Commit 0f2f8e09 authored by Nijsse, Bart's avatar Nijsse, Bart
Browse files

add database names to the output names

parent 2dd80284
......@@ -3,13 +3,6 @@
cwlVersion: v1.2
class: CommandLineTool
# hints:
# SoftwareRequirement:
# packages:
# kraken2:
# version: ["2.1.2"]
# specs: ["https://anaconda.org/bioconda/kraken2"]
baseCommand: [ /unlock/infrastructure/binaries/kraken2-2.0.9-beta/kraken2 ]
label: "Kraken2 metagenomics read classification"
......@@ -21,16 +14,11 @@ doc: |
requirements:
- class: InlineJavascriptRequirement
- class: InitialWorkDirRequirement
listing:
- entry: "$({class: 'Directory', listing: []})"
entryname: "kraken2_output"
writable: true
arguments:
- valueFrom: kraken2_output/$(inputs.identifier)_kraken2.txt
- valueFrom: $(inputs.identifier)_$(inputs.database.split( '/' ).pop())_kraken2.txt
prefix: --output
- valueFrom: kraken2_output/$(inputs.identifier)_kraken2_report.txt
- valueFrom: $(inputs.identifier)_$(inputs.database.split( '/' ).pop())_kraken2_report.txt
prefix: --report
- "--report-zero-counts"
- "--use-names"
......@@ -96,18 +84,14 @@ inputs:
default: false
outputs:
kraken2_outdir:
type: Directory
outputBinding:
glob: kraken2_output
standard_report:
type: File
outputBinding:
glob: kraken2_output/$(inputs.identifier)_kraken2.txt
glob: $(inputs.identifier)_$(inputs.database.split( '/' ).pop())_kraken2.txt
sample_report:
type: File
outputBinding:
glob: kraken2_output/$(inputs.identifier)_kraken2_report.txt
glob: $(inputs.identifier)_$(inputs.database.split( '/' ).pop())_kraken2_report.txt
s:author:
- class: s:Person
......
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