Repository navigation
Port ISOFORMSWITCHANALYZER to the nf-core module structure and update IsoformSwitchAnalyzeR to 2.12.0 #281
New issue
Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.
By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We鈥檒l occasionally send you account related emails.
Already on GitHub? Sign in to your account
Merged
Merged
Changes from all commits
Commits
Show all changes
4 commits
Select commit
Hold shift + click to select a range
File filter
Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
There are no files selected for viewing
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,115 @@ | ||
| %%metro title: nf-core/rnasplice | ||
| %%metro logo: nf-core-rnasplice_logo_light.png | nf-core-rnasplice_logo_dark.png | ||
| %%metro style: nfcore | ||
| %%metro center_ports: true | ||
| %%metro compact_offsets: true | ||
| %%metro files: fastq_in | FASTQ | Reads | ||
| %%metro file: genome_bam_in | BAM | Genome | ||
| %%metro file: transcriptome_bam_in | BAM | Transcriptome | ||
| %%metro dir: salmon_in | Salmon | Quant | ||
| %%metro file: bigwig_out | BW | Coverage | ||
| %%metro file: report_out | HTML | MultiQC | ||
| %%metro off_track: genome_bam_in, transcriptome_bam_in, salmon_in | ||
| %%metro line: deu | Differential exon usage (DEU) | #e63946 | ||
| %%metro line: dtu | Differential transcript usage (DTU) | #4361ee | ||
| %%metro line: event | Event-based splicing | #f39c12 | ||
| %%metro line: qc | QC & visualisation | #2db572 | ||
| %%metro legend: bl | ||
| %%metro grid: preprocessing | 0,0 | ||
| %%metro grid: alignment | 1,0 | ||
| %%metro grid: quantification | 1,1 | ||
| %%metro grid: exon_analysis | 2,0 | ||
| %%metro grid: transcript_analysis | 2,1 | ||
| %%metro grid: reporting | 3,0 | ||
|
|
||
| graph LR | ||
| subgraph preprocessing [Pre-processing] | ||
| fastq_in[ ] | ||
| cat_fastq[cat] | ||
| fastqc_raw[FastQC] | ||
| trimgalore[Trim Galore!] | ||
| fastqc_trim[FastQC] | ||
|
|
||
| fastq_in -->|deu,dtu,event,qc| cat_fastq | ||
| cat_fastq -->|deu,dtu,event,qc| fastqc_raw | ||
| fastqc_raw -->|deu,dtu,event,qc| trimgalore | ||
| trimgalore -->|deu,dtu,event,qc| fastqc_trim | ||
| end | ||
|
|
||
| subgraph alignment [Genome alignment] | ||
| genome_bam_in[ ] | ||
| star[STAR] | ||
| samtools[SAMtools] | ||
|
|
||
| star -->|deu,event,qc| samtools | ||
| genome_bam_in -->|deu,event,qc| samtools | ||
| end | ||
|
|
||
| subgraph quantification [Transcript quantification] | ||
| transcriptome_bam_in[ ] | ||
| salmon_in[ ] | ||
| salmon[Salmon] | ||
| tximport[tximport] | ||
|
|
||
| transcriptome_bam_in -->|dtu,event| salmon | ||
| salmon -->|dtu,event| tximport | ||
| salmon_in -->|dtu,event| tximport | ||
| end | ||
|
|
||
| subgraph exon_analysis [Exon & junction based analysis] | ||
| htseq[HTSeq] | ||
| dexseq_exon[DEXSeq] | ||
| featurecounts[featureCounts] | ||
| edger[edgeR] | ||
| rmats[rMATS] | ||
| regtools[regtools] | ||
| leafcutter[LeafCutter] | ||
|
|
||
| htseq -->|deu| dexseq_exon | ||
| featurecounts -->|deu| edger | ||
| regtools -->|event| leafcutter | ||
| end | ||
|
|
||
| subgraph transcript_analysis [Transcript based analysis] | ||
| drimseq[DRIMSeq] | ||
| dexseq_dtu[DEXSeq] | ||
| stager[stageR] | ||
| isar[IsoformSwitchAnalyzeR] | ||
| suppa_events[SUPPA events] | ||
| suppa_psi[SUPPA PSI] | ||
