Commit 934bf3f2 authored by Nijsse, Bart's avatar Nijsse, Bart
Browse files

new combined and more complete table of bins

parent 22425219
......@@ -10,35 +10,60 @@ doc: |
+ table of the bins and their respective assembly contigs names.
requirements:
- class: InlineJavascriptRequirement
- 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 $@
baseCommand: ["bash", "script.sh"] # see requirements
inputs:
identifier:
type: string
doc: Identifier for this dataset used in this workflow
label: identifier used
label: identifier used
bin_dir:
type: Directory
doc: folder containing bins in fasta format from metagenomic binning
label: bins folder
doc: Directory containing bins in fasta format from metagenomic binning
label: Bins directory
inputBinding:
prefix: "--bin_dir"
bin_depths:
type: File
doc: MetaBAT2 aggregateDepths file
label: bin depths
inputBinding:
prefix: "--bin_depths"
busco_dir:
type: Directory
doc: Directory containing BUSCO reports
label: BUSCO folder
inputBinding:
prefix: "--busco_dir"
checkm:
type: File
doc: CheckM report file
label: CheckM report
inputBinding:
prefix: "--checkm"
arguments:
- "$(inputs.bin_dir)"
baseCommand: [bash, "/unlock/infrastructure/binaries/scripts/metagenomics/bin_assembly_stats.sh"]
stdout: $(inputs.identifier)_binAssemblyStats.tsv
- prefix: "--output_file"
valueFrom: $(inputs.identifier)_bin_summary.tsv
outputs:
binStats:
type: File
outputBinding:
glob: $(inputs.identifier)_binAssemblyStats.tsv
binContigs:
bin_summary:
type: File
outputBinding:
glob: binContigs.tsv
glob: $(inputs.identifier)_bin_summary.tsv
s:author:
- class: s:Person
......
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