.command.sh - Workdir - NFCORE_RNAFUSION:RNAFUSION:TRIM_WORKFLOW:FASTQC_FOR_FASTP (dna_s739)

File Info

Filename: .command.sh
Full Path: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/4c/b4afc88a70a9b14fe611a5a2a8f830/.command.sh
Size: 497 bytes
Task: NFCORE_RNAFUSION:RNAFUSION:TRIM_WORKFLOW:FASTQC_FOR_FASTP (dna_s739)
Attempt

Content

#!/bin/bash -euo pipefail
printf "%s %s\n" dna_s739_1.fastp.fastq.gz dna_s739_trimmed_1.gz dna_s739_2.fastp.fastq.gz dna_s739_trimmed_2.gz | while read old_name new_name; do
    [ -f "${new_name}" ] || ln -s $old_name $new_name
done

fastqc \
    --quiet \
    --threads 2 \
    dna_s739_trimmed_1.gz dna_s739_trimmed_2.gz

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