont/test_hifiasm_flye_hic.bp.hap2.p_ctg.gfa", "test_hifiasm_flye_hic/assembly/hifiasm_ont/test_hifiasm_flye_hic.bp.p_ctg.gfa", "test_hifiasm_flye_hic/assembly/hifiasm_ont/test_hifiasm_flye_hic.bp.p_utg.gfa", "test_hifiasm_flye_hic/assembly/hifiasm_ont/test_hifiasm_flye_hic.bp.r_utg.gfa", "test_hifiasm_flye_hic/assembly/hifiasm_ont/test_hifiasm_flye_hic.ec.bin", + "test_hifiasm_flye_hic/assembly/hifiasm_ont/test_hifiasm_flye_hic.fa.gz", "test_hifiasm_flye_hic/assembly/hifiasm_ont/test_hifiasm_flye_hic.ovlp.reverse.bin", "test_hifiasm_flye_hic/assembly/hifiasm_ont/test_hifiasm_flye_hic.ovlp.source.bin", "test_hifiasm_flye_hic/assembly/hifiasm_ont/test_hifiasm_flye_hic.stderr.log", @@ -1575,11 +1548,11 @@ "test_hifiasm_flye_hic/assembly/ragtag/test_hifiasm_flye_hic_assembly_patch.patch.agp", "test_hifiasm_flye_hic/assembly/ragtag/test_hifiasm_flye_hic_assembly_patch.patch.err", "test_hifiasm_flye_hic/assembly/ragtag/test_hifiasm_flye_hic_assembly_patch.patch.fa", + "test_hifiasm_flye_hic/assembly/ragtag/test_hifiasm_flye_hic_assembly_patch.patch.fa.gz", "test_hifiasm_flye_hic/assembly/ragtag/test_hifiasm_flye_hic_assembly_patch.rename.agp", "test_hifiasm_flye_hic/assembly/ragtag/test_hifiasm_flye_hic_assembly_patch.rename.fa", - "test_hifiasm_flye_hic/bgzip", - "test_hifiasm_flye_hic/bgzip/out", - "test_hifiasm_flye_hic/bgzip/out/test_hifiasm_flye_hic_assembly_patch.patch.fa.gz", + "test_hifiasm_flye_hic/assembly/test_hifiasm_flye_hic_assembly.gff3", + "test_hifiasm_flye_hic/assembly/test_hifiasm_flye_hic_assembly.unmapped.txt", "test_hifiasm_flye_hic/gfa2fa", "test_hifiasm_flye_hic/gfa2fa/test_hifiasm_flye_hic.fa", "test_hifiasm_flye_hic/hic_reads", @@ -1619,12 +1592,12 @@ "test_hifiasm_flye_hic/scaffold/hic/markdup/test_hifiasm_flye_hic_hic_dedup.MarkDuplicates.metrics.txt", "test_hifiasm_flye_hic/scaffold/hic/markdup/test_hifiasm_flye_hic_hic_dedup.bai", "test_hifiasm_flye_hic/scaffold/hic/markdup/test_hifiasm_flye_hic_hic_dedup.bam", + "test_hifiasm_flye_hic/scaffold/hic/test_hifiasm_flye_hic_links.gff3", + "test_hifiasm_flye_hic/scaffold/hic/test_hifiasm_flye_hic_links.unmapped.txt", "test_hifiasm_flye_hic/scaffold/hic/yahs", "test_hifiasm_flye_hic/scaffold/hic/yahs/index", "test_hifiasm_flye_hic/scaffold/hic/yahs/index/test_hifiasm_flye_hic_assembly_patch.patch.fa.gz.fai", "test_hifiasm_flye_hic/scaffold/hic/yahs/index/test_hifiasm_flye_hic_assembly_patch.patch.fa.gz.gzi", - "test_hifiasm_flye_hic/scaffold/hic/yahs/out", - "test_hifiasm_flye_hic/scaffold/hic/yahs/out/test_hifiasm_flye_hic_hic_scaffolds_final.fa.gz", "test_hifiasm_flye_hic/scaffold/hic/yahs/test_hifiasm_flye_hic_hic.bin", "test_hifiasm_flye_hic/scaffold/hic/yahs/test_hifiasm_flye_hic_hic.log", "test_hifiasm_flye_hic/scaffold/hic/yahs/test_hifiasm_flye_hic_hic_inital_break_01.agp", @@ -1632,18 +1605,17 @@ "test_hifiasm_flye_hic/scaffold/hic/yahs/test_hifiasm_flye_hic_hic_r02_break.agp", "test_hifiasm_flye_hic/scaffold/hic/yahs/test_hifiasm_flye_hic_hic_scaffolds_final.agp", "test_hifiasm_flye_hic/scaffold/hic/yahs/test_hifiasm_flye_hic_hic_scaffolds_final.fa", + "test_hifiasm_flye_hic/scaffold/hic/yahs/test_hifiasm_flye_hic_hic_scaffolds_final.fa.gz", "test_hifiasm_ul", "test_hifiasm_ul/assembly", "test_hifiasm_ul/assembly/hifiasm", - "test_hifiasm_ul/assembly/hifiasm/fasta", - "test_hifiasm_ul/assembly/hifiasm/fasta/out", - "test_hifiasm_ul/assembly/hifiasm/fasta/out/test_hifiasm_ul.fa.gz", "test_hifiasm_ul/assembly/hifiasm/test_hifiasm_ul.bp.hap1.p_ctg.gfa", "test_hifiasm_ul/assembly/hifiasm/test_hifiasm_ul.bp.hap2.p_ctg.gfa", "test_hifiasm_ul/assembly/hifiasm/test_hifiasm_ul.bp.p_ctg.gfa", "test_hifiasm_ul/assembly/hifiasm/test_hifiasm_ul.bp.p_utg.gfa", "test_hifiasm_ul/assembly/hifiasm/test_hifiasm_ul.bp.r_utg.gfa", "test_hifiasm_ul/assembly/hifiasm/test_hifiasm_ul.ec.bin", + "test_hifiasm_ul/assembly/hifiasm/test_hifiasm_ul.fa.gz", "test_hifiasm_ul/assembly/hifiasm/test_hifiasm_ul.ovlp.reverse.bin", "test_hifiasm_ul/assembly/hifiasm/test_hifiasm_ul.ovlp.source.bin", "test_hifiasm_ul/assembly/hifiasm/test_hifiasm_ul.re.uidx.bin", @@ -1690,20 +1662,20 @@ "test_hifiasm_ul/scaffold/longstitch/assembly.cut250.tigmint.fa.k32.w100.z1000.trimmed_scafs.path", "test_hifiasm_ul/scaffold/longstitch/assembly.cut250.tigmint.fa.k32.w100.z1000.trimmed_scafs.tsv", "test_hifiasm_ul/scaffold/longstitch/assembly.cut250.tigmint.fa.k32.w100.z1000.verbose_mapping.tsv", - "test_hifiasm_ul/scaffold/longstitch/out", - "test_hifiasm_ul/scaffold/longstitch/out/test_hifiasm_ul_longstitch.tigmint-ntLink-arks.fa.gz", "test_hifiasm_ul/scaffold/longstitch/test_hifiasm_ul_longstitch.tigmint-ntLink-arks.fa", + "test_hifiasm_ul/scaffold/longstitch/test_hifiasm_ul_longstitch.tigmint-ntLink-arks.fa.gz", "test_hifiasm_ul/scaffold/longstitch/versions.yml", "test_ont_flye", "test_ont_flye/assembly", "test_ont_flye/assembly/flye", - "test_ont_flye/assembly/flye/out", - "test_ont_flye/assembly/flye/out/test_ont_flye.assembly.fa.gz", + "test_ont_flye/assembly/flye/test_ont_flye.assembly.fa.gz", "test_ont_flye/assembly/flye/test_ont_flye.assembly_graph.gfa.gz", "test_ont_flye/assembly/flye/test_ont_flye.assembly_graph.gv.gz", "test_ont_flye/assembly/flye/test_ont_flye.assembly_info.txt", "test_ont_flye/assembly/flye/test_ont_flye.flye.log", "test_ont_flye/assembly/flye/test_ont_flye.params.json", + "test_ont_flye/assembly/test_ont_flye_assembly.gff3", + "test_ont_flye/assembly/test_ont_flye_assembly.unmapped.txt", "test_ont_flye/reads", "test_ont_flye/reads/fastplong", "test_ont_flye/reads/fastplong/hifi", @@ -1719,18 +1691,18 @@ "test_ont_hifiasm", "test_ont_hifiasm/assembly", "test_ont_hifiasm/assembly/hifiasm_ont", - "test_ont_hifiasm/assembly/hifiasm_ont/fasta", - "test_ont_hifiasm/assembly/hifiasm_ont/fasta/out", - "test_ont_hifiasm/assembly/hifiasm_ont/fasta/out/test_ont_hifiasm.fa.gz", "test_ont_hifiasm/assembly/hifiasm_ont/test_ont_hifiasm.bp.hap1.p_ctg.gfa", "test_ont_hifiasm/assembly/hifiasm_ont/test_ont_hifiasm.bp.hap2.p_ctg.gfa", "test_ont_hifiasm/assembly/hifiasm_ont/test_ont_hifiasm.bp.p_ctg.gfa", "test_ont_hifiasm/assembly/hifiasm_ont/test_ont_hifiasm.bp.p_utg.gfa", "test_ont_hifiasm/assembly/hifiasm_ont/test_ont_hifiasm.bp.r_utg.gfa", "test_ont_hifiasm/assembly/hifiasm_ont/test_ont_hifiasm.ec.bin", + "test_ont_hifiasm/assembly/hifiasm_ont/test_ont_hifiasm.fa.gz", "test_ont_hifiasm/assembly/hifiasm_ont/test_ont_hifiasm.ovlp.reverse.bin", "test_ont_hifiasm/assembly/hifiasm_ont/test_ont_hifiasm.ovlp.source.bin", "test_ont_hifiasm/assembly/hifiasm_ont/test_ont_hifiasm.stderr.log", + "test_ont_hifiasm/assembly/test_ont_hifiasm_assembly.gff3", + "test_ont_hifiasm/assembly/test_ont_hifiasm_assembly.unmapped.txt", "test_ont_hifiasm/gfa2fa", "test_ont_hifiasm/gfa2fa/test_ont_hifiasm.fa", "test_ont_hifiasm/reads", @@ -1747,23 +1719,22 @@ "test_ont_hifiasm/reads/fastplong/ont/test_ont_hifiasm_ont.fastplong.log", "test_ont_hifiasm/scaffold", "test_ont_hifiasm/scaffold/ragtag", - "test_ont_hifiasm/scaffold/ragtag/out", - "test_ont_hifiasm/scaffold/ragtag/out/test_ont_hifiasm_ragtag.fa.gz", "test_ont_hifiasm/scaffold/ragtag/test_ont_hifiasm_ragtag.agp", "test_ont_hifiasm/scaffold/ragtag/test_ont_hifiasm_ragtag.fa", + "test_ont_hifiasm/scaffold/ragtag/test_ont_hifiasm_ragtag.fa.gz", + "test_ont_hifiasm/scaffold/ragtag/test_ont_hifiasm_ragtag.gff3", "test_ont_hifiasm/scaffold/ragtag/test_ont_hifiasm_ragtag.stats", + "test_ont_hifiasm/scaffold/ragtag/test_ont_hifiasm_ragtag.unmapped.txt", "test_ont_hifiasm_hic", "test_ont_hifiasm_hic/assembly", "test_ont_hifiasm_hic/assembly/hifiasm_ont", - "test_ont_hifiasm_hic/assembly/hifiasm_ont/fasta", - "test_ont_hifiasm_hic/assembly/hifiasm_ont/fasta/out", - "test_ont_hifiasm_hic/assembly/hifiasm_ont/fasta/out/test_ont_hifiasm_hic.fa.gz", "test_ont_hifiasm_hic/assembly/hifiasm_ont/test_ont_hifiasm_hic.bp.hap1.p_ctg.gfa", "test_ont_hifiasm_hic/assembly/hifiasm_ont/test_ont_hifiasm_hic.bp.hap2.p_ctg.gfa", "test_ont_hifiasm_hic/assembly/hifiasm_ont/test_ont_hifiasm_hic.bp.p_ctg.gfa", "test_ont_hifiasm_hic/assembly/hifiasm_ont/test_ont_hifiasm_hic.bp.p_utg.gfa", "test_ont_hifiasm_hic/assembly/hifiasm_ont/test_ont_hifiasm_hic.bp.r_utg.gfa", "test_ont_hifiasm_hic/assembly/hifiasm_ont/test_ont_hifiasm_hic.ec.bin", + "test_ont_hifiasm_hic/assembly/hifiasm_ont/test_ont_hifiasm_hic.fa.gz", "test_ont_hifiasm_hic/assembly/hifiasm_ont/test_ont_hifiasm_hic.ovlp.reverse.bin", "test_ont_hifiasm_hic/assembly/hifiasm_ont/test_ont_hifiasm_hic.ovlp.source.bin", "test_ont_hifiasm_hic/assembly/hifiasm_ont/test_ont_hifiasm_hic.stderr.log", @@ -1810,19 +1781,18 @@ "test_ont_hifiasm_hic/scaffold/hic/yahs/index", "test_ont_hifiasm_hic/scaffold/hic/yahs/index/test_ont_hifiasm_hic.fa.gz.fai", "test_ont_hifiasm_hic/scaffold/hic/yahs/index/test_ont_hifiasm_hic.fa.gz.gzi", - "test_ont_hifiasm_hic/scaffold/hic/yahs/out", - "test_ont_hifiasm_hic/scaffold/hic/yahs/out/test_ont_hifiasm_hic_hic_scaffolds_final.fa.gz", "test_ont_hifiasm_hic/scaffold/hic/yahs/test_ont_hifiasm_hic_hic.bin", "test_ont_hifiasm_hic/scaffold/hic/yahs/test_ont_hifiasm_hic_hic.log", "test_ont_hifiasm_hic/scaffold/hic/yahs/test_ont_hifiasm_hic_hic_inital_break_01.agp", "test_ont_hifiasm_hic/scaffold/hic/yahs/test_ont_hifiasm_hic_hic_r01_break.agp", "test_ont_hifiasm_hic/scaffold/hic/yahs/test_ont_hifiasm_hic_hic_r02_break.agp", "test_ont_hifiasm_hic/scaffold/hic/yahs/test_ont_hifiasm_hic_hic_scaffolds_final.agp", - "test_ont_hifiasm_hic/scaffold/hic/yahs/test_ont_hifiasm_hic_hic_scaffolds_final.fa" + "test_ont_hifiasm_hic/scaffold/hic/yahs/test_ont_hifiasm_hic_hic_scaffolds_final.fa", + "test_ont_hifiasm_hic/scaffold/hic/yahs/test_ont_hifiasm_hic_hic_scaffolds_final.fa.gz" ], [ + "nf-core-genomeqc-in.csv:md5,a54f349d2518c3d324e12658b60d1f71", "test_flye_hifiasm.params.json:md5,afa91c041bce5e190f4a699d11b69db6", - "test_flye_hifiasm.fa.gz:md5,77e3d5af48175c784bfd217048fe271b", "test_flye_hifiasm.bp.hap1.p_ctg.gfa:md5,46ee70869884ad585165bd48081414e9", "test_flye_hifiasm.bp.hap2.p_ctg.gfa:md5,7792865547989d6d284f640425c4e36c", "test_flye_hifiasm.bp.p_ctg.gfa:md5,8fe65466d76815ffe1663ff6d8f2e8d1", @@ -1834,11 +1804,12 @@ "test_flye_hifiasm_hifi.fastplong.json:md5,0e20fedb8dfe0646232060da502883ee", "test_flye_hifiasm_ont.fastplong.json:md5,826cc5a321dd130a2f2c53cdb1a345b2", "test_hifi_flye.params.json:md5,54b576cb6d4d27656878a7fd3657bde9", + "test_hifi_flye_assembly.unmapped.txt:md5,d41d8cd98f00b204e9800998ecf8427e", "test_hifi_flye_hifi.fastplong.json:md5,daad59b32b84b79c29c274ed20f03cce", "test_hifi_flye_ont.fastplong.json:md5,198eb762846548340557f5f861f10c11", "test_hifi_flye_ragtag.fa:md5,79d2708ebfdbd7b766b9e7c6ee795d5b", "test_hifi_flye_ragtag.stats:md5,25325bb3c27246be0934f38f291b57b2", - "test_hifi_hifiasm.fa.gz:md5,77e3d5af48175c784bfd217048fe271b", + "test_hifi_flye_ragtag.unmapped.txt:md5,d41d8cd98f00b204e9800998ecf8427e", "test_hifi_hifiasm.bp.hap1.p_ctg.gfa:md5,46ee70869884ad585165bd48081414e9", "test_hifi_hifiasm.bp.hap2.p_ctg.gfa:md5,7792865547989d6d284f640425c4e36c", "test_hifi_hifiasm.bp.p_ctg.gfa:md5,8fe65466d76815ffe1663ff6d8f2e8d1", @@ -1848,7 +1819,6 @@ "test_hifi_hifiasm_hifi.fastplong.json:md5,e58f896e9b70344ae4e607324c2c6742", "test_hifi_hifiasm_ont.fastplong.json:md5,eedbb98c4d3870f38320d75b21c86604", "test_hifiasm_flye.params.json:md5,54b576cb6d4d27656878a7fd3657bde9", - "test_hifiasm_flye.fa.gz:md5,35d9e542fb372022a36ecf4854467e80", "test_hifiasm_flye.bp.hap1.p_ctg.gfa:md5,c9a084903ea872a7ac28f3bbd5eee8f3", "test_hifiasm_flye.bp.hap2.p_ctg.gfa:md5,d41d8cd98f00b204e9800998ecf8427e", "test_hifiasm_flye.bp.p_ctg.gfa:md5,d78f7a647429b254d9d46aab4d1306a0", @@ -1859,11 +1829,11 @@ "test_hifiasm_flye_assembly_patch.patch.err:md5,d41d8cd98f00b204e9800998ecf8427e", "test_hifiasm_flye_assembly_patch.patch.fa:md5,6ff15d809eaa0ecf6381400cdd7f0770", "test_hifiasm_flye_assembly_patch.rename.fa:md5,48208c6df370a225c6f54f378d7a8e39", + "test_hifiasm_flye_assembly.unmapped.txt:md5,e99c39c4afff7b433fb3973359dae6a4", "test_hifiasm_flye.fa:md5,35d9e542fb372022a36ecf4854467e80", "test_hifiasm_flye_hifi.fastplong.json:md5,2671b946d2bf533341b86a9f2424e5c3", "test_hifiasm_flye_ont.fastplong.json:md5,924d11a05764994135ff5de294052a02", "test_hifiasm_flye_hic.params.json:md5,54b576cb6d4d27656878a7fd3657bde9", - "test_hifiasm_flye_hic.fa.gz:md5,35d9e542fb372022a36ecf4854467e80", "test_hifiasm_flye_hic.bp.hap1.p_ctg.gfa:md5,c9a084903ea872a7ac28f3bbd5eee8f3", "test_hifiasm_flye_hic.bp.hap2.p_ctg.gfa:md5,d41d8cd98f00b204e9800998ecf8427e", "test_hifiasm_flye_hic.bp.p_ctg.gfa:md5,d78f7a647429b254d9d46aab4d1306a0", @@ -1874,6 +1844,7 @@ "test_hifiasm_flye_hic_assembly_patch.patch.err:md5,d41d8cd98f00b204e9800998ecf8427e", "test_hifiasm_flye_hic_assembly_patch.patch.fa:md5,6ff15d809eaa0ecf6381400cdd7f0770", "test_hifiasm_flye_hic_assembly_patch.rename.fa:md5,48208c6df370a225c6f54f378d7a8e39", + "test_hifiasm_flye_hic_assembly.unmapped.txt:md5,e99c39c4afff7b433fb3973359dae6a4", "test_hifiasm_flye_hic.fa:md5,35d9e542fb372022a36ecf4854467e80", "test_hifiasm_flye_hic_hicreads.fastp.json:md5,639daa4b554b8562208d2f7dff3a118f", "test_hifiasm_flye_hic_hifi.fastplong.json:md5,1c4764224854af4537899de86c8e2e56", @@ -1887,11 +1858,10 @@ "test_hifiasm_flye_hic_bwamem.bam:md5,837f8fbfbaf79b1049093e62a23a02b2", "test_hifiasm_flye_hic_hic_dedup.bai:md5,aeda4dd1092e5ae65a44c90faa2a4e86", "test_hifiasm_flye_hic_hic_dedup.bam:md5,d93aabe7dbda135b1562eeef7808d347", + "test_hifiasm_flye_hic_links.unmapped.txt:md5,e99c39c4afff7b433fb3973359dae6a4", "test_hifiasm_flye_hic_assembly_patch.patch.fa.gz.fai:md5,06f2947d7897ca8a7c6f30a81bd6bdcc", "test_hifiasm_flye_hic_assembly_patch.patch.fa.gz.gzi:md5,251cd3924556d6f48e9d5127bdd15ee2", - "test_hifiasm_flye_hic_hic_scaffolds_final.fa.gz:md5,3ac2a0232e899bcb28b72e3c4f1c2d79", "test_hifiasm_flye_hic_hic_scaffolds_final.fa:md5,3ac2a0232e899bcb28b72e3c4f1c2d79", - "test_hifiasm_ul.fa.gz:md5,77e3d5af48175c784bfd217048fe271b", "test_hifiasm_ul.bp.hap1.p_ctg.gfa:md5,46ee70869884ad585165bd48081414e9", "test_hifiasm_ul.bp.hap2.p_ctg.gfa:md5,7792865547989d6d284f640425c4e36c", "test_hifiasm_ul.bp.p_ctg.gfa:md5,8fe65466d76815ffe1663ff6d8f2e8d1", @@ -1902,20 +1872,21 @@ "test_hifiasm_ul_ont.fastplong.json:md5,86da6d58ac4630bfeae3ee08014ecb0b", "versions.yml:md5,c6c0c66defcf12c9bd29c649fbef58af", "test_ont_flye.params.json:md5,afa91c041bce5e190f4a699d11b69db6", + "test_ont_flye_assembly.unmapped.txt:md5,d41d8cd98f00b204e9800998ecf8427e", "test_ont_flye_hifi.fastplong.json:md5,9205a4cf65cce249429badc208348349", "test_ont_flye_ont.fastplong.json:md5,e418b2481ade21bc45e77d1437bad913", - "test_ont_hifiasm.fa.gz:md5,35d9e542fb372022a36ecf4854467e80", "test_ont_hifiasm.bp.hap1.p_ctg.gfa:md5,c9a084903ea872a7ac28f3bbd5eee8f3", "test_ont_hifiasm.bp.hap2.p_ctg.gfa:md5,d41d8cd98f00b204e9800998ecf8427e", "test_ont_hifiasm.bp.p_ctg.gfa:md5,d78f7a647429b254d9d46aab4d1306a0", "test_ont_hifiasm.bp.p_utg.gfa:md5,e2b6621386edda1636dfb84ddd676ea8", "test_ont_hifiasm.bp.r_utg.gfa:md5,e2b6621386edda1636dfb84ddd676ea8", + "test_ont_hifiasm_assembly.unmapped.txt:md5,e99c39c4afff7b433fb3973359dae6a4", "test_ont_hifiasm.fa:md5,35d9e542fb372022a36ecf4854467e80", "test_ont_hifiasm_hifi.fastplong.json:md5,91878df7edc2b07a885c103f260fc70e", "test_ont_hifiasm_ont.fastplong.json:md5,e97714274268b5a30be4d9851f2b61b3", "test_ont_hifiasm_ragtag.fa:md5,51f2975257b49657716d2ca7cc6d5fe2", "test_ont_hifiasm_ragtag.stats:md5,466273b499384b2c781c83dc583b8c99", - "test_ont_hifiasm_hic.fa.gz:md5,35d9e542fb372022a36ecf4854467e80", + "test_ont_hifiasm_ragtag.unmapped.txt:md5,e99c39c4afff7b433fb3973359dae6a4", "test_ont_hifiasm_hic.bp.hap1.p_ctg.gfa:md5,c9a084903ea872a7ac28f3bbd5eee8f3", "test_ont_hifiasm_hic.bp.hap2.p_ctg.gfa:md5,d41d8cd98f00b204e9800998ecf8427e", "test_ont_hifiasm_hic.bp.p_ctg.gfa:md5,d78f7a647429b254d9d46aab4d1306a0", @@ -1936,11 +1907,10 @@ "test_ont_hifiasm_hic_hic_dedup.bam:md5,9246dec2c1b6d6f4fd37383ddda244cb", "test_ont_hifiasm_hic.fa.gz.fai:md5,3f23b28c147c40cb4f1d6571cf2dc045", "test_ont_hifiasm_hic.fa.gz.gzi:md5,a5721349018bd8e33902a3e18ef9f530", - "test_ont_hifiasm_hic_hic_scaffolds_final.fa.gz:md5,3ac2a0232e899bcb28b72e3c4f1c2d79", "test_ont_hifiasm_hic_hic_scaffolds_final.fa:md5,3ac2a0232e899bcb28b72e3c4f1c2d79" ] ], - "timestamp": "2026-07-21T11:16:49.003340709", + "timestamp": "2026-08-28T15:26:50.323204919", "meta": { "nf-test": "0.9.5", "nextflow": "25.10.4" @@ -1948,7 +1918,7 @@ }, "-profile test_quast": { "content": [ - 80, + 88, { "ADD_RG": { "picard": "3.4.0" @@ -2010,6 +1980,9 @@ "HIFIASM_ONT": { "hifasm": "0.25.0-r726" }, + "LIFTOFF": { + "liftoff": "1.6.3" + }, "MARKDUP": { "picard": "3.4.0" }, @@ -2027,6 +2000,8 @@ } }, [ + "genomeqc_samplesheet", + "genomeqc_samplesheet/nf-core-genomeqc-in.csv", "pipeline_info", "pipeline_info/nf_core_pipeline_software_versions.yml", "report", @@ -2034,23 +2009,20 @@ "test_flye_hifiasm", "test_flye_hifiasm/assembly", "test_flye_hifiasm/assembly/flye", - "test_flye_hifiasm/assembly/flye/out", - "test_flye_hifiasm/assembly/flye/out/test_flye_hifiasm.assembly.fa.gz", + "test_flye_hifiasm/assembly/flye/test_flye_hifiasm.assembly.fa.gz", "test_flye_hifiasm/assembly/flye/test_flye_hifiasm.assembly_graph.gfa.gz", "test_flye_hifiasm/assembly/flye/test_flye_hifiasm.assembly_graph.gv.gz", "test_flye_hifiasm/assembly/flye/test_flye_hifiasm.assembly_info.txt", "test_flye_hifiasm/assembly/flye/test_flye_hifiasm.flye.log", "test_flye_hifiasm/assembly/flye/test_flye_hifiasm.params.json", "test_flye_hifiasm/assembly/hifiasm", - "test_flye_hifiasm/assembly/hifiasm/fasta", - "test_flye_hifiasm/assembly/hifiasm/fasta/out", - "test_flye_hifiasm/assembly/hifiasm/fasta/out/test_flye_hifiasm.fa.gz", "test_flye_hifiasm/assembly/hifiasm/test_flye_hifiasm.bp.hap1.p_ctg.gfa", "test_flye_hifiasm/assembly/hifiasm/test_flye_hifiasm.bp.hap2.p_ctg.gfa", "test_flye_hifiasm/assembly/hifiasm/test_flye_hifiasm.bp.p_ctg.gfa", "test_flye_hifiasm/assembly/hifiasm/test_flye_hifiasm.bp.p_utg.gfa", "test_flye_hifiasm/assembly/hifiasm/test_flye_hifiasm.bp.r_utg.gfa", "test_flye_hifiasm/assembly/hifiasm/test_flye_hifiasm.ec.bin", + "test_flye_hifiasm/assembly/hifiasm/test_flye_hifiasm.fa.gz", "test_flye_hifiasm/assembly/hifiasm/test_flye_hifiasm.ovlp.reverse.bin", "test_flye_hifiasm/assembly/hifiasm/test_flye_hifiasm.ovlp.source.bin", "test_flye_hifiasm/assembly/hifiasm/test_flye_hifiasm.stderr.log", @@ -2061,11 +2033,9 @@ "test_flye_hifiasm/assembly/ragtag/test_flye_hifiasm_assembly_patch.patch.agp", "test_flye_hifiasm/assembly/ragtag/test_flye_hifiasm_assembly_patch.patch.err", "test_flye_hifiasm/assembly/ragtag/test_flye_hifiasm_assembly_patch.patch.fa", + "test_flye_hifiasm/assembly/ragtag/test_flye_hifiasm_assembly_patch.patch.fa.gz", "test_flye_hifiasm/assembly/ragtag/test_flye_hifiasm_assembly_patch.rename.agp", "test_flye_hifiasm/assembly/ragtag/test_flye_hifiasm_assembly_patch.rename.fa", - "test_flye_hifiasm/bgzip", - "test_flye_hifiasm/bgzip/out", - "test_flye_hifiasm/bgzip/out/test_flye_hifiasm_assembly_patch.patch.fa.gz", "test_flye_hifiasm/gfa2fa", "test_flye_hifiasm/gfa2fa/test_flye_hifiasm.fa", "test_flye_hifiasm/reads", @@ -2082,21 +2052,21 @@ "test_flye_hifiasm/reads/fastplong/ont/test_flye_hifiasm_ont.fastplong.log", "test_flye_hifiasm/scaffold", "test_flye_hifiasm/scaffold/ragtag", - "test_flye_hifiasm/scaffold/ragtag/out", - "test_flye_hifiasm/scaffold/ragtag/out/test_flye_hifiasm_ragtag.fa.gz", "test_flye_hifiasm/scaffold/ragtag/test_flye_hifiasm_ragtag.agp", "test_flye_hifiasm/scaffold/ragtag/test_flye_hifiasm_ragtag.fa", + "test_flye_hifiasm/scaffold/ragtag/test_flye_hifiasm_ragtag.fa.gz", "test_flye_hifiasm/scaffold/ragtag/test_flye_hifiasm_ragtag.stats", "test_hifi_flye", "test_hifi_flye/assembly", "test_hifi_flye/assembly/flye", - "test_hifi_flye/assembly/flye/out", - "test_hifi_flye/assembly/flye/out/test_hifi_flye.assembly.fa.gz", + "test_hifi_flye/assembly/flye/test_hifi_flye.assembly.fa.gz", "test_hifi_flye/assembly/flye/test_hifi_flye.assembly_graph.gfa.gz", "test_hifi_flye/assembly/flye/test_hifi_flye.assembly_graph.gv.gz", "test_hifi_flye/assembly/flye/test_hifi_flye.assembly_info.txt", "test_hifi_flye/assembly/flye/test_hifi_flye.flye.log", "test_hifi_flye/assembly/flye/test_hifi_flye.params.json", + "test_hifi_flye/assembly/test_hifi_flye_assembly.gff3", + "test_hifi_flye/assembly/test_hifi_flye_assembly.unmapped.txt", "test_hifi_flye/reads", "test_hifi_flye/reads/fastplong", "test_hifi_flye/reads/fastplong/hifi", @@ -2111,23 +2081,22 @@ "test_hifi_flye/reads/fastplong/ont/test_hifi_flye_ont.fastplong.log", "test_hifi_flye/scaffold", "test_hifi_flye/scaffold/ragtag", - "test_hifi_flye/scaffold/ragtag/out", - "test_hifi_flye/scaffold/ragtag/out/test_hifi_flye_ragtag.fa.gz", "test_hifi_flye/scaffold/ragtag/test_hifi_flye_ragtag.agp", "test_hifi_flye/scaffold/ragtag/test_hifi_flye_ragtag.fa", + "test_hifi_flye/scaffold/ragtag/test_hifi_flye_ragtag.fa.gz", + "test_hifi_flye/scaffold/ragtag/test_hifi_flye_ragtag.gff3", "test_hifi_flye/scaffold/ragtag/test_hifi_flye_ragtag.stats", + "test_hifi_flye/scaffold/ragtag/test_hifi_flye_ragtag.unmapped.txt", "test_hifi_hifiasm", "test_hifi_hifiasm/assembly", "test_hifi_hifiasm/assembly/hifiasm", - "test_hifi_hifiasm/assembly/hifiasm/fasta", - "test_hifi_hifiasm/assembly/hifiasm/fasta/out", - "test_hifi_hifiasm/assembly/hifiasm/fasta/out/test_hifi_hifiasm.fa.gz", "test_hifi_hifiasm/assembly/hifiasm/test_hifi_hifiasm.bp.hap1.p_ctg.gfa", "test_hifi_hifiasm/assembly/hifiasm/test_hifi_hifiasm.bp.hap2.p_ctg.gfa", "test_hifi_hifiasm/assembly/hifiasm/test_hifi_hifiasm.bp.p_ctg.gfa", "test_hifi_hifiasm/assembly/hifiasm/test_hifi_hifiasm.bp.p_utg.gfa", "test_hifi_hifiasm/assembly/hifiasm/test_hifi_hifiasm.bp.r_utg.gfa", "test_hifi_hifiasm/assembly/hifiasm/test_hifi_hifiasm.ec.bin", + "test_hifi_hifiasm/assembly/hifiasm/test_hifi_hifiasm.fa.gz", "test_hifi_hifiasm/assembly/hifiasm/test_hifi_hifiasm.ovlp.reverse.bin", "test_hifi_hifiasm/assembly/hifiasm/test_hifi_hifiasm.ovlp.source.bin", "test_hifi_hifiasm/assembly/hifiasm/test_hifi_hifiasm.stderr.log", @@ -2148,23 +2117,20 @@ "test_hifiasm_flye", "test_hifiasm_flye/assembly", "test_hifiasm_flye/assembly/flye", - "test_hifiasm_flye/assembly/flye/out", - "test_hifiasm_flye/assembly/flye/out/test_hifiasm_flye.assembly.fa.gz", + "test_hifiasm_flye/assembly/flye/test_hifiasm_flye.assembly.fa.gz", "test_hifiasm_flye/assembly/flye/test_hifiasm_flye.assembly_graph.gfa.gz", "test_hifiasm_flye/assembly/flye/test_hifiasm_flye.assembly_graph.gv.gz", "test_hifiasm_flye/assembly/flye/test_hifiasm_flye.assembly_info.txt", "test_hifiasm_flye/assembly/flye/test_hifiasm_flye.flye.log", "test_hifiasm_flye/assembly/flye/test_hifiasm_flye.params.json", "test_hifiasm_flye/assembly/hifiasm_ont", - "test_hifiasm_flye/assembly/hifiasm_ont/fasta", - "test_hifiasm_flye/assembly/hifiasm_ont/fasta/out", - "test_hifiasm_flye/assembly/hifiasm_ont/fasta/out/test_hifiasm_flye.fa.gz", "test_hifiasm_flye/assembly/hifiasm_ont/test_hifiasm_flye.bp.hap1.p_ctg.gfa", "test_hifiasm_flye/assembly/hifiasm_ont/test_hifiasm_flye.bp.hap2.p_ctg.gfa", "test_hifiasm_flye/assembly/hifiasm_ont/test_hifiasm_flye.bp.p_ctg.gfa", "test_hifiasm_flye/assembly/hifiasm_ont/test_hifiasm_flye.bp.p_utg.gfa", "test_hifiasm_flye/assembly/hifiasm_ont/test_hifiasm_flye.bp.r_utg.gfa", "test_hifiasm_flye/assembly/hifiasm_ont/test_hifiasm_flye.ec.bin", + "test_hifiasm_flye/assembly/hifiasm_ont/test_hifiasm_flye.fa.gz", "test_hifiasm_flye/assembly/hifiasm_ont/test_hifiasm_flye.ovlp.reverse.bin", "test_hifiasm_flye/assembly/hifiasm_ont/test_hifiasm_flye.ovlp.source.bin", "test_hifiasm_flye/assembly/hifiasm_ont/test_hifiasm_flye.stderr.log", @@ -2175,11 +2141,11 @@ "test_hifiasm_flye/assembly/ragtag/test_hifiasm_flye_assembly_patch.patch.agp", "test_hifiasm_flye/assembly/ragtag/test_hifiasm_flye_assembly_patch.patch.err", "test_hifiasm_flye/assembly/ragtag/test_hifiasm_flye_assembly_patch.patch.fa", + "test_hifiasm_flye/assembly/ragtag/test_hifiasm_flye_assembly_patch.patch.fa.gz", "test_hifiasm_flye/assembly/ragtag/test_hifiasm_flye_assembly_patch.rename.agp", "test_hifiasm_flye/assembly/ragtag/test_hifiasm_flye_assembly_patch.rename.fa", - "test_hifiasm_flye/bgzip", - "test_hifiasm_flye/bgzip/out", - "test_hifiasm_flye/bgzip/out/test_hifiasm_flye_assembly_patch.patch.fa.gz", + "test_hifiasm_flye/assembly/test_hifiasm_flye_assembly.gff3", + "test_hifiasm_flye/assembly/test_hifiasm_flye_assembly.unmapped.txt", "test_hifiasm_flye/gfa2fa", "test_hifiasm_flye/gfa2fa/test_hifiasm_flye.fa", "test_hifiasm_flye/reads", @@ -2197,23 +2163,20 @@ "test_hifiasm_flye_hic", "test_hifiasm_flye_hic/assembly", "test_hifiasm_flye_hic/assembly/flye", - "test_hifiasm_flye_hic/assembly/flye/out", - "test_hifiasm_flye_hic/assembly/flye/out/test_hifiasm_flye_hic.assembly.fa.gz", + "test_hifiasm_flye_hic/assembly/flye/test_hifiasm_flye_hic.assembly.fa.gz", "test_hifiasm_flye_hic/assembly/flye/test_hifiasm_flye_hic.assembly_graph.gfa.gz", "test_hifiasm_flye_hic/assembly/flye/test_hifiasm_flye_hic.assembly_graph.gv.gz", "test_hifiasm_flye_hic/assembly/flye/test_hifiasm_flye_hic.assembly_info.txt", "test_hifiasm_flye_hic/assembly/flye/test_hifiasm_flye_hic.flye.log", "test_hifiasm_flye_hic/assembly/flye/test_hifiasm_flye_hic.params.json", "test_hifiasm_flye_hic/assembly/hifiasm_ont", - "test_hifiasm_flye_hic/assembly/hifiasm_ont/fasta", - "test_hifiasm_flye_hic/assembly/hifiasm_ont/fasta/out", - "test_hifiasm_flye_hic/assembly/hifiasm_ont/fasta/out/test_hifiasm_flye_hic.fa.gz", "test_hifiasm_flye_hic/assembly/hifiasm_ont/test_hifiasm_flye_hic.bp.hap1.p_ctg.gfa", "test_hifiasm_flye_hic/assembly/hifiasm_ont/test_hifiasm_flye_hic.bp.hap2.p_ctg.gfa", "test_hifiasm_flye_hic/assembly/hifiasm_ont/test_hifiasm_flye_hic.bp.p_ctg.gfa", "test_hifiasm_flye_hic/assembly/hifiasm_ont/test_hifiasm_flye_hic.bp.p_utg.gfa", "test_hifiasm_flye_hic/assembly/hifiasm_ont/test_hifiasm_flye_hic.bp.r_utg.gfa", "test_hifiasm_flye_hic/assembly/hifiasm_ont/test_hifiasm_flye_hic.ec.bin", + "test_hifiasm_flye_hic/assembly/hifiasm_ont/test_hifiasm_flye_hic.fa.gz", "test_hifiasm_flye_hic/assembly/hifiasm_ont/test_hifiasm_flye_hic.ovlp.reverse.bin", "test_hifiasm_flye_hic/assembly/hifiasm_ont/test_hifiasm_flye_hic.ovlp.source.bin", "test_hifiasm_flye_hic/assembly/hifiasm_ont/test_hifiasm_flye_hic.stderr.log", @@ -2224,11 +2187,11 @@ "test_hifiasm_flye_hic/assembly/ragtag/test_hifiasm_flye_hic_assembly_patch.patch.agp", "test_hifiasm_flye_hic/assembly/ragtag/test_hifiasm_flye_hic_assembly_patch.patch.err", "test_hifiasm_flye_hic/assembly/ragtag/test_hifiasm_flye_hic_assembly_patch.patch.fa", + "test_hifiasm_flye_hic/assembly/ragtag/test_hifiasm_flye_hic_assembly_patch.patch.fa.gz", "test_hifiasm_flye_hic/assembly/ragtag/test_hifiasm_flye_hic_assembly_patch.rename.agp", "test_hifiasm_flye_hic/assembly/ragtag/test_hifiasm_flye_hic_assembly_patch.rename.fa", - "test_hifiasm_flye_hic/bgzip", - "test_hifiasm_flye_hic/bgzip/out", - "test_hifiasm_flye_hic/bgzip/out/test_hifiasm_flye_hic_assembly_patch.patch.fa.gz", + "test_hifiasm_flye_hic/assembly/test_hifiasm_flye_hic_assembly.gff3", + "test_hifiasm_flye_hic/assembly/test_hifiasm_flye_hic_assembly.unmapped.txt", "test_hifiasm_flye_hic/gfa2fa", "test_hifiasm_flye_hic/gfa2fa/test_hifiasm_flye_hic.fa", "test_hifiasm_flye_hic/hic_reads", @@ -2268,12 +2231,12 @@ "test_hifiasm_flye_hic/scaffold/hic/markdup/test_hifiasm_flye_hic_hic_dedup.MarkDuplicates.metrics.txt", "test_hifiasm_flye_hic/scaffold/hic/markdup/test_hifiasm_flye_hic_hic_dedup.bai", "test_hifiasm_flye_hic/scaffold/hic/markdup/test_hifiasm_flye_hic_hic_dedup.bam", + "test_hifiasm_flye_hic/scaffold/hic/test_hifiasm_flye_hic_links.gff3", + "test_hifiasm_flye_hic/scaffold/hic/test_hifiasm_flye_hic_links.unmapped.txt", "test_hifiasm_flye_hic/scaffold/hic/yahs", "test_hifiasm_flye_hic/scaffold/hic/yahs/index", "test_hifiasm_flye_hic/scaffold/hic/yahs/index/test_hifiasm_flye_hic_assembly_patch.patch.fa.gz.fai", "test_hifiasm_flye_hic/scaffold/hic/yahs/index/test_hifiasm_flye_hic_assembly_patch.patch.fa.gz.gzi", - "test_hifiasm_flye_hic/scaffold/hic/yahs/out", - "test_hifiasm_flye_hic/scaffold/hic/yahs/out/test_hifiasm_flye_hic_hic_scaffolds_final.fa.gz", "test_hifiasm_flye_hic/scaffold/hic/yahs/test_hifiasm_flye_hic_hic.bin", "test_hifiasm_flye_hic/scaffold/hic/yahs/test_hifiasm_flye_hic_hic.log", "test_hifiasm_flye_hic/scaffold/hic/yahs/test_hifiasm_flye_hic_hic_inital_break_01.agp", @@ -2281,18 +2244,17 @@ "test_hifiasm_flye_hic/scaffold/hic/yahs/test_hifiasm_flye_hic_hic_r02_break.agp", "test_hifiasm_flye_hic/scaffold/hic/yahs/test_hifiasm_flye_hic_hic_scaffolds_final.agp", "test_hifiasm_flye_hic/scaffold/hic/yahs/test_hifiasm_flye_hic_hic_scaffolds_final.fa", + "test_hifiasm_flye_hic/scaffold/hic/yahs/test_hifiasm_flye_hic_hic_scaffolds_final.fa.gz", "test_hifiasm_ul", "test_hifiasm_ul/assembly", "test_hifiasm_ul/assembly/hifiasm", - "test_hifiasm_ul/assembly/hifiasm/fasta", - "test_hifiasm_ul/assembly/hifiasm/fasta/out", - "test_hifiasm_ul/assembly/hifiasm/fasta/out/test_hifiasm_ul.fa.gz", "test_hifiasm_ul/assembly/hifiasm/test_hifiasm_ul.bp.hap1.p_ctg.gfa", "test_hifiasm_ul/assembly/hifiasm/test_hifiasm_ul.bp.hap2.p_ctg.gfa", "test_hifiasm_ul/assembly/hifiasm/test_hifiasm_ul.bp.p_ctg.gfa", "test_hifiasm_ul/assembly/hifiasm/test_hifiasm_ul.bp.p_utg.gfa", "test_hifiasm_ul/assembly/hifiasm/test_hifiasm_ul.bp.r_utg.gfa", "test_hifiasm_ul/assembly/hifiasm/test_hifiasm_ul.ec.bin", + "test_hifiasm_ul/assembly/hifiasm/test_hifiasm_ul.fa.gz", "test_hifiasm_ul/assembly/hifiasm/test_hifiasm_ul.ovlp.reverse.bin", "test_hifiasm_ul/assembly/hifiasm/test_hifiasm_ul.ovlp.source.bin", "test_hifiasm_ul/assembly/hifiasm/test_hifiasm_ul.re.uidx.bin", @@ -2339,20 +2301,20 @@ "test_hifiasm_ul/scaffold/longstitch/assembly.cut250.tigmint.fa.k32.w100.z1000.trimmed_scafs.path", "test_hifiasm_ul/scaffold/longstitch/assembly.cut250.tigmint.fa.k32.w100.z1000.trimmed_scafs.tsv", "test_hifiasm_ul/scaffold/longstitch/assembly.cut250.tigmint.fa.k32.w100.z1000.verbose_mapping.tsv", - "test_hifiasm_ul/scaffold/longstitch/out", - "test_hifiasm_ul/scaffold/longstitch/out/test_hifiasm_ul_longstitch.tigmint-ntLink-arks.fa.gz", "test_hifiasm_ul/scaffold/longstitch/test_hifiasm_ul_longstitch.tigmint-ntLink-arks.fa", + "test_hifiasm_ul/scaffold/longstitch/test_hifiasm_ul_longstitch.tigmint-ntLink-arks.fa.gz", "test_hifiasm_ul/scaffold/longstitch/versions.yml", "test_ont_flye", "test_ont_flye/assembly", "test_ont_flye/assembly/flye", - "test_ont_flye/assembly/flye/out", - "test_ont_flye/assembly/flye/out/test_ont_flye.assembly.fa.gz", + "test_ont_flye/assembly/flye/test_ont_flye.assembly.fa.gz", "test_ont_flye/assembly/flye/test_ont_flye.assembly_graph.gfa.gz", "test_ont_flye/assembly/flye/test_ont_flye.assembly_graph.gv.gz", "test_ont_flye/assembly/flye/test_ont_flye.assembly_info.txt", "test_ont_flye/assembly/flye/test_ont_flye.flye.log", "test_ont_flye/assembly/flye/test_ont_flye.params.json", + "test_ont_flye/assembly/test_ont_flye_assembly.gff3", + "test_ont_flye/assembly/test_ont_flye_assembly.unmapped.txt", "test_ont_flye/reads", "test_ont_flye/reads/fastplong", "test_ont_flye/reads/fastplong/hifi", @@ -2368,18 +2330,18 @@ "test_ont_hifiasm", "test_ont_hifiasm/assembly", "test_ont_hifiasm/assembly/hifiasm_ont", - "test_ont_hifiasm/assembly/hifiasm_ont/fasta", - "test_ont_hifiasm/assembly/hifiasm_ont/fasta/out", - "test_ont_hifiasm/assembly/hifiasm_ont/fasta/out/test_ont_hifiasm.fa.gz", "test_ont_hifiasm/assembly/hifiasm_ont/test_ont_hifiasm.bp.hap1.p_ctg.gfa", "test_ont_hifiasm/assembly/hifiasm_ont/test_ont_hifiasm.bp.hap2.p_ctg.gfa", "test_ont_hifiasm/assembly/hifiasm_ont/test_ont_hifiasm.bp.p_ctg.gfa", "test_ont_hifiasm/assembly/hifiasm_ont/test_ont_hifiasm.bp.p_utg.gfa", "test_ont_hifiasm/assembly/hifiasm_ont/test_ont_hifiasm.bp.r_utg.gfa", "test_ont_hifiasm/assembly/hifiasm_ont/test_ont_hifiasm.ec.bin", + "test_ont_hifiasm/assembly/hifiasm_ont/test_ont_hifiasm.fa.gz", "test_ont_hifiasm/assembly/hifiasm_ont/test_ont_hifiasm.ovlp.reverse.bin", "test_ont_hifiasm/assembly/hifiasm_ont/test_ont_hifiasm.ovlp.source.bin", "test_ont_hifiasm/assembly/hifiasm_ont/test_ont_hifiasm.stderr.log", + "test_ont_hifiasm/assembly/test_ont_hifiasm_assembly.gff3", + "test_ont_hifiasm/assembly/test_ont_hifiasm_assembly.unmapped.txt", "test_ont_hifiasm/gfa2fa", "test_ont_hifiasm/gfa2fa/test_ont_hifiasm.fa", "test_ont_hifiasm/reads", @@ -2396,23 +2358,22 @@ "test_ont_hifiasm/reads/fastplong/ont/test_ont_hifiasm_ont.fastplong.log", "test_ont_hifiasm/scaffold", "test_ont_hifiasm/scaffold/ragtag", - "test_ont_hifiasm/scaffold/ragtag/out", - "test_ont_hifiasm/scaffold/ragtag/out/test_ont_hifiasm_ragtag.fa.gz", "test_ont_hifiasm/scaffold/ragtag/test_ont_hifiasm_ragtag.agp", "test_ont_hifiasm/scaffold/ragtag/test_ont_hifiasm_ragtag.fa", + "test_ont_hifiasm/scaffold/ragtag/test_ont_hifiasm_ragtag.fa.gz", + "test_ont_hifiasm/scaffold/ragtag/test_ont_hifiasm_ragtag.gff3", "test_ont_hifiasm/scaffold/ragtag/test_ont_hifiasm_ragtag.stats", + "test_ont_hifiasm/scaffold/ragtag/test_ont_hifiasm_ragtag.unmapped.txt", "test_ont_hifiasm_hic", "test_ont_hifiasm_hic/assembly", "test_ont_hifiasm_hic/assembly/hifiasm_ont", - "test_ont_hifiasm_hic/assembly/hifiasm_ont/fasta", - "test_ont_hifiasm_hic/assembly/hifiasm_ont/fasta/out", - "test_ont_hifiasm_hic/assembly/hifiasm_ont/fasta/out/test_ont_hifiasm_hic.fa.gz", "test_ont_hifiasm_hic/assembly/hifiasm_ont/test_ont_hifiasm_hic.bp.hap1.p_ctg.gfa", "test_ont_hifiasm_hic/assembly/hifiasm_ont/test_ont_hifiasm_hic.bp.hap2.p_ctg.gfa", "test_ont_hifiasm_hic/assembly/hifiasm_ont/test_ont_hifiasm_hic.bp.p_ctg.gfa", "test_ont_hifiasm_hic/assembly/hifiasm_ont/test_ont_hifiasm_hic.bp.p_utg.gfa", "test_ont_hifiasm_hic/assembly/hifiasm_ont/test_ont_hifiasm_hic.bp.r_utg.gfa", "test_ont_hifiasm_hic/assembly/hifiasm_ont/test_ont_hifiasm_hic.ec.bin", + "test_ont_hifiasm_hic/assembly/hifiasm_ont/test_ont_hifiasm_hic.fa.gz", "test_ont_hifiasm_hic/assembly/hifiasm_ont/test_ont_hifiasm_hic.ovlp.reverse.bin", "test_ont_hifiasm_hic/assembly/hifiasm_ont/test_ont_hifiasm_hic.ovlp.source.bin", "test_ont_hifiasm_hic/assembly/hifiasm_ont/test_ont_hifiasm_hic.stderr.log", @@ -2459,19 +2420,18 @@ "test_ont_hifiasm_hic/scaffold/hic/yahs/index", "test_ont_hifiasm_hic/scaffold/hic/yahs/index/test_ont_hifiasm_hic.fa.gz.fai", "test_ont_hifiasm_hic/scaffold/hic/yahs/index/test_ont_hifiasm_hic.fa.gz.gzi", - "test_ont_hifiasm_hic/scaffold/hic/yahs/out", - "test_ont_hifiasm_hic/scaffold/hic/yahs/out/test_ont_hifiasm_hic_hic_scaffolds_final.fa.gz", "test_ont_hifiasm_hic/scaffold/hic/yahs/test_ont_hifiasm_hic_hic.bin", "test_ont_hifiasm_hic/scaffold/hic/yahs/test_ont_hifiasm_hic_hic.log", "test_ont_hifiasm_hic/scaffold/hic/yahs/test_ont_hifiasm_hic_hic_inital_break_01.agp", "test_ont_hifiasm_hic/scaffold/hic/yahs/test_ont_hifiasm_hic_hic_r01_break.agp", "test_ont_hifiasm_hic/scaffold/hic/yahs/test_ont_hifiasm_hic_hic_r02_break.agp", "test_ont_hifiasm_hic/scaffold/hic/yahs/test_ont_hifiasm_hic_hic_scaffolds_final.agp", - "test_ont_hifiasm_hic/scaffold/hic/yahs/test_ont_hifiasm_hic_hic_scaffolds_final.fa" + "test_ont_hifiasm_hic/scaffold/hic/yahs/test_ont_hifiasm_hic_hic_scaffolds_final.fa", + "test_ont_hifiasm_hic/scaffold/hic/yahs/test_ont_hifiasm_hic_hic_scaffolds_final.fa.gz" ], [ + "nf-core-genomeqc-in.csv:md5,fec7340f5774b7a47fda549c99ae1732", "test_flye_hifiasm.params.json:md5,afa91c041bce5e190f4a699d11b69db6", - "test_flye_hifiasm.fa.gz:md5,77e3d5af48175c784bfd217048fe271b", "test_flye_hifiasm.bp.hap1.p_ctg.gfa:md5,46ee70869884ad585165bd48081414e9", "test_flye_hifiasm.bp.hap2.p_ctg.gfa:md5,7792865547989d6d284f640425c4e36c", "test_flye_hifiasm.bp.p_ctg.gfa:md5,8fe65466d76815ffe1663ff6d8f2e8d1", @@ -2483,11 +2443,12 @@ "test_flye_hifiasm_hifi.fastplong.json:md5,0e20fedb8dfe0646232060da502883ee", "test_flye_hifiasm_ont.fastplong.json:md5,826cc5a321dd130a2f2c53cdb1a345b2", "test_hifi_flye.params.json:md5,54b576cb6d4d27656878a7fd3657bde9", + "test_hifi_flye_assembly.unmapped.txt:md5,d41d8cd98f00b204e9800998ecf8427e", "test_hifi_flye_hifi.fastplong.json:md5,daad59b32b84b79c29c274ed20f03cce", "test_hifi_flye_ont.fastplong.json:md5,198eb762846548340557f5f861f10c11", "test_hifi_flye_ragtag.fa:md5,79d2708ebfdbd7b766b9e7c6ee795d5b", "test_hifi_flye_ragtag.stats:md5,25325bb3c27246be0934f38f291b57b2", - "test_hifi_hifiasm.fa.gz:md5,77e3d5af48175c784bfd217048fe271b", + "test_hifi_flye_ragtag.unmapped.txt:md5,d41d8cd98f00b204e9800998ecf8427e", "test_hifi_hifiasm.bp.hap1.p_ctg.gfa:md5,46ee70869884ad585165bd48081414e9", "test_hifi_hifiasm.bp.hap2.p_ctg.gfa:md5,7792865547989d6d284f640425c4e36c", "test_hifi_hifiasm.bp.p_ctg.gfa:md5,8fe65466d76815ffe1663ff6d8f2e8d1", @@ -2497,7 +2458,6 @@ "test_hifi_hifiasm_hifi.fastplong.json:md5,e58f896e9b70344ae4e607324c2c6742", "test_hifi_hifiasm_ont.fastplong.json:md5,eedbb98c4d3870f38320d75b21c86604", "test_hifiasm_flye.params.json:md5,54b576cb6d4d27656878a7fd3657bde9", - "test_hifiasm_flye.fa.gz:md5,35d9e542fb372022a36ecf4854467e80", "test_hifiasm_flye.bp.hap1.p_ctg.gfa:md5,c9a084903ea872a7ac28f3bbd5eee8f3", "test_hifiasm_flye.bp.hap2.p_ctg.gfa:md5,d41d8cd98f00b204e9800998ecf8427e", "test_hifiasm_flye.bp.p_ctg.gfa:md5,d78f7a647429b254d9d46aab4d1306a0", @@ -2508,11 +2468,11 @@ "test_hifiasm_flye_assembly_patch.patch.err:md5,d41d8cd98f00b204e9800998ecf8427e", "test_hifiasm_flye_assembly_patch.patch.fa:md5,6ff15d809eaa0ecf6381400cdd7f0770", "test_hifiasm_flye_assembly_patch.rename.fa:md5,48208c6df370a225c6f54f378d7a8e39", + "test_hifiasm_flye_assembly.unmapped.txt:md5,e99c39c4afff7b433fb3973359dae6a4", "test_hifiasm_flye.fa:md5,35d9e542fb372022a36ecf4854467e80", "test_hifiasm_flye_hifi.fastplong.json:md5,2671b946d2bf533341b86a9f2424e5c3", "test_hifiasm_flye_ont.fastplong.json:md5,924d11a05764994135ff5de294052a02", "test_hifiasm_flye_hic.params.json:md5,54b576cb6d4d27656878a7fd3657bde9", - "test_hifiasm_flye_hic.fa.gz:md5,35d9e542fb372022a36ecf4854467e80", "test_hifiasm_flye_hic.bp.hap1.p_ctg.gfa:md5,c9a084903ea872a7ac28f3bbd5eee8f3", "test_hifiasm_flye_hic.bp.hap2.p_ctg.gfa:md5,d41d8cd98f00b204e9800998ecf8427e", "test_hifiasm_flye_hic.bp.p_ctg.gfa:md5,d78f7a647429b254d9d46aab4d1306a0", @@ -2523,6 +2483,7 @@ "test_hifiasm_flye_hic_assembly_patch.patch.err:md5,d41d8cd98f00b204e9800998ecf8427e", "test_hifiasm_flye_hic_assembly_patch.patch.fa:md5,6ff15d809eaa0ecf6381400cdd7f0770", "test_hifiasm_flye_hic_assembly_patch.rename.fa:md5,48208c6df370a225c6f54f378d7a8e39", + "test_hifiasm_flye_hic_assembly.unmapped.txt:md5,e99c39c4afff7b433fb3973359dae6a4", "test_hifiasm_flye_hic.fa:md5,35d9e542fb372022a36ecf4854467e80", "test_hifiasm_flye_hic_hicreads.fastp.json:md5,639daa4b554b8562208d2f7dff3a118f", "test_hifiasm_flye_hic_hifi.fastplong.json:md5,1c4764224854af4537899de86c8e2e56", @@ -2536,11 +2497,10 @@ "test_hifiasm_flye_hic_bwamem.bam:md5,837f8fbfbaf79b1049093e62a23a02b2", "test_hifiasm_flye_hic_hic_dedup.bai:md5,aeda4dd1092e5ae65a44c90faa2a4e86", "test_hifiasm_flye_hic_hic_dedup.bam:md5,d93aabe7dbda135b1562eeef7808d347", + "test_hifiasm_flye_hic_links.unmapped.txt:md5,e99c39c4afff7b433fb3973359dae6a4", "test_hifiasm_flye_hic_assembly_patch.patch.fa.gz.fai:md5,06f2947d7897ca8a7c6f30a81bd6bdcc", "test_hifiasm_flye_hic_assembly_patch.patch.fa.gz.gzi:md5,251cd3924556d6f48e9d5127bdd15ee2", - "test_hifiasm_flye_hic_hic_scaffolds_final.fa.gz:md5,3ac2a0232e899bcb28b72e3c4f1c2d79", "test_hifiasm_flye_hic_hic_scaffolds_final.fa:md5,3ac2a0232e899bcb28b72e3c4f1c2d79", - "test_hifiasm_ul.fa.gz:md5,77e3d5af48175c784bfd217048fe271b", "test_hifiasm_ul.bp.hap1.p_ctg.gfa:md5,46ee70869884ad585165bd48081414e9", "test_hifiasm_ul.bp.hap2.p_ctg.gfa:md5,7792865547989d6d284f640425c4e36c", "test_hifiasm_ul.bp.p_ctg.gfa:md5,8fe65466d76815ffe1663ff6d8f2e8d1", @@ -2551,20 +2511,21 @@ "test_hifiasm_ul_ont.fastplong.json:md5,86da6d58ac4630bfeae3ee08014ecb0b", "versions.yml:md5,c6c0c66defcf12c9bd29c649fbef58af", "test_ont_flye.params.json:md5,afa91c041bce5e190f4a699d11b69db6", + "test_ont_flye_assembly.unmapped.txt:md5,d41d8cd98f00b204e9800998ecf8427e", "test_ont_flye_hifi.fastplong.json:md5,9205a4cf65cce249429badc208348349", "test_ont_flye_ont.fastplong.json:md5,e418b2481ade21bc45e77d1437bad913", - "test_ont_hifiasm.fa.gz:md5,35d9e542fb372022a36ecf4854467e80", "test_ont_hifiasm.bp.hap1.p_ctg.gfa:md5,c9a084903ea872a7ac28f3bbd5eee8f3", "test_ont_hifiasm.bp.hap2.p_ctg.gfa:md5,d41d8cd98f00b204e9800998ecf8427e", "test_ont_hifiasm.bp.p_ctg.gfa:md5,d78f7a647429b254d9d46aab4d1306a0", "test_ont_hifiasm.bp.p_utg.gfa:md5,e2b6621386edda1636dfb84ddd676ea8", "test_ont_hifiasm.bp.r_utg.gfa:md5,e2b6621386edda1636dfb84ddd676ea8", + "test_ont_hifiasm_assembly.unmapped.txt:md5,e99c39c4afff7b433fb3973359dae6a4", "test_ont_hifiasm.fa:md5,35d9e542fb372022a36ecf4854467e80", "test_ont_hifiasm_hifi.fastplong.json:md5,91878df7edc2b07a885c103f260fc70e", "test_ont_hifiasm_ont.fastplong.json:md5,e97714274268b5a30be4d9851f2b61b3", "test_ont_hifiasm_ragtag.fa:md5,51f2975257b49657716d2ca7cc6d5fe2", "test_ont_hifiasm_ragtag.stats:md5,466273b499384b2c781c83dc583b8c99", - "test_ont_hifiasm_hic.fa.gz:md5,35d9e542fb372022a36ecf4854467e80", + "test_ont_hifiasm_ragtag.unmapped.txt:md5,e99c39c4afff7b433fb3973359dae6a4", "test_ont_hifiasm_hic.bp.hap1.p_ctg.gfa:md5,c9a084903ea872a7ac28f3bbd5eee8f3", "test_ont_hifiasm_hic.bp.hap2.p_ctg.gfa:md5,d41d8cd98f00b204e9800998ecf8427e", "test_ont_hifiasm_hic.bp.p_ctg.gfa:md5,d78f7a647429b254d9d46aab4d1306a0", @@ -2585,11 +2546,10 @@ "test_ont_hifiasm_hic_hic_dedup.bam:md5,9246dec2c1b6d6f4fd37383ddda244cb", "test_ont_hifiasm_hic.fa.gz.fai:md5,3f23b28c147c40cb4f1d6571cf2dc045", "test_ont_hifiasm_hic.fa.gz.gzi:md5,a5721349018bd8e33902a3e18ef9f530", - "test_ont_hifiasm_hic_hic_scaffolds_final.fa.gz:md5,3ac2a0232e899bcb28b72e3c4f1c2d79", "test_ont_hifiasm_hic_hic_scaffolds_final.fa:md5,3ac2a0232e899bcb28b72e3c4f1c2d79" ] ], - "timestamp": "2026-07-21T11:11:36.406160676", + "timestamp": "2026-08-28T15:21:45.78029328", "meta": { "nf-test": "0.9.5", "nextflow": "25.10.4" From 209d5a222fda9102337684ac250f60ed38aec1cc Mon Sep 17 00:00:00 2001 From: Niklas Schandry Date: Fri, 28 Aug 2026 15:33:13 +0200 Subject: [PATCH 12/17] remove debug comments from workflow --- workflows/genomeassembler.nf | 51 ------------------------------------ 1 file changed, 51 deletions(-) diff --git a/workflows/genomeassembler.nf b/workflows/genomeassembler.nf index f42e8b72..8beb1332 100644 --- a/workflows/genomeassembler.nf +++ b/workflows/genomeassembler.nf @@ -232,58 +232,7 @@ workflow GENOMEASSEMBLER { Prepare a samplesheet that is ready to use with nf-core/genomeqc. This uses the published output paths, not the workdir files. */ - /* - def ch_assembly_manifest = ch_main_scaffolded - .map { it -> - def meta = it.meta - def candidates = [ - // A list of filenames, corresponding and the candidate output folder - [ meta.scaffolds ? meta.scaffolds.ragtag ?: null : null, 'scaffold/ragtag' ], - [ meta.scaffolds ? meta.scaffolds.hic ?: null : null, 'scaffold/hic/yahs' ], - [ meta.scaffolds ? meta.scaffolds.longstitch ?: null : null, 'scaffold/longstitch' ], - [ meta.scaffolds ? meta.scaffolds.links ?: null : null, 'scaffold/links' ], - [ meta.polished ? meta.polished.pilon ?: null : null, 'polish/pilon' ], - [ meta.polished ? meta.polished.medaka ?: null : null, 'polish/medaka' ], - [ meta.polished ? meta.polished.dorado ?: null : null, 'polish/dorado' ], - [ meta.assembly, { - // Assembly publishdirs are a bit more specific - meta.strategy == "single" ? ( - meta.assembler_ont == "flye" || meta.assembler_hifi == "flye" - ? 