.command.sh - Workdir - DAQ:FASTQ_NGSCHECKMATE:NGSCHECKMATE_FASTQ (1136_6G2-T1-TDNA-1_A23MHWWLT4_1)

File Info

Filename: .command.sh
Full Path: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/90/4e889970aceac96cbff732f6dd3169/.command.sh
Size: 367 bytes
Task: DAQ:FASTQ_NGSCHECKMATE:NGSCHECKMATE_FASTQ (1136_6G2-T1-TDNA-1_A23MHWWLT4_1)
Attempt

Content

#!/bin/bash -Ceuo pipefail
ngscheckmate_fastq \
    -1 1136_6G2-T1-TDNA-1_A23MHWWLT4_1_R1.fastq.gz \
    -2 1136_6G2-T1-TDNA-1_A23MHWWLT4_1_R2.fastq.gz \
    SNP_GRCh38_hg38_wChr.pt \
    -p 4 \
    -s 0.05 \
    > 1136_6G2-T1-TDNA-1_A23MHWWLT4_1.vaf

cat <<-END_VERSIONS > versions.yml
"DAQ:FASTQ_NGSCHECKMATE:NGSCHECKMATE_FASTQ":
    ngscheckmate: 1.0
END_VERSIONS