File Info

Filename
.command.sh
Full Path
s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/16/ab39a9c1b8ed7c37c61cfb28e6fe20/.command.sh
Size
850 bytes
Task
NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MANTA_FUSION:MANTA_FUSION_ANNOTATE (659_bQZ-T1-TDNA-1_B23KFCWLT4_1_vs_659_bQZ-N1-BDNA-1_B23KGCJLT4_1)
Attempt

Content

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#!/bin/bash -Ceuo pipefail
annotateFusionVcf.py \
    --vcf 659_bQZ-T1-TDNA-1_B23KFCWLT4_1_vs_659_bQZ-N1-BDNA-1_B23KGCJLT4_1.manta_fusion.somatic_sv.vcf.gz \
    --genes protein_coding_genes.bed \
    --actionable-bed foresight_panel_for_manta.bed \
    --out 659_bQZ-T1-TDNA-1_B23KFCWLT4_1_vs_659_bQZ-N1-BDNA-1_B23KGCJLT4_1.manta_fusion.somatic_sv.annotated.vcf

bgzip  659_bQZ-T1-TDNA-1_B23KFCWLT4_1_vs_659_bQZ-N1-BDNA-1_B23KGCJLT4_1.manta_fusion.somatic_sv.annotated.vcf
tabix -p vcf 659_bQZ-T1-TDNA-1_B23KFCWLT4_1_vs_659_bQZ-N1-BDNA-1_B23KGCJLT4_1.manta_fusion.somatic_sv.annotated.vcf.gz

cat <<-END_VERSIONS > versions.yml
"NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MANTA_FUSION:MANTA_FUSION_ANNOTATE":
    python: $( python3 --version 2>&1 | sed 's/Python //' )
    annotateFusionVcf: "1.0.0"
END_VERSIONS