.command.sh - Workdir - NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:SCARHRD (custom_Sig_18_tumor_normal)

File Info

Filename: .command.sh
Full Path: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/db/c6bc34ed5de5a47a33922742bc3424/.command.sh
Size: 434 bytes
Task: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:SCARHRD (custom_Sig_18_tumor_normal)
Attempt

Content

#!/bin/bash -Ceuo pipefail
source /opt/conda/etc/profile.d/conda.sh && \
conda activate env_scarhrd && \
scarhrd_cli.py \
    --segments custom_Sig_18_tumor_normal.segments.csv \
    --ploidy custom_Sig_18_tumor_normal.purity_ploidy.csv \
    --sample-id custom_Sig_18_tumor_normal \
    --out-dir ./ \


cat <<-END_VERSIONS > versions.yml
"NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:SCARHRD":
    scarHRD: 0.6.2
END_VERSIONS