File Info

Filename
.command.sh
Full Path
s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/7f/6fd8beaaeb7c787d5ae1ea3cb072e8/.command.sh
Size
631 bytes
Task
NFCORE_RNAFUSION:RNAFUSION:FUSIONINSPECTOR_WORKFLOW:ARRIBA_VISUALISATION (659_bIB-T1-TRNA-1_B23MHV2LT4_1)
Attempt

Content

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#!/bin/bash -euo pipefail
draw_fusions.R \
    --fusions=659_bIB-T1-TRNA-1_B23MHV2LT4_1.FusionInspector.fusions.tsv \
    --alignments=659_bIB-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam \
    --output=659_bIB-T1-TRNA-1_B23MHV2LT4_1_combined_fusions_arriba_visualisation.pdf \
    --annotation=ref_annot.gtf \
     --cytobands=cytobands_hg38_GRCh38_v2.4.0.tsv \
    --proteinDomains=protein_domains_hg38_GRCh38_v2.4.0.gff3 \


cat <<-END_VERSIONS > versions.yml
"NFCORE_RNAFUSION:RNAFUSION:FUSIONINSPECTOR_WORKFLOW:ARRIBA_VISUALISATION":
    arriba: $(arriba -h | grep 'Version:' 2>&1 |  sed 's/Version: //')
END_VERSIONS