Improved ext.args consolidation for STAR and TRIMGALORE #1248
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I did manually test the change with the test profile and providing 
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Thank your for doing this, @MatthiasZepper. I think it follows the principle of "least surprise". Don't know how easy it would be, but if you wanted to avoid people inadvertently overwriting preset options, you could test for that and issue a warning. I don't consider it strictly necessary, though -- people who use this option should know what they are doing. |
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pinin4fjords
approved these changes
Apr 15, 2024
| params.save_unaligned ? '--outReadsUnmapped Fastx' : '', | ||
| params.extra_star_align_args ? params.extra_star_align_args.split("\\s(?=--)") : '' | ||
| ].flatten().unique(false).join(' ').trim() } | ||
| ext.args = { |
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Principle makes sense.
Would it make more sense to factor out maps and merge from there? Like the following (untested).
ext.args = {
// Function to convert argument strings into a map
def argsToMap(String args) {
args.split("\\s(?=--)").collectEntries {
def (key, value) = it.trim().split(/\s+/, 2)
[(key): value]
}
}
// Initialize the map with preset arguments
def preset_args_map = argsToMap('''
--quantMode TranscriptomeSAM
--twopassMode Basic
--outSAMtype BAM Unsorted
--readFilesCommand zcat
--runRNGseed 0
--outFilterMultimapNmax 20
--alignSJDBoverhangMin 1
--outSAMattributes NH HI AS NM MD
--quantTranscriptomeBan Singleend
--outSAMstrandField intronMotif
${params.save_unaligned ? '--outReadsUnmapped Fastx' : ''}
'''.trim())
// Convert extra arguments into a map
def extra_args_map = params.extra_star_align_args ? argsToMap(params.extra_star_align_args) : [:]
// Merge maps: extra arguments override preset arguments
def final_args_map = preset_args_map + extra_args_map
// Convert the map back to a list and then to a single string
final_args_map.collect { key, value -> "${key} ${value}" }.join(' ').trim()
}
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Either way is fine with me.
Since I do know neither Java nor Groovy (why is Nextflow not pythonic :-/ ?!?) I was just happy that I could nudge the AI into coming up with something that worked. But it is true, using a map is an elegant solution, because it avoids repeatedly looping over the preset arguments for each extra argument.
…sets from the config.
…ion for the local STAR alignment subworkflow.
…ion for the FastQC-UMItools-Trimgalore subworkflow..
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Seems the tests are failing. Before I try to troubleshoot code in a language I do not know... do you, Jonathan, right away know where the problem is? |
subworkflows/nf-core/fastq_fastqc_umitools_trimgalore/nextflow.config
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Co-authored-by: Jonathan Manning <jonathan.manning@seqera.io>
That looks much better! Thank you very much! There are two tests failing, but to me, it doesn't seem that this is anyway related to this PR. |
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Occasionally, people were surprised that parameters provided to
extra_star_align_argscould still conflict with the default configuration (e.g. #1046).As a convenience parameter, I felt that it should never take precedence over the actual module configuration, because it seemed more error-prone to silently overwrite the module config with something that (as the parameter name suggests) is meant to be extra. Hence, I preferred that a custom module config should be used.
However, I said that I would be open to reconsider and since now also @tdanhorn and @CharlotteAnne suggested that change, I gave in. This PR now improves the
extra_argsparameter consolidation so it can override presets from the config.PR checklist
nf-core lint).nextflow run . -profile test,docker --outdir <OUTDIR>).nextflow run . -profile debug,test,docker --outdir <OUTDIR>).CHANGELOG.mdis updated.