.command.sh - Workdir - NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:SCARHRD (HCC1395_tumor_vs_HCC1395_BL)

File Info

Filename: .command.sh
Full Path: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/0e/e5389f1f7ffb69cc3ebeeed16d3f25/.command.sh
Size: 437 bytes
Task: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:SCARHRD (HCC1395_tumor_vs_HCC1395_BL)
Attempt

Content

#!/bin/bash -Ceuo pipefail
source /opt/conda/etc/profile.d/conda.sh && \
conda activate env_scarhrd && \
scarhrd_cli.py \
    --segments HCC1395_tumor_vs_HCC1395_BL.segments.csv \
    --ploidy HCC1395_tumor_vs_HCC1395_BL.purity_ploidy.csv \
    --sample-id HCC1395_tumor_vs_HCC1395_BL \
    --out-dir ./ \


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