diff --git a/CHANGELOG.md b/CHANGELOG.md index 63598fc3..d1b037d5 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) + [#212](https://github.com/nf-core/genomeassembler/pull/212) - bumped medaka to 2.2.2 @@ -33,7 +37,7 @@ 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) diff --git a/conf/modules/assembly.config b/conf/modules/assembly.config index f33f81a1..9700587a 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 { @@ -49,35 +50,38 @@ 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" }, - mode: params.publish_dir_mode + 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" }, - mode: params.publish_dir_mode + path: { "${params.outdir}/${meta.id}/assembly/hifiasm_ont/" }, + 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.*' { diff --git a/docs/usage.md b/docs/usage.md index 2201199d..bd912045 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 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 Parameters for this pipeline can either be supplied **globally**, e.g: 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/subworkflows/local/scaffold/main.nf b/subworkflows/local/scaffold/main.nf index bfe33b96..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 - 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 - 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 - 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 - 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 @@ -83,70 +84,70 @@ 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 -> [ - 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 .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 -> [ - 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 .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 -> [ - 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 .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 -> [ - meta: meta_links - + _id, meta_links, meta_longstitch, meta_ragtag -> + meta_links - meta_links.subMap("scaffolds_links") + [ scaffolds: [ @@ -155,11 +156,9 @@ 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 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 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 ] } 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 c025e79d..5c276639 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" }, @@ -83,6 +86,8 @@ } }, [ + "genomeqc_samplesheet", + "genomeqc_samplesheet/nf-core-genomeqc-in.csv", "pipeline_info", "pipeline_info/nf_core_genomeassembler_software_versions.yml", "report", @@ -90,23 +95,20 @@ "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", @@ -117,11 +119,9 @@ "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", @@ -138,21 +138,21 @@ "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", @@ -167,23 +167,22 @@ "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", @@ -204,23 +203,20 @@ "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", @@ -231,11 +227,11 @@ "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", @@ -253,23 +249,20 @@ "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", @@ -280,11 +273,11 @@ "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", @@ -324,12 +317,12 @@ "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", @@ -337,18 +330,17 @@ "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", @@ -395,20 +387,20 @@ "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", @@ -424,18 +416,18 @@ "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", @@ -452,23 +444,22 @@ "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", @@ -515,19 +506,17 @@ "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" ], [ "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", @@ -539,11 +528,12 @@ "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", @@ -553,7 +543,6 @@ "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", @@ -564,11 +553,11 @@ "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", @@ -579,6 +568,7 @@ "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", @@ -592,11 +582,10 @@ "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", @@ -607,20 +596,21 @@ "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", @@ -641,11 +631,10 @@ "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": "2026-08-27T11:51:08.257214278", + "timestamp": "2026-08-31T12:18:27.860963373", "meta": { "nf-test": "0.9.5", "nextflow": "25.10.4" @@ -653,7 +642,7 @@ }, "-profile test": { "content": [ - 80, + 88, { "ADD_RG": { "picard": "3.4.0" @@ -715,6 +704,9 @@ "HIFIASM_ONT": { "hifasm": "0.25.0-r726" }, + "LIFTOFF": { + "liftoff": "1.6.3" + }, "MARKDUP": { "picard": "3.4.0" }, @@ -735,6 +727,8 @@ } }, [ + "genomeqc_samplesheet", + "genomeqc_samplesheet/nf-core-genomeqc-in.csv", "pipeline_info", "pipeline_info/nf_core_genomeassembler_software_versions.yml", "report", @@ -742,23 +736,20 @@ "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", @@ -769,11 +760,9 @@ "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", @@ -790,21 +779,21 @@ "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", @@ -819,23 +808,22 @@ "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", @@ -856,23 +844,20 @@ "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", @@ -883,11 +868,11 @@ "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", @@ -905,23 +890,20 @@ "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", @@ -932,11 +914,11 @@ "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", @@ -976,12 +958,12 @@ "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", @@ -989,18 +971,17 @@ "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", @@ -1047,20 +1028,20 @@ "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", @@ -1076,18 +1057,18 @@ "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", @@ -1104,23 +1085,22 @@ "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", @@ -1167,19 +1147,17 @@ "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" ], [ "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", @@ -1191,11 +1169,12 @@ "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", @@ -1205,7 +1184,6 @@ "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", @@ -1216,11 +1194,11 @@ "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", @@ -1231,6 +1209,7 @@ "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", @@ -1244,11 +1223,10 @@ "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", @@ -1259,20 +1237,21 @@ "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", @@ -1293,11 +1272,10 @@ "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": "2026-08-27T11:34:33.81252959", + "timestamp": "2026-08-31T11:04:15.591023109", "meta": { "nf-test": "0.9.5", "nextflow": "25.10.4" @@ -1305,7 +1283,7 @@ }, "-profile test_busco": { "content": [ - 80, + 88, { "ADD_RG": { "picard": "3.4.0" @@ -1367,6 +1345,9 @@ "HIFIASM_ONT": { "hifasm": "0.25.0-r726" }, + "LIFTOFF": { + "liftoff": "1.6.3" + }, "MARKDUP": { "picard": "3.4.0" }, @@ -1387,6 +1368,8 @@ } }, [ + "genomeqc_samplesheet", + "genomeqc_samplesheet/nf-core-genomeqc-in.csv", "pipeline_info", "pipeline_info/nf_core_genomeassembler_software_versions.yml", "report", @@ -1394,23 +1377,20 @@ "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", @@ -1421,11 +1401,9 @@ "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", @@ -1442,21 +1420,21 @@ "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", @@ -1471,23 +1449,22 @@ "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", @@ -1508,23 +1485,20 @@ "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", @@ -1535,11 +1509,11 @@ "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", @@ -1557,23 +1531,20 @@ "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", @@ -1584,11 +1555,11 @@ "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", @@ -1628,12 +1599,12 @@ "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", @@ -1641,18 +1612,17 @@ "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", @@ -1699,20 +1669,20 @@ "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", @@ -1728,18 +1698,18 @@ "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", @@ -1756,23 +1726,22 @@ "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", @@ -1819,19 +1788,17 @@ "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" ], [ "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", @@ -1843,11 +1810,12 @@ "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", @@ -1857,7 +1825,6 @@ "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", @@ -1868,11 +1835,11 @@ "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", @@ -1883,6 +1850,7 @@ "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", @@ -1896,11 +1864,10 @@ "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", @@ -1911,20 +1878,21 @@ "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", @@ -1945,11 +1913,10 @@ "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": "2026-08-27T11:45:29.31994282", + "timestamp": "2026-08-31T11:14:40.766695087", "meta": { "nf-test": "0.9.5", "nextflow": "25.10.4" @@ -1957,7 +1924,7 @@ }, "-profile test_quast": { "content": [ - 80, + 88, { "ADD_RG": { "picard": "3.4.0" @@ -2019,6 +1986,9 @@ "HIFIASM_ONT": { "hifasm": "0.25.0-r726" }, + "LIFTOFF": { + "liftoff": "1.6.3" + }, "MARKDUP": { "picard": "3.4.0" }, @@ -2039,6 +2009,8 @@ } }, [ + "genomeqc_samplesheet", + "genomeqc_samplesheet/nf-core-genomeqc-in.csv", "pipeline_info", "pipeline_info/nf_core_genomeassembler_software_versions.yml", "report", @@ -2046,23 +2018,20 @@ "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", @@ -2073,11 +2042,9 @@ "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", @@ -2094,21 +2061,21 @@ "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", @@ -2123,23 +2090,22 @@ "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", @@ -2160,23 +2126,20 @@ "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", @@ -2187,11 +2150,11 @@ "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", @@ -2209,23 +2172,20 @@ "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", @@ -2236,11 +2196,11 @@ "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", @@ -2280,12 +2240,12 @@ "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", @@ -2293,18 +2253,17 @@ "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", @@ -2351,20 +2310,20 @@ "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", @@ -2380,18 +2339,18 @@ "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", @@ -2408,23 +2367,22 @@ "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", @@ -2471,19 +2429,17 @@ "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" ], [ "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", @@ -2495,11 +2451,12 @@ "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", @@ -2509,7 +2466,6 @@ "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", @@ -2520,11 +2476,11 @@ "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", @@ -2535,6 +2491,7 @@ "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", @@ -2548,11 +2505,10 @@ "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", @@ -2563,20 +2519,21 @@ "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", @@ -2597,11 +2554,10 @@ "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": "2026-08-27T11:39:56.092238324", + "timestamp": "2026-08-31T11:09:22.682790803", "meta": { "nf-test": "0.9.5", "nextflow": "25.10.4" diff --git a/workflows/genomeassembler.nf b/workflows/genomeassembler.nf index 80a1d8be..28c9c047 100644 --- a/workflows/genomeassembler.nf +++ b/workflows/genomeassembler.nf @@ -231,6 +231,66 @@ 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 outdir_uri = file(params.outdir).toUriString() + + def ch_assembly_manifest = ch_main_scaffolded + .map { it -> + def meta = it.meta + def subout = + // Assembly publishdirs are a bit more specific + meta.strategy == "single" ? ( + meta.assembler_ont == "flye" || meta.assembler_hifi == "flye" + ? 'assembly/flye' + : 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 + ] + ] + } + .flatMap( { it -> it } ) + .filter { + _id, _stage, assembly_file, _subdir -> assembly_file != null + } + .map { + id, stage ,assembly_file, subdir -> + [ + "${id}-${stage}", + "${outdir_uri}/${id}/${subdir}/${file(assembly_file).name}" + ] + } + + ch_assembly_manifest + .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, + skip: 1 + ) + + emit: _report }