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Improved ext.args consolidation for STAR and TRIMGALORE #1248

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merged 5 commits into from
Apr 18, 2024
Merged

Improved ext.args consolidation for STAR and TRIMGALORE #1248

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fbaef17
Improve the extra_args parameter consolidation so it can override pre…
MatthiasZepper Mar 8, 2024
0d7e0f5
Changelog update.
MatthiasZepper Mar 8, 2024
934019e
Implement Jonathan Manning's map-method for extra argument consolidat…
MatthiasZepper Apr 16, 2024
8027585
Implement Jonathan Manning's map-method for extra argument consolidat…
MatthiasZepper Apr 16, 2024
6ab2e44
Apply @pinin4fjords (Jonathan Manning)'s suggestions from code review
MatthiasZepper Apr 17, 2024
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1 change: 1 addition & 0 deletions CHANGELOG.md
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Original file line number Diff line number Diff line change
Expand Up @@ -56,6 +56,7 @@ Thank you to everyone else that has contributed by reporting bugs, enhancements
- [PR #1245](https://github.com/nf-core/rnaseq/pull/1245) - nf test quantify rsem
- [PR #1246](https://github.com/nf-core/rnaseq/pull/1246) - nf-test quantify pseudoalignment
- [PR #1247](https://github.com/nf-core/rnaseq/pull/1247) - nf-test prepare_genome
- [PR #1248](https://github.com/nf-core/rnaseq/pull/1248) - Improved ext.args consolidation for STAR and TRIMGALORE extra_args parameters
- [PR #1249](https://github.com/nf-core/rnaseq/pull/1249) - Include nf-tests for rsem_merge_counts module
- [PR #1250](https://github.com/nf-core/rnaseq/pull/1250) - Remove all tags.yml files because the testing system has changed
- [PR #1251](https://github.com/nf-core/rnaseq/pull/1251) - Replace deseq2qc paths
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45 changes: 31 additions & 14 deletions subworkflows/local/align_star/nextflow.config
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@@ -1,20 +1,37 @@
if (!params.skip_alignment && params.aligner == 'star_salmon') {
process {
withName: '.*:ALIGN_STAR:STAR_ALIGN|.*:ALIGN_STAR:STAR_ALIGN_IGENOMES' {
ext.args = { [
'--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' : '',
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.

// 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]
}
}
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// Initialize the map with preconfigured values
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())

// Consolidate the extra arguments
def final_args_map = preset_args_map + (params.extra_star_align_args ? argsToMap(params.extra_star_align_args) : [:])

// Convert the map back to a list and then to a single string
final_args_map.collect { key, value -> "${key} ${value}" }.join(' ').trim()
}

publishDir = [
[
path: { "${params.outdir}/${params.aligner}/log" },
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22 changes: 18 additions & 4 deletions subworkflows/nf-core/fastq_fastqc_umitools_trimgalore/nextflow.config
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