| suppa_diff[SUPPA diffSplice] | ||
| suppa_cluster[SUPPA cluster] | ||
|
|
||
| drimseq -->|dtu| dexseq_dtu | ||
| dexseq_dtu -->|dtu| stager | ||
| suppa_events -->|event| suppa_psi | ||
| suppa_psi -->|event| suppa_diff | ||
| suppa_diff -->|event| suppa_cluster | ||
| end | ||
|
|
||
| subgraph reporting [Visualisation & reporting] | ||
| miso[MISO sashimi] | ||
| bedtools[BEDTools] | ||
| bigwig[bedGraphToBigWig] | ||
| multiqc[MultiQC] | ||
| bigwig_out[ ] | ||
| report_out[ ] | ||
|
|
||
| bedtools -->|qc| bigwig | ||
| bigwig -->|qc| bigwig_out | ||
| multiqc -->|qc| report_out | ||
| end | ||
|
|
||
| %% Inter-section edges | ||
| fastqc_trim -->|deu,dtu,event,qc| star | ||
| star -->|dtu,event| salmon | ||
| samtools -->|deu| htseq | ||
| samtools -->|deu| featurecounts | ||
| samtools -->|event| rmats | ||
| samtools -->|event| regtools | ||
| samtools -->|qc| miso | ||
| samtools -->|qc| bedtools | ||
| samtools -->|qc| multiqc | ||
| tximport -->|dtu| drimseq | ||
| tximport -->|event| suppa_events | ||
| salmon -->|dtu| isar |
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Binary file not shown.
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,7 @@ | ||
| --- | ||
| # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json | ||
| channels: | ||
| - conda-forge | ||
| - bioconda | ||
| dependencies: | ||
| - "bioconda::bioconductor-isoformswitchanalyzer=2.12.0" |
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,37 +1,47 @@ | ||
| process ISOFORMSWITCHANALYZER { | ||
| label 'process_medium' | ||
|
|
||
| conda "bioconda::bioconductor-isoformswitchanalyzer==2.2.0" | ||
| container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? | ||
| 'https://depot.galaxyproject.org/singularity/bioconductor-isoformswitchanalyzer:2.2.0--r43ha9d7317_0' : | ||
| 'biocontainers/bioconductor-isoformswitchanalyzer:2.2.0--r43ha9d7317_0' }" | ||
| conda "${moduleDir}/environment.yml" | ||
| container "${workflow.containerEngine in ['singularity', 'apptainer'] && !task.ext.singularity_pull_docker_container | ||
| ? 'https://depot.galaxyproject.org/singularity/bioconductor-isoformswitchanalyzer:2.12.0--r45hd2fad28_0' | ||
| : 'biocontainers/bioconductor-isoformswitchanalyzer:2.12.0--r45hd2fad28_0'}" | ||
|
|
||
| input: | ||
| path salmon_output | ||
| path gtf // path to gtf file | ||
| path transcript_sequences // path to isoform nt sequences fasta | ||
| path samplesheet // path samplesheet | ||
| path contrastsheet // path contrastsheet | ||
| val alpha // alpha value for differential isoform expression | ||
| val dIF // dIF cutoff value for differential isoform expression | ||
| path salmon_output // path: one Salmon quant directory per sample | ||
| path gtf // path: /path/to/genes.gtf | ||
| path transcript_sequences // path: /path/to/transcripts.fa (isoform nucleotide sequences) | ||
| path samplesheet // path: /path/to/samplesheet.csv | ||
| path contrastsheet // path: /path/to/contrastsheet.csv | ||
| val alpha // val: FDR cutoff for the isoform switch test | ||
| val dIF // val: minimum absolute difference in isoform fraction | ||
|
|
||
| output: | ||
| path "isoformswitchanalyzer_summary.csv" , emit: isoformswitchanalyzer_summary | ||
| path "isoformswitchanalyzer_isoformfeatures.csv" , emit: isoformswitchanalyzer_isoformFeatures | ||
