Commit a69a7d03 authored by Jasper Koehorst's avatar Jasper Koehorst
Browse files

kraken2 build cwl update

parent 60fafdfb
......@@ -31,8 +31,9 @@ requirements:
- entryname: script.sh
entry: |-
#!/bin/bash
PATH=/unlock/infrastructure/binaries/BLAST/ncbi-blast-2.13.0+/bin/:"$PATH"
chmod +x /unlock/infrastructure/binaries/kraken2/kraken2-v2.1.2/*
DBNAME=/Volumes/Git/m-unlock/cwl/KRAKEN2_$1
DBNAME=KRAKEN2_$1
threads=$2
/unlock/infrastructure/binaries/kraken2/kraken2-v2.1.2/kraken2-build --download-taxonomy --db $DBNAME
shift;shift;
......@@ -43,10 +44,6 @@ requirements:
done
/unlock/infrastructure/binaries/kraken2/kraken2-v2.1.2/kraken2-build --threads $threads --build --db $DBNAME
# arguments:
# - valueFrom: $(inputs.identifier)
# - valueFrom: $(inputs.threads)
# - valueFrom: $(inputs.references)
inputs:
identifier:
......
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