File Info

Filename
.command.sh
Full Path
s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/05/9bddda1b65da4a9558ce63d09935cc/.command.sh
Size
1.0 KB
Task
NFCORE_HARMONIZE:HARMONIZE:FILTER_HOTSPOT_VCF (FFPE_HD789_01_p2_gDNA_03_A23WJ5GLT4_1_vs_NA12878_c_0002_gDNA_0005_B23KYWJLT4_1)
Attempt

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#!/bin/bash -euo pipefail
filter_hotspot_vcf.py \
    --input-vcf FFPE_HD789_01_p2_gDNA_03_A23WJ5GLT4_1_vs_NA12878_c_0002_gDNA_0005_B23KYWJLT4_1.tnseq.hmnz.vcf.gz \
    --hotspot-bed FINAL_hotspot_list_07302025_hg38_sorted_w_anno_mods.bed \
    --output-vcf FFPE_HD789_01_p2_gDNA_03_A23WJ5GLT4_1_vs_NA12878_c_0002_gDNA_0005_B23KYWJLT4_1.tnseq.hotspot.hmnz.vcf

python3 -c "import pysam; pysam.tabix_compress('FFPE_HD789_01_p2_gDNA_03_A23WJ5GLT4_1_vs_NA12878_c_0002_gDNA_0005_B23KYWJLT4_1.tnseq.hotspot.hmnz.vcf', 'FFPE_HD789_01_p2_gDNA_03_A23WJ5GLT4_1_vs_NA12878_c_0002_gDNA_0005_B23KYWJLT4_1.tnseq.hotspot.hmnz.vcf.gz', force=True); pysam.tabix_index('FFPE_HD789_01_p2_gDNA_03_A23WJ5GLT4_1_vs_NA12878_c_0002_gDNA_0005_B23KYWJLT4_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