'assembly/flye' - : 'assembly/hifiasm' - ) : - meta.strategy == "hybrid" - ? 'assembly/hifiasm' - : 'assembly/ragtag' - } - ], - ] - def chosen = candidates.find { entry -> entry[0] } - if( !chosen ) - return null - def assembly_file = chosen[0] - def subdir = chosen[1] - def fasta = "${params.outdir}/${meta.id}/${subdir}/${file(assembly_file).name}" - def subdir_gff = candidates[1] ==~ "assembly" ? "assembly" : candidates[1] - def gff = "${params.outdir}/${meta.id}/${subdir_gff}/*.gff3" - def annotation = files(gff) ? files(gff).first() : null - [ meta.id, fasta ] - } - .filter { row -> row != null } - ch_assembly_manifest.view {it -> "MANIFEST: $it"} - ch_assembly_manifest - .filter( { it -> it[2] != null} ) - .map {sample, fasta, annotation -> [sample,fasta,annotation].join(",")} - .map { rows -> "species,fasta,gff\n" + rows + "\n" } - .collectFile( - name: "nf-core-genomeqc-in-gff.csv", - storeDir: "${params.outdir}/genomeqc_samplesheet", - keepHeader: true, - skip: 1 - ) - - */ def outdir_uri = file(params.outdir).toUriString() def ch_assembly_manifest = ch_main_scaffolded From 94d3d6b57b8b843647ec47dafb2b9962824f642f Mon Sep 17 00:00:00 2001 From: Niklas Schandry Date: Fri, 28 Aug 2026 15:45:34 +0200 Subject: [PATCH 13/17] merge error in changelog --- CHANGELOG.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index bae1da80..d1b037d5 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -22,7 +22,7 @@ Pull requests in reverse chronological order since v1.1.0 [#215](https://github.com/nf-core/genomeassembler/pull/215) - Prepare samplesheet for downstream QC with [nf-core/genomeqc](https://nf-co.re/genomeqc) -- + [#212](https://github.com/nf-core/genomeassembler/pull/212) - bumped medaka to 2.2.2 From 5521bed78c2bb825934e8681d72b257dd3821e7a Mon Sep 17 00:00:00 2001 From: Niklas Schandry Date: Mon, 31 Aug 2026 09:07:21 +0200 Subject: [PATCH 14/17] sort genomeqc samplesheet, regenerate snapshot --- tests/default.nf.test.snap | 16 ++++++++-------- workflows/genomeassembler.nf | 1 + 2 files changed, 9 insertions(+), 8 deletions(-) diff --git a/tests/default.nf.test.snap b/tests/default.nf.test.snap index dd06ed59..5c75f4f3 100644 --- a/tests/default.nf.test.snap +++ b/tests/default.nf.test.snap @@ -516,7 +516,7 @@ "test_ont_hifiasm_hic/scaffold/hic/yahs/test_ont_hifiasm_hic_hic_scaffolds_final.fa.gz" ], [ - "nf-core-genomeqc-in.csv:md5,ee60673c5c108c08220d3e7a9ad2926c", + "nf-core-genomeqc-in.csv:md5,1504281a0bc3142cecc39abe81e7a47f", "test_flye_hifiasm.params.json:md5,afa91c041bce5e190f4a699d11b69db6", "test_flye_hifiasm.bp.hap1.p_ctg.gfa:md5,46ee70869884ad585165bd48081414e9", "test_flye_hifiasm.bp.hap2.p_ctg.gfa:md5,7792865547989d6d284f640425c4e36c", @@ -635,7 +635,7 @@ "test_ont_hifiasm_hic_hic_scaffolds_final.fa:md5,3ac2a0232e899bcb28b72e3c4f1c2d79" ] ], - "timestamp": "2026-08-28T15:31:58.143500933", + "timestamp": "2026-08-31T09:06:52.960597627", "meta": { "nf-test": "0.9.5", "nextflow": "25.10.4" @@ -1158,7 +1158,7 @@ "test_ont_hifiasm_hic/scaffold/hic/yahs/test_ont_hifiasm_hic_hic_scaffolds_final.fa.gz" ], [ - "nf-core-genomeqc-in.csv:md5,dfd339a042d4be575d4d61924100de3e", + "nf-core-genomeqc-in.csv:md5,298dcf1cce8dcd6dda74bd12c4a86f7f", "test_flye_hifiasm.params.json:md5,afa91c041bce5e190f4a699d11b69db6", "test_flye_hifiasm.bp.hap1.p_ctg.gfa:md5,46ee70869884ad585165bd48081414e9", "test_flye_hifiasm.bp.hap2.p_ctg.gfa:md5,7792865547989d6d284f640425c4e36c", @@ -1277,7 +1277,7 @@ "test_ont_hifiasm_hic_hic_scaffolds_final.fa:md5,3ac2a0232e899bcb28b72e3c4f1c2d79" ] ], - "timestamp": "2026-08-28T15:16:42.348431261", + "timestamp": "2026-08-31T08:51:16.105004153", "meta": { "nf-test": "0.9.5", "nextflow": "25.10.4" @@ -1800,7 +1800,7 @@ "test_ont_hifiasm_hic/scaffold/hic/yahs/test_ont_hifiasm_hic_hic_scaffolds_final.fa.gz" ], [ - "nf-core-genomeqc-in.csv:md5,a54f349d2518c3d324e12658b60d1f71", + "nf-core-genomeqc-in.csv:md5,8ece939fc6172e4cb687b2f2c854113b", "test_flye_hifiasm.params.json:md5,afa91c041bce5e190f4a699d11b69db6", "test_flye_hifiasm.bp.hap1.p_ctg.gfa:md5,46ee70869884ad585165bd48081414e9", "test_flye_hifiasm.bp.hap2.p_ctg.gfa:md5,7792865547989d6d284f640425c4e36c", @@ -1919,7 +1919,7 @@ "test_ont_hifiasm_hic_hic_scaffolds_final.fa:md5,3ac2a0232e899bcb28b72e3c4f1c2d79" ] ], - "timestamp": "2026-08-28T15:26:50.323204919", + "timestamp": "2026-08-31T09:01:35.555117899", "meta": { "nf-test": "0.9.5", "nextflow": "25.10.4" @@ -2442,7 +2442,7 @@ "test_ont_hifiasm_hic/scaffold/hic/yahs/test_ont_hifiasm_hic_hic_scaffolds_final.fa.gz" ], [ - "nf-core-genomeqc-in.csv:md5,fec7340f5774b7a47fda549c99ae1732", + "nf-core-genomeqc-in.csv:md5,a9d6b5aa51ea95d0d553a78532dc8aa2", "test_flye_hifiasm.params.json:md5,afa91c041bce5e190f4a699d11b69db6", "test_flye_hifiasm.bp.hap1.p_ctg.gfa:md5,46ee70869884ad585165bd48081414e9", "test_flye_hifiasm.bp.hap2.p_ctg.gfa:md5,7792865547989d6d284f640425c4e36c", @@ -2561,7 +2561,7 @@ "test_ont_hifiasm_hic_hic_scaffolds_final.fa:md5,3ac2a0232e899bcb28b72e3c4f1c2d79" ] ], - "timestamp": "2026-08-28T15:21:45.78029328", + "timestamp": "2026-08-31T08:56:25.205437395", "meta": { "nf-test": "0.9.5", "nextflow": "25.10.4" diff --git a/workflows/genomeassembler.nf b/workflows/genomeassembler.nf index 883b9f3b..c6806e98 100644 --- a/workflows/genomeassembler.nf +++ b/workflows/genomeassembler.nf @@ -283,6 +283,7 @@ workflow GENOMEASSEMBLER { .map {sample, fasta -> [sample,fasta].join(",")} .map { rows -> "assembly,fasta\n" + rows + "\n" } .collectFile( + sort: true, name: "nf-core-genomeqc-in.csv", storeDir: "${params.outdir}/genomeqc_samplesheet", keepHeader: true, From a8e5588d3f1932ddde6adf753326dbe4a76f87d5 Mon Sep 17 00:00:00 2001 From: Niklas Schandry Date: Mon, 31 Aug 2026 12:18:36 +0200 Subject: [PATCH 15/17] genomeqc samplesheet contains paths.. test shape, regenerate snapshot --- nextflow.config | 2 +- nf-test.config | 5 +---- tests/.nftignore | 1 + tests/default.nf.test | 13 +++++++++++++ tests/default.nf.test.snap | 12 ++++-------- 5 files changed, 20 insertions(+), 13 deletions(-) diff --git a/nextflow.config b/nextflow.config index 17951b50..5d20ab88 100644 --- a/nextflow.config +++ b/nextflow.config @@ -31,7 +31,7 @@ params { config_profile_description = null custom_config_version = 'master' - custom_config_base = "https://raw.githubusercontent.com/nf-core/configs/${params.custom_config_version}" + custom_config_base = "https://raw.githubusercontent.com/nf-core/configs/refs/heads/${params.custom_config_version}" config_profile_contact = null config_profile_url = null diff --git a/nf-test.config b/nf-test.config index 2835a825..f829c149 100644 --- a/nf-test.config +++ b/nf-test.config @@ -1,22 +1,18 @@ config { // location for all nf-test tests testsDir = "." - testsDir = "." // nf-test directory including temporary files for each test workDir = System.getenv("NFT_WORKDIR") ?: ".nf-test" - workDir = System.getenv("NFT_WORKDIR") ?: ".nf-test" // location of an optional nextflow.config file specific for executing tests configFile = "tests/nextflow.config" - configFile = "tests/nextflow.config" // ignore tests coming from the nf-core/modules repo ignore = ['modules/nf-core/**/tests/*', 'subworkflows/nf-core/**/tests/*'] // run all test with defined profile(s) from the main nextflow.config profile = "test" - profile = "test" // list of filenames or patterns that should be trigger a full test run triggers = [ @@ -35,5 +31,6 @@ config { // load the necessary plugins plugins { load "nft-utils@0.0.3" + load "nft-csv@0.1.0" } } diff --git a/tests/.nftignore b/tests/.nftignore index 59e0a7e3..819302a4 100644 --- a/tests/.nftignore +++ b/tests/.nftignore @@ -17,3 +17,4 @@ test_flye_hifiasm/scaffold/ragtag/test_flye_hifiasm_ragtag.stats **/assembly.cut250.tigmint.