.command.sh - Workdir - TASTER_FREQ (one.markdup.bam)

File Info

Filename: .command.sh
Full Path: s3://natera-rnd-fsdx-dev-nextflow-scratch-01/work/2f/6591d360df6c3d77bf2fe1170559ab/.command.sh
Size: 398 bytes
Task: TASTER_FREQ (one.markdup.bam)
Attempt

Content

#!/bin/bash -Ceuo pipefail
set -euo pipefail
/usr/local/bin/make_freq_file \
    --bam-file 'one.markdup.bam' \
    --output-file one.markduped.freqs.txt \
    --duplex one.markduped.freqs.duplex.txt \
    --reference-file 'hg38.fa' \
    --bed-file 'small_padded.bed' \
    --unpad-bed-file 'small.bed' \
    --threads 4 \
    --duplex-tag "XX" \
    --min-bq 30 \
    --min-mapq 30 \
    --tabix