From b4b58591427023961452664ec5bcfad9a28ace37 Mon Sep 17 00:00:00 2001 From: "Thiseas C. Lamnidis" Date: Wed, 27 Jul 2022 14:28:37 +0200 Subject: [PATCH 1/3] Add path call in pileupcaller bams --- main.nf | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/main.nf b/main.nf index e1c7d7b1e..a289208c6 100644 --- a/main.nf +++ b/main.nf @@ -2502,7 +2502,7 @@ process genotyping_pileupcaller { params.run_genotyping && params.genotyping_tool == 'pileupcaller' input: - tuple samplename, libraryid, lane, seqtype, organism, strandedness, udg, bam, bai from ch_prepped_for_pileupcaller_double.mix(ch_prepped_for_pileupcaller_single) + tuple samplename, libraryid, lane, seqtype, organism, strandedness, udg, path(bam), path(bai) from ch_prepped_for_pileupcaller_double.mix(ch_prepped_for_pileupcaller_single) file fasta from ch_fasta_for_genotyping_pileupcaller.collect() file fai from ch_fai_for_pileupcaller.collect() file dict from ch_dict_for_pileupcaller.collect() From 637cd73c3a695290379212cfde1cd10b286b9398 Mon Sep 17 00:00:00 2001 From: "Thiseas C. Lamnidis" Date: Thu, 28 Jul 2022 18:21:57 +0200 Subject: [PATCH 2/3] fix pileupcaller path input. paths in bamtrim. --- main.nf | 32 +++++++++++++++++++++++++++++--- 1 file changed, 29 insertions(+), 3 deletions(-) diff --git a/main.nf b/main.nf index a289208c6..419cd7cc2 100644 --- a/main.nf +++ b/main.nf @@ -1787,7 +1787,7 @@ if (params.run_bam_filtering) { def seqtype = it[3] def organism = it[4] def strandedness = it[5] - def udg = it[6] + def udg = it[6] def stats = file(it[7]) def poststats = file("$projectDir/assets/nf-core_eager_dummy.txt") @@ -2229,7 +2229,7 @@ process bam_trim { tuple samplename, libraryid, lane, seqtype, organism, strandedness, udg, path(bam), path(bai) from ch_bamutils_decision.totrim output: - tuple samplename, libraryid, lane, seqtype, organism, strandedness, udg, file("*.trimmed.bam"), file("*.trimmed.bam.{bai,csi}") into ch_trimmed_from_bamutils + tuple samplename, libraryid, lane, seqtype, organism, strandedness, udg, path("*.trimmed.bam"), path("*.trimmed.bam.{bai,csi}") into ch_trimmed_from_bamutils script: def softclip = params.bamutils_softclip ? '-c' : '' @@ -2261,7 +2261,7 @@ ch_trimmed_formerge = ch_bamutils_decision.notrim def seqtype = it[3] def organism = it[4] def strandedness = it[5] - def udg = it[6] + def udg = it[6] def bam = it[7].flatten() def bai = it[8].flatten() @@ -2487,10 +2487,36 @@ ch_damagemanipulation_for_genotyping_pileupcaller // Create pileupcaller input tuples ch_input_for_genotyping_pileupcaller.singleStranded .groupTuple(by:[5]) + .map{ + def samplename = it[0] + def libraryid = it[1] + def lane = it[2] + def seqtype = it[3] + def organism = it[4] + def strandedness = it[5] + def udg = it[6] + def bam = it[7].flatten() + def bai = it[8].flatten() + + [samplename, libraryid, lane, seqtype, organism, strandedness, udg, bam, bai ] + } .set {ch_prepped_for_pileupcaller_single} ch_input_for_genotyping_pileupcaller.doubleStranded .groupTuple(by:[5]) + .map{ + def samplename = it[0] + def libraryid = it[1] + def lane = it[2] + def seqtype = it[3] + def organism = it[4] + def strandedness = it[5] + def udg = it[6] + def bam = it[7].flatten() + def bai = it[8].flatten() + + [samplename, libraryid, lane, seqtype, organism, strandedness, udg, bam, bai ] + } .set {ch_prepped_for_pileupcaller_double} process genotyping_pileupcaller { From 4f19b50770101dc3dbbc4f717fc2b3b89261e842 Mon Sep 17 00:00:00 2001 From: "Thiseas C. Lamnidis" Date: Thu, 28 Jul 2022 18:32:39 +0200 Subject: [PATCH 3/3] Update CHANGELOG.md --- CHANGELOG.md | 1 + 1 file changed, 1 insertion(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index 884bbefa1..e3d240390 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -19,6 +19,7 @@ and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0. - [#895](https://github.com/nf-core/eager/issues/895) Output documentation typo fix and added location of output docs in pipeline summary (♥ to @RodrigoBarquera for reporting) - [#897](https://github.com/nf-core/eager/issues/897) Fix pipeline crash if no Kraken2 results generated (♥ to @alexandregilardet for reporting) - [#899](https://github.com/nf-core/eager/issues/897) Fix pipeline crash for circulargenerator if reference file does not end in .fasta (♥ to @scarlhoff for reporting) +- Fix staging of input bams for genotyping_pileupcaller process. Downstream changes from changes introduced when fixing endorspy caching. ### `Dependencies`