File Info

Filename
.command.sh
Full Path
s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a3/f40d613b9dea405f68703e663f89d3/.command.sh
Size
975 bytes
Task
NFCORE_HARMONIZE:HARMONIZE:FILTER_HOTSPOT_VCF (1136_814-N1-BDNA-1_A23WGJTLT4_1_vs_1136_814-N1-BDNA-1_A237CFYLT3_1)
Attempt

Content

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#!/bin/bash -euo pipefail
filter_hotspot_vcf.py \
    --input-vcf 1136_814-N1-BDNA-1_A23WGJTLT4_1_vs_1136_814-N1-BDNA-1_A237CFYLT3_1.tnseq.hmnz.vcf.gz \
    --hotspot-bed FINAL_hotspot_list_07302025_hg38_sorted_w_anno_mods.bed \
    --output-vcf 1136_814-N1-BDNA-1_A23WGJTLT4_1_vs_1136_814-N1-BDNA-1_A237CFYLT3_1.tnseq.hotspot.hmnz.vcf

python3 -c "import pysam; pysam.tabix_compress('1136_814-N1-BDNA-1_A23WGJTLT4_1_vs_1136_814-N1-BDNA-1_A237CFYLT3_1.tnseq.hotspot.hmnz.vcf', '1136_814-N1-BDNA-1_A23WGJTLT4_1_vs_1136_814-N1-BDNA-1_A237CFYLT3_1.tnseq.hotspot.hmnz.vcf.gz', force=True); pysam.tabix_index('1136_814-N1-BDNA-1_A23WGJTLT4_1_vs_1136_814-N1-BDNA-1_A237CFYLT3_1.tnseq.hotspot.hmnz.vcf.gz', preset='vcf', force=True)"

cat <<-END_VERSIONS > versions.yml
"NFCORE_HARMONIZE:HARMONIZE:FILTER_HOTSPOT_VCF":
    python: $(python --version | sed 's/Python //')
    filter_hotspot_vcf: "1.0.0"
    pysam: $(python3 -c "import pysam; print(pysam.__version__)")
END_VERSIONS