From 583a91ec13c0e808acde4d828f8bd31aa03cbca2 Mon Sep 17 00:00:00 2001 From: WackerO Date: Tue, 28 Jun 2022 09:01:11 +0200 Subject: [PATCH 01/24] Started to work on the umi stuff --- .github/workflows/ci.yml | 1 + tests/test_umi.yml | 97 ++++++++++++++++++++-------------------- 2 files changed, 49 insertions(+), 49 deletions(-) diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index c08a2348f..b4eee053a 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -58,6 +58,7 @@ jobs: - "tiddit" - "trimming" - "tumor_normal_pair" + - "umi" - "variantcalling_channel" steps: diff --git a/tests/test_umi.yml b/tests/test_umi.yml index 73206f622..a107cd85a 100644 --- a/tests/test_umi.yml +++ b/tests/test_umi.yml @@ -1,7 +1,7 @@ - name: Run UMI Quiaseq test - command: nextflow run main.nf -profile test,umi_quiaseq,docker + command: nextflow run main.nf -profile test,umi,docker tags: - - umi_quiaseq + # - umi_quiaseq - umi files: - path: results/fastqtobam/1234N-SRR7545951_umi_converted.bam @@ -44,50 +44,49 @@ md5sum: 709872fc2910431b1e8b7074bfe38c67 - path: results/samtools/1234N-SRR7545951.unmapped_singleton.fq.gz md5sum: 709872fc2910431b1e8b7074bfe38c67 - -- name: Run UMI TSO test - command: nextflow run main.nf -profile test,umi_tso,docker - tags: - - umi_tso - - umi - files: - - path: results/fastqtobam/1234N-HT1080_umi_converted.bam - md5sum: aaf4b9a80f4b780d93820df8b536c531 - - path: results/bam2fastq/1234N-HT1080_interleaved.fq.gz - md5sum: b037fe8e180e805226485d9bea4a69e5 - - path: results/callumiconsensus/1234N-HT1080_umi-consensus.bam - md5sum: 807bfe6a82eabdf29aaf8bc6a832f0cd - - path: results/cat/1234N-HT1080_1.merged.fastq.gz - md5sum: c8f0d1308df4c46c0716ccfe76f78fb4 - - path: results/cat/1234N-HT1080_2.merged.fastq.gz - md5sum: 1b42767b2d5dbc99e447c41d6d2418ab - - path: results/groupreadsbyumi/1234N-HT1080_umi-grouped.bam - md5sum: c9c76b410ba208fea76c79cecfb45241 - - path: results/groupreadsbyumi/1234N-HT1080_umi_histogram.txt - md5sum: 3dec92ae49763c10c0b2e79827d25ffb - - path: results/samblaster/1234N-HT1080_unsorted_tagged.bam - md5sum: 628bd970fa00615fb9f841bad7c8f597 - - path: results/samtools/1234N-HT1080.map_map.bam - md5sum: 2689e640c3ededf70228a44ee4b1de48 - - path: results/samtools/1234N-HT1080.map_unmap.bam - md5sum: 37300fea69f7c400220a03ca5854d04b - - path: results/samtools/1234N-HT1080.mapped_1.fq.gz - md5sum: 709872fc2910431b1e8b7074bfe38c67 - - path: results/samtools/1234N-HT1080.mapped_2.fq.gz - md5sum: 709872fc2910431b1e8b7074bfe38c67 - - path: results/samtools/1234N-HT1080.mapped_other.fq.gz - md5sum: 709872fc2910431b1e8b7074bfe38c67 - - path: results/samtools/1234N-HT1080.mapped_singleton.fq.gz - md5sum: 709872fc2910431b1e8b7074bfe38c67 - - path: results/samtools/1234N-HT1080.unmap_map.bam - md5sum: 6267d0ed8274e1fa7aad8d1e71d98696 - - path: results/samtools/1234N-HT1080.unmap_unmap.bam - md5sum: 32ed07aa23900f5722e5983a646a5ac2 - - path: results/samtools/1234N-HT1080.unmapped_1.fq.gz - md5sum: d9a7a279c05563a37d9a5a6938be68fb - - path: results/samtools/1234N-HT1080.unmapped_2.fq.gz - md5sum: afe191dcd48360f96bdb583fa60ff400 - - path: results/samtools/1234N-HT1080.unmapped_other.fq.gz - md5sum: 709872fc2910431b1e8b7074bfe38c67 - - path: results/samtools/1234N-HT1080.unmapped_singleton.fq.gz - md5sum: 709872fc2910431b1e8b7074bfe38c67 +# - name: Run UMI TSO test +# command: nextflow run main.nf -profile test,umi_tso,docker +# tags: +# - umi_tso +# - umi +# files: +# - path: results/fastqtobam/1234N-HT1080_umi_converted.bam +# md5sum: aaf4b9a80f4b780d93820df8b536c531 +# - path: results/bam2fastq/1234N-HT1080_interleaved.fq.gz +# md5sum: b037fe8e180e805226485d9bea4a69e5 +# - path: results/callumiconsensus/1234N-HT1080_umi-consensus.bam +# md5sum: 807bfe6a82eabdf29aaf8bc6a832f0cd +# - path: results/cat/1234N-HT1080_1.merged.fastq.gz +# md5sum: c8f0d1308df4c46c0716ccfe76f78fb4 +# - path: results/cat/1234N-HT1080_2.merged.fastq.gz +# md5sum: 1b42767b2d5dbc99e447c41d6d2418ab +# - path: results/groupreadsbyumi/1234N-HT1080_umi-grouped.bam +# md5sum: