From 2fb885ed8273f84c8f804386cbf9ca15a8ebe507 Mon Sep 17 00:00:00 2001
From: Dominik Brilhaus <brilhaus@nfdi4plants.org>
Date: Thu, 20 Mar 2025 16:10:02 +0100
Subject: [PATCH] add metadata to kallisto
---
workflows/kallisto/kallisto-index.cwl | 33 +++++++++++++++++++++++----
1 file changed, 29 insertions(+), 4 deletions(-)
diff --git a/workflows/kallisto/kallisto-index.cwl b/workflows/kallisto/kallisto-index.cwl
index d35f520..977cbab 100644
--- a/workflows/kallisto/kallisto-index.cwl
+++ b/workflows/kallisto/kallisto-index.cwl
@@ -2,18 +2,42 @@
cwlVersion: v1.2
class: CommandLineTool
+label: Kallisto index
+doc: |
+ Builds a kallisto index
+
+ Usage: kallisto index [arguments] FASTA-files
+
+ Required argument:
+ -i, --index=STRING Filename for the kallisto index to be constructed
+
+ Optional argument:
+ -k, --kmer-size=INT k-mer (odd) length (default: 31, max value: 63)
+ -t, --threads=INT Number of threads to use (default: 1)
+ -d, --d-list=STRING Path to a FASTA-file containing sequences to mask from quantification
+ --make-unique Replace repeated target names with unique names
+ --aa Generate index from a FASTA-file containing amino acid sequences
+ --distinguish Generate index where sequences are distinguished by the sequence name
+ -T, --tmp=STRING Temporary directory (default: tmp)
+ -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)
+
hints:
DockerRequirement:
dockerPull: quay.io/biocontainers/kallisto:0.51.1--ha4fb952_1
SoftwareRequirement:
packages:
kallisto:
- version: [ "0.50.0" ]
- specs: [ https://identifiers.org/biotools/kallisto ]
+ version: [ "0.51.1" ]
+ specs:
+ - https://identifiers.org/rrid/RRID:SCR_016582
+ - https://identifiers.org/biotools/kallisto
requirements:
- class: InlineJavascriptRequirement
+baseCommand: [kallisto, index]
+
inputs:
InputFiles:
type: File[]
@@ -41,8 +65,6 @@ inputs:
inputBinding:
prefix: "--make-unique"
-baseCommand: [kallisto, index]
-
outputs:
index:
type: File
@@ -51,5 +73,8 @@ outputs:
$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
--
GitLab