Commit 5b982b0f authored by Jasper Koehorst's avatar Jasper Koehorst
Browse files

multiqc reporting update

parent 75611fdb
......@@ -3,45 +3,49 @@
cwlVersion: v1.0
class: CommandLineTool
label: "FASTQC run"
label: "MultiQC reporting"
requirements:
- class: InlineJavascriptRequirement
- class: InitialWorkDirRequirement
listing:
- entry: "$({class: 'Directory', listing: []})"
entryname: $(inputs.step)_QualityControl
writable: true
InlineJavascriptRequirement: {}
InitialWorkDirRequirement:
listing:
- entry: "$({class: 'Directory', listing: []})"
entryname: "medaka_output"
writable: true
- entryname: script.sh
entry: |-
#!/bin/bash
source /root/miniconda/bin/activate
conda init bash
conda activate /unlock/infrastructure/conda/multiqc_v1.12.0
multiqc --filename multiqc_report $@
doc: |
Performs quality control on FASTQ file
Generates a MultiQC report of a given folder
stdout: fastqc.log
stderr: fastqc.error
# stdout: multiqc.log
# stderr: multiqc.error
inputs:
step:
type: int
doc: workflow step number
label: The step number in the workflow
fastqs:
type: File[]
doc: FastQ file directory
label: FASTQ file directory
folder:
type: string
doc: Directory path to be processed by MultiQC
label: MultiQC directory
inputBinding:
position: 100
arguments: ["/unlock/infrastructure/binaries/fastqc_v0.11.9/fastqc", "--outdir", $(inputs.step)_QualityControl]
baseCommand: ["bash", "script.sh"]
# arguments: ["multiqc","--filename","multiqc_report"]
outputs:
info:
type: stdout
error:
type: stderr
upload:
type: Directory
# info:
# type: stdout
# error:
# type: stderr
multiqc:
type: File
outputBinding:
glob: $(inputs.step)_QualityControl
glob: multiqc_report.*
s:author:
- class: s:Person
......@@ -55,7 +59,7 @@ s:author:
s:citation: https://m-unlock.nl
s:codeRepository: https://gitlab.com/m-unlock/cwl
s:dateCreated: "2020-00-00"
s:dateCreated: "2022-00-00"
s:license: https://spdx.org/licenses/Apache-2.0
s:copyrightHolder: "UNLOCK - Unlocking Microbial Potential"
......
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