.command.sh - Workdir - NFCORE_RNAFUSION:RNAFUSION:FASTQC (rna_s1221_S42)

File Info

Filename: .command.sh
Full Path: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/df/ce337fea0365b398bfbc4383e2f8b7/.command.sh
Size: 497 bytes
Task: NFCORE_RNAFUSION:RNAFUSION:FASTQC (rna_s1221_S42)
Attempt

Content

#!/bin/bash -euo pipefail
printf "%s %s\n" rna_s1221_S42_rna_s1221_S42_R1_001.fastq.gz rna_s1221_S42_1.gz rna_s1221_S42_rna_s1221_S42_R2_001.fastq.gz rna_s1221_S42_2.gz | while read old_name new_name; do
    [ -f "${new_name}" ] || ln -s $old_name $new_name
done

fastqc \
    --quiet \
    --threads 2 \
    rna_s1221_S42_1.gz rna_s1221_S42_2.gz

cat <<-END_VERSIONS > versions.yml
"NFCORE_RNAFUSION:RNAFUSION:FASTQC":
    fastqc: $( fastqc --version | sed '/FastQC v/!d; s/.*v//' )
END_VERSIONS