* **/*.assembly.fa **/*MarkDuplicates.metrics.txt +**/nf-core-genomeqc-in.csv diff --git a/tests/default.nf.test b/tests/default.nf.test index 2d7a017a..e0b340d6 100644 --- a/tests/default.nf.test +++ b/tests/default.nf.test @@ -4,6 +4,7 @@ nextflow_pipeline { script "../main.nf" tag "pipeline" + test("-profile test") { when { @@ -18,6 +19,9 @@ nextflow_pipeline { // stable_content: All files in ${params.outdir}/ with stable content def stable_content = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/.nftignore') assert workflow.success + def genomeqc_infile = path("$outputDir/genomeqc_samplesheet/nf-core-genomeqc-in.csv").csv + assert genomeqc_infile.rowCount == 15 + assert genomeqc_infile.columnCount == 2 assertAll( { assert snapshot( // Number of successful tasks @@ -46,6 +50,9 @@ nextflow_pipeline { // stable_content: All files in ${params.outdir}/ with stable content def stable_content = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/.nftignore') assert workflow.success + def genomeqc_infile = path("$outputDir/genomeqc_samplesheet/nf-core-genomeqc-in.csv").csv() + assert genomeqc_infile.rowCount == 15 + assert genomeqc_infile.columnCount == 2 assertAll( { assert snapshot( // Number of successful tasks @@ -74,6 +81,9 @@ nextflow_pipeline { // stable_content: All files in ${params.outdir}/ with stable content def stable_content = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/.nftignore') assert workflow.success + def genomeqc_infile = path("$outputDir/genomeqc_samplesheet/nf-core-genomeqc-in.csv").csv() + assert genomeqc_infile.rowCount == 15 + assert genomeqc_infile.columnCount == 2 assertAll( { assert snapshot( // Number of successful tasks @@ -101,6 +111,9 @@ nextflow_pipeline { def stable_path = getAllFilesFromDir(params.outdir, relative: true, includeDir: true, ignore: ['pipeline_info/*.{html,json,txt}']) // stable_content: All files in ${params.outdir}/ with stable content def stable_content = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/.nftignore') + def genomeqc_infile = path("$outputDir/genomeqc_samplesheet/nf-core-genomeqc-in.csv").csv() + assert genomeqc_infile.rowCount == 15 + assert genomeqc_infile.columnCount == 2 assert workflow.success assertAll( { assert snapshot( diff --git a/tests/default.nf.test.snap b/tests/default.nf.test.snap index 5c75f4f3..5c276639 100644 --- a/tests/default.nf.test.snap +++ b/tests/default.nf.test.snap @@ -516,7 +516,6 @@ "test_ont_hifiasm_hic/scaffold/hic/yahs/test_ont_hifiasm_hic_hic_scaffolds_final.fa.gz" ], [ - "nf-core-genomeqc-in.csv:md5,1504281a0bc3142cecc39abe81e7a47f", "test_flye_hifiasm.params.json:md5,afa91c041bce5e190f4a699d11b69db6", "test_flye_hifiasm.bp.hap1.p_ctg.gfa:md5,46ee70869884ad585165bd48081414e9", "test_flye_hifiasm.bp.hap2.p_ctg.gfa:md5,7792865547989d6d284f640425c4e36c", @@ -635,7 +634,7 @@ "test_ont_hifiasm_hic_hic_scaffolds_final.fa:md5,3ac2a0232e899bcb28b72e3c4f1c2d79" ] ], - "timestamp": "2026-08-31T09:06:52.960597627", + "timestamp": "2026-08-31T12:18:27.860963373", "meta": { "nf-test": "0.9.5", "nextflow": "25.10.4" @@ -1158,7 +1157,6 @@ "test_ont_hifiasm_hic/scaffold/hic/yahs/test_ont_hifiasm_hic_hic_scaffolds_final.fa.gz" ], [ - "nf-core-genomeqc-in.csv:md5,298dcf1cce8dcd6dda74bd12c4a86f7f", "test_flye_hifiasm.params.json:md5,afa91c041bce5e190f4a699d11b69db6", "test_flye_hifiasm.bp.hap1.p_ctg.gfa:md5,46ee70869884ad585165bd48081414e9", "test_flye_hifiasm.bp.hap2.p_ctg.gfa:md5,7792865547989d6d284f640425c4e36c", @@ -1277,7 +1275,7 @@ "test_ont_hifiasm_hic_hic_scaffolds_final.fa:md5,3ac2a0232e899bcb28b72e3c4f1c2d79" ] ], - "timestamp": "2026-08-31T08:51:16.105004153", + "timestamp": "2026-08-31T11:04:15.591023109", "meta": { "nf-test": "0.9.5", "nextflow": "25.10.4" @@ -1800,7 +1798,6 @@ "test_ont_hifiasm_hic/scaffold/hic/yahs/test_ont_hifiasm_hic_hic_scaffolds_final.fa.gz" ], [ - "nf-core-genomeqc-in.csv:md5,8ece939fc6172e4cb687b2f2c854113b", "test_flye_hifiasm.params.json:md5,afa91c041bce5e190f4a699d11b69db6", "test_flye_hifiasm.bp.hap1.p_ctg.gfa:md5,46ee70869884ad585165bd48081414e9", "test_flye_hifiasm.bp.hap2.p_ctg.gfa:md5,7792865547989d6d284f640425c4e36c", @@ -1919,7 +1916,7 @@ "test_ont_hifiasm_hic_hic_scaffolds_final.fa:md5,3ac2a0232e899bcb28b72e3c4f1c2d79" ] ], - "timestamp": "2026-08-31T09:01:35.555117899", + "timestamp": "2026-08-31T11:14:40.766695087", "meta": { "nf-test": "0.9.5", "nextflow": "25.10.4" @@ -2442,7 +2439,6 @@ "test_ont_hifiasm_hic/scaffold/hic/yahs/test_ont_hifiasm_hic_hic_scaffolds_final.fa.gz" ], [ - "nf-core-genomeqc-in.csv:md5,a9d6b5aa51ea95d0d553a78532dc8aa2", "test_flye_hifiasm.params.json:md5,afa91c041bce5e190f4a699d11b69db6", "test_flye_hifiasm.bp.hap1.p_ctg.gfa:md5,46ee70869884ad585165bd48081414e9", "test_flye_hifiasm.bp.hap2.p_ctg.gfa:md5,7792865547989d6d284f640425c4e36c", @@ -2561,7 +2557,7 @@ "test_ont_hifiasm_hic_hic_scaffolds_final.fa:md5,3ac2a0232e899bcb28b72e3c4f1c2d79" ] ], - "timestamp": "2026-08-31T08:56:25.205437395", + "timestamp": "2026-08-31T11:09:22.682790803", "meta": { "nf-test": "0.9.5", "nextflow": "25.10.4" From b553faeb4c06765b4c5396e1169630ebc97739df Mon Sep 17 00:00:00 2001 From: Niklas Schandry Date: Mon, 31 Aug 2026 12:59:14 +0200 Subject: [PATCH 16/17] revert change to custom_config_base --- nextflow.config | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/nextflow.config b/nextflow.config index 5d20ab88..17951b50 100644 --- a/nextflow.config +++ b/nextflow.config @@ -31,7 +31,7 @@ params { config_profile_description = null custom_config_version = 'master' - custom_config_base = "https://raw.githubusercontent.com/nf-core/configs/refs/heads/${params.custom_config_version}" + custom_config_base = "https://raw.githubusercontent.com/nf-core/configs/${params.custom_config_version}" config_profile_contact = null config_profile_url = null From 010eae19641d6ba08c7311fb0346860210788413 Mon Sep 17 00:00:00 2001 From: Niklas Schandry Date: Tue, 1 Sep 2026 10:37:42 +0200 Subject: [PATCH 17/17] Update workflows/genomeassembler.nf Co-authored-by: Daniel Lundin --- workflows/genomeassembler.nf | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/workflows/genomeassembler.nf b/workflows/genomeassembler.nf index c6806e98..28c9c047 100644 --- a/workflows/genomeassembler.nf +++ b/workflows/genomeassembler.nf @@ -269,7 +269,7 @@ workflow GENOMEASSEMBLER { } .flatMap( { it -> it } ) .filter { - _id, _stage, file, _subdir -> file != null + _id, _stage, assembly_file, _subdir -> assembly_file != null } .map { id, stage ,assembly_file, subdir ->