modules
modules copied to clipboard
nf-core
Use `eval` to collect version
Nextflow 24.02.0-edge brings with it two new features which should give much cleaner syntax for collecting tool versions: channel topics using topic (see https://github.com/nf-core/modules/issues/4517) and eval. They are designed to work together nicely, but are technically separate features.
- Docs for
eval: https://nextflow.io/docs/latest/process.html#output-type-eval - Blog post about
evalandtopic: https://nextflow.io/blog/2024/nextflow-2404-highlights.html#process-eval-outputs - Example pipeline change: https://github.com/nf-core/fetchngs/pull/312
The blog post contains a basic example of how this can be used to collect versions:
process FASTQC {
input:
tuple val(meta), path(reads)
output:
tuple val(meta), path('*.html'), emit: html
tuple val("${task.process}"), val('fastqc'), eval('fastqc --version'), topic: versions
"""
fastqc $reads
"""
}
workflow {
Channel.topic('versions')
| unique()
| collectFile(name: 'collated_versions.yml')
| CUSTOM_DUMPSOFTWAREVERSIONS
}
Needs some thought about how we approach these changes - may be best to do a bulk change everywhere in one go, as it affects multiple code locations (modules and pipelines).
See comment: https://github.com/nf-core/modules/issues/4517#issuecomment-2194150864
An example that might need to be taken into consideration is that, in the nf-module for bwa, the command used to retrieve the version information is bwa 2>&1 and that command always returns exit code 1, and so I guess eval('bwa 2>&1') will always fail.
If the result of the version-retrieving command is pipped into sed like here, and the eval-statement over in the fastqc-module in the nf-core/repo would be something like eval('fastqc --version | sed \'/FastQC v/!d; s/.*v//'\')(Not sure about the syntax for escaping the single quotation mark (') but nevermind.), then Nextflow might not detect if the command fastqc --version | sed \'/FastQC v/!d; s/.*v//') has failed, because <some_failing_cmd> | sed '/FastQC v/!d; s/.*v//' seems to always return exit code 0.
