rm

cwl/metagenomics/bin_assembly_stats.cwl

-#!/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/