From aa2d07c42ae4e451711a4147264782d567576e88 Mon Sep 17 00:00:00 2001 From: James Fellows Yates Date: Wed, 13 Apr 2022 14:19:19 +0200 Subject: [PATCH] Fix merge cockup --- .github/workflows/ci.yml | 2 +- conf/test.config | 2 +- nextflow.config | 2 +- nextflow_schema.json | 2 +- workflows/taxprofiler.nf | 13 +++++-------- 5 files changed, 9 insertions(+), 12 deletions(-) diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index b18e601..a1ece72 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -41,7 +41,7 @@ jobs: - "--shortread_complexityfilter_tool prinseq" - "--perform_runmerging" - "--perform_runmerging --shortread_clipmerge_mergepairs" - - "--shortread_complexityfilter false --shortread_hostremoval" + - "--shortread_complexityfilter false --perform_shortread_hostremoval" steps: - name: Check out pipeline code diff --git a/conf/test.config b/conf/test.config index 1d08d91..8f12312 100644 --- a/conf/test.config +++ b/conf/test.config @@ -31,6 +31,6 @@ params { perform_shortread_clipmerge = true perform_longread_clip = false perform_shortread_complexityfilter = true - shortread_hostremoval = true + perform_shortread_hostremoval = true shortread_hostremoval_reference = 'https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/homo_sapiens/genome/genome.fasta' } diff --git a/nextflow.config b/nextflow.config index 6b0a79d..94c5837 100644 --- a/nextflow.config +++ b/nextflow.config @@ -81,7 +81,7 @@ params { save_runmerged_reads = false // Host Removal - shortread_hostremoval = false + perform_shortread_hostremoval = false shortread_hostremoval_reference = null shortread_hostremoval_index = null diff --git a/nextflow_schema.json b/nextflow_schema.json index 07295e3..cf0edab 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -359,7 +359,7 @@ "perform_runmerging": { "type": "boolean" }, - "shortread_hostremoval": { + "perform_shortread_hostremoval": { "type": "boolean" }, "shortread_hostremoval_reference": { diff --git a/workflows/taxprofiler.nf b/workflows/taxprofiler.nf index 894a1e1..9fe8cc8 100644 --- a/workflows/taxprofiler.nf +++ b/workflows/taxprofiler.nf @@ -22,11 +22,10 @@ if (params.databases) { ch_databases = file(params.databases) } else { exit 1, ' 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." 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" -// TODO Add check if index but no reference exit 1 -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." } +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." } 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." } -if (params.shortread_hostremoval_reference ) { ch_reference = file(params.shortread_hostremoval_reference) } else { ch_reference = [] } +if (params.shortread_hostremoval_reference ) { ch_reference = file(params.shortread_hostremoval_reference) } if (params.shortread_hostremoval_index ) { ch_reference_index = file(params.shortread_hostremoval_index ) } else { ch_reference_index = [] } /* @@ -140,15 +139,13 @@ workflow TAXPROFILER { SUBWORKFLOW: HOST REMOVAL */ - if ( params.shortread_hostremoval ) { + if ( params.perform_shortread_hostremoval ) { ch_shortreads_hostremoved = SHORTREAD_HOSTREMOVAL ( ch_shortreads_filtered, ch_reference, ch_reference_index ).reads ch_versions = ch_versions.mix(SHORTREAD_HOSTREMOVAL.out.versions.first()) } else { ch_shortreads_hostremoved = ch_shortreads_filtered } - */ - if ( params.perform_runmerging ) { ch_reads_for_cat_branch = ch_shortreads_hostremoved @@ -225,11 +222,11 @@ workflow TAXPROFILER { ch_versions = ch_versions.mix( SHORTREAD_COMPLEXITYFILTERING.out.versions ) } - if (params.shortread_hostremoval) { + if (params.perform_shortread_hostremoval) { ch_multiqc_files = ch_multiqc_files.mix(SHORTREAD_HOSTREMOVAL.out.mqc.collect{it[1]}.ifEmpty([])) ch_versions = ch_versions.mix(SHORTREAD_HOSTREMOVAL.out.versions) } - + if (params.perform_runmerging){ ch_versions = ch_versions.mix(CAT_FASTQ.out.versions) }