| path "switchlist.rds" , emit: switchlist_rds | ||
| path "results" , emit: results | ||
| tuple val("${task.process}"), val('r-base'), eval('R --version 2>&1 | head -n 1 | sed "s/^.*version //; s/ .*$//"'), topic: versions, emit: versions_R | ||
| tuple val("${task.process}"), val('bioconductor-isoformswitchanalyzer'), eval('Rscript -e "library(IsoformSwitchAnalyzeR); cat(as.character(packageVersion(\'IsoformSwitchAnalyzeR\')))"'), topic: versions, emit: versions_isoformswitchanalyzer | ||
|
|
||
| path "isoformswitchanalyzer_summary.csv" , emit: isoformswitchanalyzer_summary | ||
| path "isoformswitchanalyzer_isoformfeatures.csv", emit: isoformswitchanalyzer_isoformFeatures | ||
| path "switchlist.rds" , emit: switchlist_rds | ||
| path "results" , emit: results | ||
| path "versions.yml" , topic: versions, emit: versions_isoformswitchanalyzer | ||
|
|
||
| when: | ||
| task.ext.when == null || task.ext.when | ||
|
|
||
| script: | ||
| template 'run_isoformswitchanalyzer.R' | ||
|
|
||
| stub: | ||
| def args = task.ext.args ?: '' | ||
| """ | ||
| echo ${args} | ||
|
|
||
| mkdir -p results | ||
| touch isoformswitchanalyzer_summary.csv | ||
| touch isoformswitchanalyzer_isoformfeatures.csv | ||
| touch switchlist.rds | ||
|
|
||
| run_isoformswitchanalyzer.R ${gtf} ${transcript_sequences} ${samplesheet} ${contrastsheet} ${alpha} ${dIF} ${args} | ||
| cat <<-END_VERSIONS > versions.yml | ||
| "${task.process}": | ||
| r-base: \$(R --version 2>&1 | head -n 1 | sed 's/^.*version //; s/ .*\$//') | ||
| bioconductor-isoformswitchanalyzer: \$(Rscript -e "library(IsoformSwitchAnalyzeR); cat(as.character(packageVersion('IsoformSwitchAnalyzeR')))") | ||
| END_VERSIONS | ||
| """ | ||
| } |
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,116 @@ | ||
| # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json | ||
| name: "isoformswitchanalyzer" | ||
| description: Identify isoform switches between conditions from Salmon quantifications | ||
| with IsoformSwitchAnalyzeR, predict their functional consequences and plot the top | ||
| switching genes of every contrast | ||
| keywords: | ||
| - IsoformSwitchAnalyzeR | ||
| - isoform switch | ||
| - differential transcript usage | ||
| - alternative splicing | ||
| - salmon | ||
| tools: | ||
| - "IsoformSwitchAnalyzeR": | ||
| description: "Analysis of alternative splicing and isoform switches with predicted | ||
| functional consequences (e.g. gain/loss of protein domains etc.) from quantification | ||
| of all types of RNASeq by tools such as Kallisto, Salmon, StringTie, Cufflinks/Cuffdiff | ||
| etc." | ||
| homepage: "https://bioconductor.org/packages/IsoformSwitchAnalyzeR" | ||
| documentation: "https://bioconductor.org/packages/release/bioc/vignettes/IsoformSwitchAnalyzeR/inst/doc/IsoformSwitchAnalyzeR.html" | ||
| tool_dev_url: "https://github.com/kvittingseerup/IsoformSwitchAnalyzeR" | ||
| doi: "10.1093/bioinformatics/btz247" | ||
| licence: ["GPL-2.0-or-later"] | ||
| identifier: biotools:isoformswitchanalyzer | ||
|
|
||
| input: | ||
| - salmon_output: | ||
| type: directory | ||
| description: One Salmon quant directory per sample, each holding a `quant.sf`. | ||
| The directory names must match the `sample` column of the samplesheet | ||
| pattern: "*" | ||
| - gtf: | ||
| type: file | ||
| description: GTF annotation the transcripts were quantified against | ||
