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Fix refactored 2.4.3 auxiliary files to value channels #873

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Merged
jfy133 merged 2 commits into from
Apr 6, 2022
Merged

Fix refactored 2.4.3 auxiliary files to value channels #873

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57764c0
Change auxilary files from queue to value channels
jfy133 Apr 5, 2022
43db446
New style changelog
jfy133 Apr 5, 2022
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2 changes: 2 additions & 0 deletions CHANGELOG.md
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Original file line number Diff line number Diff line change
Expand Up @@ -9,6 +9,8 @@ and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.

### `Fixed`

- Fixed some auxiliary files (adapater list, snpcapture/pileupcaller/sexdeterrmine BED files, and pileupCaller SNP file, PMD reference mask) in some cases only be used against one sample (❤ to @meganemichel for reporting, fix by @jfy133)

### `Dependencies`

### `Deprecated`
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22 changes: 12 additions & 10 deletions main.nf
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Expand Up @@ -238,45 +238,47 @@ if ( !params.clip_adapters_list ) {
Channel
.fromPath("$projectDir/assets/nf-core_eager_dummy2.txt", checkIfExists: true)
.ifEmpty { exit 1, "[nf-core/eager] error: adapters list file not found. Please check input. Supplied: --clip_adapters_list '${params.clip_adapters_list}'." }
.collect()
.set {ch_adapterlist}
} else {
Channel
.fromPath("${params.clip_adapters_list}", checkIfExists: true)
.ifEmpty { exit 1, "[nf-core/eager] error: adapters list file not found. Please check input. Supplied: --clip_adapters_list '${params.clip_adapters_list}'." }
.collect()
.set {ch_adapterlist}
}

if ( params.snpcapture_bed ) {
Channel.fromPath(params.snpcapture_bed, checkIfExists: true).set { ch_snpcapture_bed }
ch_snpcapture_bed = Channel.fromPath(params.snpcapture_bed, checkIfExists: true).collect()
} else {
Channel.fromPath("$projectDir/assets/nf-core_eager_dummy.txt").set { ch_snpcapture_bed }
ch_snpcapture_bed = Channel.fromPath("$projectDir/assets/nf-core_eager_dummy.txt").collect()
}

// Set up channel with pmdtools reference mask bedfile
if (!params.pmdtools_reference_mask) {
ch_bedfile_for_reference_masking = Channel.fromPath("$projectDir/assets/nf-core_eager_dummy.txt")
ch_bedfile_for_reference_masking = Channel.fromPath("$projectDir/assets/nf-core_eager_dummy.txt").collect()
} else {
ch_bedfile_for_reference_masking = Channel.fromPath(params.pmdtools_reference_mask, checkIfExists: true)
ch_bedfile_for_reference_masking = Channel.fromPath(params.pmdtools_reference_mask, checkIfExists: true).collect()
}

// SexDetermination channel set up and bedfile validation
if (!params.sexdeterrmine_bedfile) {
ch_bed_for_sexdeterrmine = Channel.fromPath("$projectDir/assets/nf-core_eager_dummy.txt")
ch_bed_for_sexdeterrmine = Channel.fromPath("$projectDir/assets/nf-core_eager_dummy.txt").collect()
} else {
ch_bed_for_sexdeterrmine = Channel.fromPath(params.sexdeterrmine_bedfile, checkIfExists: true)
ch_bed_for_sexdeterrmine = Channel.fromPath(params.sexdeterrmine_bedfile, checkIfExists: true).collect()
}

// pileupCaller channel generation and input checks for 'random sampling' genotyping
if (!params.pileupcaller_bedfile) {
ch_bed_for_pileupcaller = Channel.fromPath("$projectDir/assets/nf-core_eager_dummy.txt")
ch_bed_for_pileupcaller = Channel.fromPath("$projectDir/assets/nf-core_eager_dummy.txt").collect()
} else {
ch_bed_for_pileupcaller = Channel.fromPath(params.pileupcaller_bedfile, checkIfExists: true)
ch_bed_for_pileupcaller = Channel.fromPath(params.pileupcaller_bedfile, checkIfExists: true).collect()
}

if (!params.pileupcaller_snpfile) {
ch_snp_for_pileupcaller = Channel.fromPath("$projectDir/assets/nf-core_eager_dummy2.txt")
ch_snp_for_pileupcaller = Channel.fromPath("$projectDir/assets/nf-core_eager_dummy2.txt").collect()
} else {
ch_snp_for_pileupcaller = Channel.fromPath(params.pileupcaller_snpfile, checkIfExists: true)
ch_snp_for_pileupcaller = Channel.fromPath(params.pileupcaller_snpfile, checkIfExists: true).collect()
}

// Create input channel for MALT database directory, checking directory exists
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