File Info
- Filename
- .command.sh
- Full Path
- s3://natera-rnd-fsdx-dev-nextflow-scratch-01/work/de/45ea01ec0d91b007bfc63ed0f10d95/.command.sh
- Size
- 351 bytes
- Task
- BWA_MEM (four)
- Attempt
Content
View in new tab#!/bin/bash -Ceuo pipefail
set -euo pipefail
RG=$(printf '@RG\tID:%s\tSM:%s\tPL:ILLUMINA\tLB:%s' 'four' 'four' 'four')
bwa-mem2 mem -t 4 -K 50000000 -R "$RG" 'hg38.fa' 'nf_gui_test_two.1.fastp.fq.gz' 'nf_gui_test_two.2.fastp.fq.gz' \
| samtools sort -@4 -m 768M --no-PG -o four.sorted.bam -
samtools index -@ 4 four.sorted.bam four.sorted.bam.bai