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Commit 02d24942 authored by Dominik Brilhaus's avatar Dominik Brilhaus
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add cwl metadata

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1 merge request!19Arc cwl
Pipeline #9525 passed
This commit is part of merge request !19. Comments created here will be created in the context of that merge request.
......@@ -16,9 +16,9 @@ steps:
in:
fastq: fastq
finaloutdir: finaloutdir
out: [outdir]
out: [fastqc_outdir]
outputs:
outdir:
fastqc_outdir:
type: Directory
outputSource: fastqc/outdir
\ No newline at end of file
outputSource: fastqc/fastqc_outdir
\ No newline at end of file
......@@ -2,12 +2,14 @@
cwlVersion: v1.2
class: CommandLineTool
label: Run fastqc on raw reads in FASTQ format (single or paired end) or aligned reads in BAM.
label: FastQC - A high throughput sequence QC analysis tool
doc: |
simplified from: https://github.com/common-workflow-library/bio-cwl-tools/blob/66f620da5b0a11e934a6da83272205a2516bcd91/fastqc/fastqc_1.cwl
Original docs: https://www.bioinformatics.babraham.ac.uk/projects/fastqc/
Run fastqc on raw reads in FASTQ format (single or paired end) or aligned reads in BAM.
This CWL was adapted from: https://github.com/common-workflow-library/bio-cwl-tools/blob/66f620da5b0a11e934a6da83272205a2516bcd91/fastqc/fastqc_1.cwl
hints:
ResourceRequirement:
......@@ -18,11 +20,13 @@ hints:
SoftwareRequirement:
packages:
fastqc:
specs: [ https://identifiers.org/biotools/fastqc ]
specs:
- https://identifiers.org/biotools/fastqc
- - https://identifiers.org/rrid/RRID:SCR_014583
version: [ "0.11.9" ]
baseCommand: "fastqc"
arguments:
- valueFrom: $(runtime.outdir)
prefix: "-o"
......@@ -46,3 +50,13 @@ outputs:
outputBinding:
glob: "*_fastqc.html"
$namespaces:
edam: https://edamontology.org/
s: https://schema.org/
$schemas:
- https://edamontology.org/EDAM_1.18.owl
s:license: https://spdx.org/licenses/GPL-3.0-or-later
cwlVersion: v1.2
class: ExpressionTool
label: Collect files in a directory
label: Gather files
doc: |
Takes Files (e.g. from a workflow step) and yields them in a desired directory.
Helper tool to organize workflow outputs
Takes an array of files (e.g. from a workflow step) and yields them in a destination directory.
Adapted from: https://github.com/common-workflow-language/cwl-v1.1/blob/a22b7580c6b50e77c0a181ca59d3828dd5c69143/tests/dir7.cwl
requirements:
- class: InlineJavascriptRequirement
inputs:
files: File[]
inFiles: File[]
destination: string
expression: |
${
return {"outDir": {
"class": "Directory",
"basename": inputs.destination,
"listing": inputs.files
"listing": inputs.inFiles
} };
}
outputs:
......
......@@ -18,15 +18,17 @@ steps:
fastq: fastq
out: [fastqc_zip, fastqc_html]
collectFiles:
run: ./collectFilesInDir.cwl
run: ./gather-files.cwl
in:
destination: finaloutdir
files:
source: [fastqc/fastqc_html, fastqc/fastqc_zip]
inFiles:
source:
- fastqc/fastqc_html
- fastqc/fastqc_zip
linkMerge: merge_flattened
destination: finaloutdir
out: [outDir]
outputs:
outdir:
fastqc_outdir:
type: Directory
outputSource: collectFiles/outDir
\ No newline at end of file
......@@ -2,8 +2,8 @@ cwlVersion: v1.2
class: ExpressionTool
label: Gather directories
doc: |
Helper tool to organize
Helper tool to organize workflow outputs
Takes an array of directories (e.g. from a workflow step) and yields them in a destination directory.
Adapted from: https://github.com/common-workflow-language/cwl-v1.1/blob/a22b7580c6b50e77c0a181ca59d3828dd5c69143/tests/dir7.cwl
......
......@@ -26,6 +26,8 @@ doc: |
-m, --min-size=INT Length of minimizers (default: automatically chosen)
-e, --ec-max-size=INT Maximum number of targets in an equivalence class (default: no maximum)
This CWL was adapted from: https://github.com/common-workflow-library/bio-cwl-tools/commit/91c42fb809ce18eafe16155cca0abf362270c0fe
hints:
DockerRequirement:
dockerPull: quay.io/biocontainers/kallisto:0.51.1--ha4fb952_1
......
......@@ -37,6 +37,9 @@ doc: |
--verbose Print out progress information every 1M proccessed reads
This CWL was adapted from: https://github.com/common-workflow-library/bio-cwl-tools/commit/91c42fb809ce18eafe16155cca0abf362270c0fe
hints:
DockerRequirement:
dockerPull: quay.io/biocontainers/kallisto:0.51.1--ha4fb952_1
......
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