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Fix merge cockup
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parent
70f94603b0
commit
aa2d07c42a
5 changed files with 9 additions and 12 deletions
2
.github/workflows/ci.yml
vendored
2
.github/workflows/ci.yml
vendored
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@ -41,7 +41,7 @@ jobs:
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- "--shortread_complexityfilter_tool prinseq"
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- "--perform_runmerging"
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- "--perform_runmerging --shortread_clipmerge_mergepairs"
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- "--shortread_complexityfilter false --shortread_hostremoval"
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- "--shortread_complexityfilter false --perform_shortread_hostremoval"
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steps:
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- name: Check out pipeline code
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@ -31,6 +31,6 @@ params {
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perform_shortread_clipmerge = true
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perform_longread_clip = false
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perform_shortread_complexityfilter = true
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shortread_hostremoval = true
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perform_shortread_hostremoval = true
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shortread_hostremoval_reference = 'https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/homo_sapiens/genome/genome.fasta'
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}
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@ -81,7 +81,7 @@ params {
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save_runmerged_reads = false
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// Host Removal
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shortread_hostremoval = false
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perform_shortread_hostremoval = false
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shortread_hostremoval_reference = null
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shortread_hostremoval_index = null
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@ -359,7 +359,7 @@
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"perform_runmerging": {
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"type": "boolean"
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},
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"shortread_hostremoval": {
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"perform_shortread_hostremoval": {
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"type": "boolean"
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},
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"shortread_hostremoval_reference": {
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@ -22,11 +22,10 @@ if (params.databases) { ch_databases = file(params.databases) } else { exit 1, '
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if (params.shortread_clipmerge_mergepairs && params.run_malt ) log.warn "[nf-core/taxprofiler] warning: MALT does not accept uncollapsed paired-reads. Pairs will be profiled as separate files."
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if (params.shortread_clipmerge_excludeunmerged && !params.shortread_clipmerge_mergepairs) exit 1, "[nf-core/taxprofiler] error: cannot include unmerged reads when merging not turned on. Please specify --shortread_clipmerge_mergepairs"
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// TODO Add check if index but no reference exit 1
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if (params.shortread_hostremoval && !params.shortread_hostremoval_reference) { exit 1, "[nf-core/taxprofiler] error: --shortread_hostremoval requested but no --shortread_hostremoval_reference FASTA supplied. Check input." }
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if (params.perform_shortread_hostremoval && !params.shortread_hostremoval_reference) { exit 1, "[nf-core/taxprofiler] error: --shortread_hostremoval requested but no --shortread_hostremoval_reference FASTA supplied. Check input." }
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if (!params.shortread_hostremoval_reference && params.shortread_hostremoval_reference_index) { exit 1, "[nf-core/taxprofiler] error: --shortread_hostremoval_index provided but no --shortread_hostremoval_reference FASTA supplied. Check input." }
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if (params.shortread_hostremoval_reference ) { ch_reference = file(params.shortread_hostremoval_reference) } else { ch_reference = [] }
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if (params.shortread_hostremoval_reference ) { ch_reference = file(params.shortread_hostremoval_reference) }
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if (params.shortread_hostremoval_index ) { ch_reference_index = file(params.shortread_hostremoval_index ) } else { ch_reference_index = [] }
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/*
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@ -140,15 +139,13 @@ workflow TAXPROFILER {
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SUBWORKFLOW: HOST REMOVAL
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*/
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if ( params.shortread_hostremoval ) {
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if ( params.perform_shortread_hostremoval ) {
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ch_shortreads_hostremoved = SHORTREAD_HOSTREMOVAL ( ch_shortreads_filtered, ch_reference, ch_reference_index ).reads
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ch_versions = ch_versions.mix(SHORTREAD_HOSTREMOVAL.out.versions.first())
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} else {
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ch_shortreads_hostremoved = ch_shortreads_filtered
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}
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*/
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if ( params.perform_runmerging ) {
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ch_reads_for_cat_branch = ch_shortreads_hostremoved
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@ -225,7 +222,7 @@ workflow TAXPROFILER {
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ch_versions = ch_versions.mix( SHORTREAD_COMPLEXITYFILTERING.out.versions )
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}
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if (params.shortread_hostremoval) {
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if (params.perform_shortread_hostremoval) {
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ch_multiqc_files = ch_multiqc_files.mix(SHORTREAD_HOSTREMOVAL.out.mqc.collect{it[1]}.ifEmpty([]))
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ch_versions = ch_versions.mix(SHORTREAD_HOSTREMOVAL.out.versions)
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}
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