Commit a03625f7 authored by Nijsse, Bart's avatar Nijsse, Bart
Browse files

rm

parent 6581cec5
#!/usr/bin/env cwl-runner
cwlVersion: v1.2
class: CommandLineTool
label: "Bin assembly stats"
doc: |
Table of all bins and there assembly statistics like size, N50, etc..
+ table of the bins and their respective assembly contigs names.
requirements:
- class: InlineJavascriptRequirement
- class: InitialWorkDirRequirement
listing:
- entry: "$({class: 'Directory', listing: []})"
entryname: "Bins summary table"
writable: true
- entryname: script.sh
entry: |-
#!/bin/bash
source /unlock/infrastructure/venv/bin/activate
python3 /unlock/infrastructure/binaries/scripts/metagenomics/bins_summary.py $@
baseCommand: ["bash", "script.sh"] # see requirements
inputs:
identifier:
type: string
doc: Identifier for this dataset used in this workflow
label: identifier used
bin_dir:
type: Directory
doc: Directory containing bins in fasta format from metagenomic binning
label: Bins directory
inputBinding:
prefix: "--bin_dir"
bin_depths:
type: File
doc: MetaBAT2 aggregateDepths file
label: bin depths
inputBinding:
prefix: "--bin_depths"
busco_dir:
type: Directory
doc: Directory containing BUSCO reports
label: BUSCO folder
inputBinding:
prefix: "--busco_dir"
checkm:
type: File
doc: CheckM report file
label: CheckM report
inputBinding:
prefix: "--checkm"
arguments:
- prefix: "--output_file"
valueFrom: $(inputs.identifier)_bin_summary.tsv
outputs:
bin_summary:
type: File
outputBinding:
glob: $(inputs.identifier)_bin_summary.tsv
s:author:
- class: s:Person
s:identifier: https://orcid.org/0000-0001-8172-8981
s:email: mailto:jasper.koehorst@wur.nl
s:name: Jasper Koehorst
- class: s:Person
s:identifier: https://orcid.org/0000-0001-9524-5964
s:email: mailto:bart.nijsse@wur.nl
s:name: Bart Nijsse
s:citation: https://m-unlock.nl
s:codeRepository: https://gitlab.com/m-unlock/cwl
s:dateCreated: "2021-00-00"
s:license: https://spdx.org/licenses/Apache-2.0
s:copyrightHolder: "UNLOCK - Unlocking Microbial Potential"
$namespaces:
s: https://schema.org/
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