From be876f99ab2b1de9129a70f94ce022c2a8a59cdd Mon Sep 17 00:00:00 2001
From: Dominik Brilhaus <brilhaus@nfdi4plants.org>
Date: Thu, 20 Mar 2025 17:23:10 +0100
Subject: [PATCH] add more cwl metadata
---
workflows/kallisto/gather-dirs.cwl | 9 ++++++
workflows/kallisto/kallisto-index.cwl | 6 +++-
workflows/kallisto/kallisto-quant.cwl | 41 ++++++++++++++++++++++++++-
workflows/kallisto/kallisto-test.cwl | 18 ------------
4 files changed, 54 insertions(+), 20 deletions(-)
delete mode 100644 workflows/kallisto/kallisto-test.cwl
diff --git a/workflows/kallisto/gather-dirs.cwl b/workflows/kallisto/gather-dirs.cwl
index c7a13f5..a11ef77 100644
--- a/workflows/kallisto/gather-dirs.cwl
+++ b/workflows/kallisto/gather-dirs.cwl
@@ -1,12 +1,20 @@
cwlVersion: v1.2
class: ExpressionTool
+label: Gather directories
doc: |
+ Helper tool to organize
+
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
+
requirements:
- class: InlineJavascriptRequirement
+
inputs:
inDirs: Directory[]
destinationDir: string
+
expression: |
${
return {"outDir": {
@@ -15,5 +23,6 @@ expression: |
"listing": inputs.inDirs
} };
}
+
outputs:
outDir: Directory
\ No newline at end of file
diff --git a/workflows/kallisto/kallisto-index.cwl b/workflows/kallisto/kallisto-index.cwl
index 977cbab..e374a1f 100644
--- a/workflows/kallisto/kallisto-index.cwl
+++ b/workflows/kallisto/kallisto-index.cwl
@@ -4,6 +4,10 @@ class: CommandLineTool
label: Kallisto index
doc: |
+
+ Docs: https://pachterlab.github.io/kallisto/
+
+
Builds a kallisto index
Usage: kallisto index [arguments] FASTA-files
@@ -34,7 +38,7 @@ hints:
- https://identifiers.org/biotools/kallisto
requirements:
- - class: InlineJavascriptRequirement
+ InlineJavascriptRequirement: {}
baseCommand: [kallisto, index]
diff --git a/workflows/kallisto/kallisto-quant.cwl b/workflows/kallisto/kallisto-quant.cwl
index 692be58..8da7542 100755
--- a/workflows/kallisto/kallisto-quant.cwl
+++ b/workflows/kallisto/kallisto-quant.cwl
@@ -2,13 +2,48 @@
cwlVersion: v1.2
class: CommandLineTool
+label: Kallisto quant
+doc: |
+
+ Docs: https://pachterlab.github.io/kallisto/
+
+ Computes equivalence classes for reads and quantifies abundances
+
+ Usage: kallisto quant [arguments] FASTQ-files
+
+ Required arguments:
+ -i, --index=STRING Filename for the kallisto index to be used for
+ quantification
+ -o, --output-dir=STRING Directory to write output to
+
+ Optional arguments:
+ -b, --bootstrap-samples=INT Number of bootstrap samples (default: 0)
+ --seed=INT Seed for the bootstrap sampling (default: 42)
+ --plaintext Output plaintext instead of HDF5
+ --single Quantify single-end reads
+ --single-overhang Include reads where unobserved rest of fragment is
+ predicted to lie outside a transcript
+ --fr-stranded Strand specific reads, first read forward
+ --rf-stranded Strand specific reads, first read reverse
+ -l, --fragment-length=DOUBLE Estimated average fragment length
+ -s, --sd=DOUBLE Estimated standard deviation of fragment length
+ (default: -l, -s values are estimated from paired
+ end data, but are required when using --single)
+ -p, --priors Priors for the EM algorithm, either as raw counts or as
+ probabilities. Pseudocounts are added to raw reads to
+ prevent zero valued priors. Supplied in the same order
+ as the transcripts in the transcriptome
+ -t, --threads=INT Number of threads to use (default: 1)
+ --verbose Print out progress information every 1M proccessed reads
+
+
hints:
DockerRequirement:
dockerPull: quay.io/biocontainers/kallisto:0.51.1--ha4fb952_1
SoftwareRequirement:
packages:
kallisto:
- version: [ "0.50.0" ]
+ version: [ "0.51.1" ]
specs: [ https://identifiers.org/biotools/kallisto ]
inputs:
@@ -131,7 +166,11 @@ outputs:
outputBinding:
glob: $(runtime.outdir)/$(inputs.QuantOutfolder)
+
$namespaces:
edam: https://edamontology.org/
+ s: https://schema.org/
$schemas:
- https://edamontology.org/EDAM_1.18.owl
+
+s:license: https://spdx.org/licenses/BSD-2-Clause
diff --git a/workflows/kallisto/kallisto-test.cwl b/workflows/kallisto/kallisto-test.cwl
deleted file mode 100644
index 3a05871..0000000
--- a/workflows/kallisto/kallisto-test.cwl
+++ /dev/null
@@ -1,18 +0,0 @@
-#!/usr/bin/env cwl-runner
-cwlVersion: v1.2
-class: CommandLineTool
-
-hints:
- DockerRequirement:
- dockerPull: quay.io/biocontainers/kallisto:0.50.1--h6de1650_2
- SoftwareRequirement:
- packages:
- kallisto:
- version: [ "0.50.0" ]
- specs: [ https://identifiers.org/biotools/kallisto ]
-
-inputs: []
-
-baseCommand: [kallisto]
-
-outputs: []
\ No newline at end of file
--
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