just to follow up on my last message: (base) stefanie@bibo:*~/Biggie/JF10_HIV_r4/work/79/1330069ee4f77da8d17dcebf782816*$ cat .command.sh #!/usr/bin/env bash -C -e -u -o pipefail fq lint \ --disable-validator P001 \ HIV_RAL_6h_trimmed_1_val_1.fq.gz HIV_RAL_6h_trimmed_2_val_2.fq.gz > HIV_RAL_6h.fq_lint.txt cat <<-END_VERSIONS > versions.yml "NFCORE_RNASEQRNASEQFASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:FQ_LINT_AFTER_TRIMMING": fq: $(echo $(fq lint --version | sed 's/fq-lint //g')) END_VERSIONS