| pattern: "*.gtf" | ||
| ontologies: | ||
| - edam: "http://edamontology.org/format_2306" # GTF | ||
| - transcript_sequences: | ||
| type: file | ||
| description: Nucleotide sequences of the annotated transcripts, named by | ||
| transcript id as in the GTF | ||
| pattern: "*.{fa,fasta}" | ||
| ontologies: | ||
| - edam: "http://edamontology.org/format_1929" # FASTA | ||
| - samplesheet: | ||
| type: file | ||
| description: Comma-separated sample sheet with at least `sample` and `condition` | ||
| column headers | ||
| pattern: "*.csv" | ||
| ontologies: | ||
| - edam: "http://edamontology.org/format_3752" # CSV | ||
| - contrastsheet: | ||
| type: file | ||
| description: Comma-separated contrast sheet with `treatment` and `control` | ||
| column headers naming the conditions to compare. Every pair of conditions | ||
| is compared when the file does not exist | ||
| pattern: "*.csv" | ||
| ontologies: | ||
| - edam: "http://edamontology.org/format_3752" # CSV | ||
| - alpha: | ||
| type: float | ||
| description: FDR cutoff below which an isoform switch is called significant | ||
| - dIF: | ||
| type: float | ||
| description: Minimum absolute difference in isoform fraction between the two | ||
| conditions for an isoform switch to be called | ||
|
|
||
| output: | ||
| isoformswitchanalyzer_summary: | ||
| - "isoformswitchanalyzer_summary.csv": | ||
| type: file | ||
| description: Number of switching isoforms, switches and genes per contrast | ||
| and combined. Holds the error message instead when no switch was found | ||
| pattern: "isoformswitchanalyzer_summary.csv" | ||
| ontologies: | ||
| - edam: "http://edamontology.org/format_3752" # CSV | ||
| isoformswitchanalyzer_isoformFeatures: | ||
| - "isoformswitchanalyzer_isoformfeatures.csv": | ||
| type: file | ||
| description: The `isoformFeatures` table of the switchAnalyzeRlist with the | ||
| expression, isoform fraction, switch q-value and consequences of every | ||
| isoform in every contrast. Empty when no switch was found | ||
| pattern: "isoformswitchanalyzer_isoformfeatures.csv" | ||
| ontologies: | ||
| - edam: "http://edamontology.org/format_3752" # CSV | ||
| switchlist_rds: | ||
| - "switchlist.rds": | ||
| type: file | ||
| description: Serialised switchAnalyzeRlist object | ||
| pattern: "switchlist.rds" | ||
| results: | ||
| - "results": | ||
| type: directory | ||
| description: One subdirectory per contrast with a switch plot PDF per switching | ||
| gene, plus the common switch consequences PDF | ||
| pattern: "results" | ||
| versions_isoformswitchanalyzer: | ||
| - "versions.yml": | ||
| type: file | ||
| description: File containing software versions | ||
| pattern: "versions.yml" | ||
| ontologies: | ||
| - edam: "http://edamontology.org/format_3750" # YAML | ||
|
|
||
| topics: | ||
| versions: | ||
| - "versions.yml": | ||
| type: file | ||
| description: File containing software versions | ||
| pattern: "versions.yml" | ||
| ontologies: | ||
| - edam: "http://edamontology.org/format_3750" # YAML | ||
| authors: | ||
| - "@bensouthgate" | ||
| - "@piplus2" | ||
| maintainers: | ||
| - "@piplus2" |
Oops, something went wrong.
Oops, something went wrong.
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
Uh oh!
There was an error while loading. Please reload this page.