.command.sh - Workdir - BWA_MEM (two)

File Info

Filename: .command.sh
Full Path: s3://natera-rnd-fsdx-dev-nextflow-scratch-01/work/69/14a5e965a6fedb1c2c7f48986977e8/.command.sh
Size: 349 bytes
Task: BWA_MEM (two)
Attempt

Content

#!/bin/bash -Ceuo pipefail
set -euo pipefail
RG=$(printf '@RG\tID:%s\tSM:%s\tPL:ILLUMINA\tLB:%s' 'two' 'two' 'two')
bwa-mem2 mem -t 4 -K 50000000 -R "$RG" 'hg38.fa' 'nf_gui_test_three.1.fastp.fq.gz' 'nf_gui_test_three.2.fastp.fq.gz' \
    | samtools sort -@4 -m 768M --no-PG -o two.sorted.bam -
samtools index -@ 4 two.sorted.bam two.sorted.bam.bai