CI
1ebb61f1e8
Build pipeline: vsh-ci-dev-jsbwk
Source commit: 1e1ffb315f
Source message: Merge pull request #17 from viash-hub/add_biobox_modules
- Migrate a number of components to biobox
- Fix tests
- Reduce size of test resources
- Prepare for Viash Hub
50 lines
1.5 KiB
Bash
50 lines
1.5 KiB
Bash
#!/bin/bash
|
|
|
|
set -eo pipefail
|
|
|
|
IFS="," read -ra input <<< $par_input
|
|
|
|
single_end_params=''
|
|
if [ $par_paired == "false" ]; then
|
|
if [[ $par_fragment_length < 0 ]] || [[ ! $fragment_length_sd < 0 ]]; then
|
|
echo "fragment_length and fragment_length_sd must be set for single-end data"
|
|
exit 1
|
|
fi
|
|
single_end_params="--single --fragment-length $par_fragment_length --sd $par_fragment_length_sd"
|
|
fi
|
|
|
|
strandedness=''
|
|
if [[ "$par_extra_args" != *"--fr-stranded"* ]] && [[ "$par_extra_args" != *"--rf-stranded"* ]]; then
|
|
if [ "$par_strandedness" == 'forward' ]; then
|
|
strandedness='--fr-stranded'
|
|
elif [ "$par_strandedness" == 'reverse' ]; then
|
|
strandedness='--rf-stranded'
|
|
fi
|
|
fi
|
|
|
|
mkdir -p $par_output
|
|
echo "kallisto quant \
|
|
${meta_cpus:+--threads $meta_cpus} \
|
|
--index $par_index \
|
|
${par_gtf:+--gtf $par_gtf} \
|
|
${par_chromosomes:+--chromosomes $par_chromosomes} \
|
|
$single_end_params \
|
|
$strandedness \
|
|
$par_extra_args \
|
|
-o $par_output \
|
|
${input[*]} 2> >(tee -a ${par_output}/kallisto_quant.log >&2)"
|
|
kallisto quant \
|
|
${meta_cpus:+--threads $meta_cpus} \
|
|
--index $par_index \
|
|
${par_gtf:+--gtf $par_gtf} \
|
|
${par_chromosomes:+--chromosomes $par_chromosomes} \
|
|
$single_end_params \
|
|
$strandedness \
|
|
$par_extra_args \
|
|
-o $par_output \
|
|
${input[*]} 2> >(tee -a ${par_output}/kallisto_quant.log >&2)
|
|
|
|
mv ${par_output}/kallisto_quant.log ${par_log}
|
|
mv ${par_output}/run_info.json ${par_run_info}
|
|
cp ${par_output}/abundance.tsv ${par_quant_results_file}
|