c9c76b410ba208fea76c79cecfb45241 +# - path: results/groupreadsbyumi/1234N-HT1080_umi_histogram.txt +# md5sum: 3dec92ae49763c10c0b2e79827d25ffb +# - path: results/samblaster/1234N-HT1080_unsorted_tagged.bam +# md5sum: 628bd970fa00615fb9f841bad7c8f597 +# - path: results/samtools/1234N-HT1080.map_map.bam +# md5sum: 2689e640c3ededf70228a44ee4b1de48 +# - path: results/samtools/1234N-HT1080.map_unmap.bam +# md5sum: 37300fea69f7c400220a03ca5854d04b +# - path: results/samtools/1234N-HT1080.mapped_1.fq.gz +# md5sum: 709872fc2910431b1e8b7074bfe38c67 +# - path: results/samtools/1234N-HT1080.mapped_2.fq.gz +# md5sum: 709872fc2910431b1e8b7074bfe38c67 +# - path: results/samtools/1234N-HT1080.mapped_other.fq.gz +# md5sum: 709872fc2910431b1e8b7074bfe38c67 +# - path: results/samtools/1234N-HT1080.mapped_singleton.fq.gz +# md5sum: 709872fc2910431b1e8b7074bfe38c67 +# - path: results/samtools/1234N-HT1080.unmap_map.bam +# md5sum: 6267d0ed8274e1fa7aad8d1e71d98696 +# - path: results/samtools/1234N-HT1080.unmap_unmap.bam +# md5sum: 32ed07aa23900f5722e5983a646a5ac2 +# - path: results/samtools/1234N-HT1080.unmapped_1.fq.gz +# md5sum: d9a7a279c05563a37d9a5a6938be68fb +# - path: results/samtools/1234N-HT1080.unmapped_2.fq.gz +# md5sum: afe191dcd48360f96bdb583fa60ff400 +# - path: results/samtools/1234N-HT1080.unmapped_other.fq.gz +# md5sum: 709872fc2910431b1e8b7074bfe38c67 +# - path: results/samtools/1234N-HT1080.unmapped_singleton.fq.gz +# md5sum: 709872fc2910431b1e8b7074bfe38c67 From e7da19915653ef8d0fe0a6cf36dada192802a5c0 Mon Sep 17 00:00:00 2001 From: WackerO Date: Thu, 30 Jun 2022 08:45:29 +0200 Subject: [PATCH 02/24] Fixed bug in modules.config --- conf/modules.config | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/conf/modules.config b/conf/modules.config index 939f27168..f545f30f0 100644 --- a/conf/modules.config +++ b/conf/modules.config @@ -224,7 +224,7 @@ process { withName: 'BAM2FASTQ' { ext.args = '-T RX' - ext.when = { umi_read_structure } + ext.when = { params.umi_read_structure } } withName: 'CALLUMICONSENSUS' { From a9889a1a17e0f3a3f3135d2e0e8261af56ffb7b2 Mon Sep 17 00:00:00 2001 From: WackerO Date: Fri, 1 Jul 2022 12:28:49 +0200 Subject: [PATCH 03/24] Code seems to run now, but had to comment ou the meta id tag from samtools_view --- conf/modules.config | 16 ++++++++++++---- modules/nf-core/modules/samtools/view/main.nf | 4 ++-- 2 files changed, 14 insertions(+), 6 deletions(-) diff --git a/conf/modules.config b/conf/modules.config index f545f30f0..a24e03812 100644 --- a/conf/modules.config +++ b/conf/modules.config @@ -238,6 +238,12 @@ process { ext.args2 = '-bS' ext.prefix = {"${meta.id}.umi_unsorted"} } +// TODO: args1? args2 should be good + withName: ".*DRAGMAP_ALIGN" { + ext.args = { "-p -C -M -R ${meta.read_group}" } + ext.args2 = '-bS' + ext.prefix = {"${meta.id}.umi_unsorted"} + } } withName: 'SAMBLASTER' { @@ -247,17 +253,19 @@ process { // MAPPING if (params.step == 'mapping') { - withName: ".*GATK4_MAPPING:BWAMEM1_MEM" { + withName: ".*BWAMEM1_MEM" { ext.when = { params.aligner == "bwa-mem" } } - withName: ".*GATK4_MAPPING:BWAMEM2_MEM" { + withName: ".*BWAMEM2_MEM" { ext.when = { params.aligner == "bwa-mem2" } } - withName: ".*GATK4_MAPPING:DRAGMAP_ALIGN" { + withName: ".*DRAGMAP_ALIGN" { ext.when = { params.aligner == "dragmap" } - ext.args = { "--RGSM ${meta.read_group}" } + } + withName: ".*GATK4_MAPPING:DRAGMAP_ALIGN" { + ext.args = { "--RGSM ${meta.read_group}" } } withName: "NFCORE_SAREK:SAREK:GATK4_MAPPING:(BWAMEM.*_MEM|DRAGMAP_ALIGN)" { diff --git a/modules/nf-core/modules/samtools/view/main.nf b/modules/nf-core/modules/samtools/view/main.nf index 55194e887..62b2836c6 100644 --- a/modules/nf-core/modules/samtools/view/main.nf +++ b/modules/nf-core/modules/samtools/view/main.nf @@ -1,5 +1,5 @@ process SAMTOOLS_VIEW { - tag "$meta.id" + // tag "$meta.id" // This causes: java.lang.NullPointerException: Cannot get property 'id' on null object. -- Check script '/home/owacker/git/sarek/./workflows/../subworkflows/nf-core/../../modules/nf-core/modules/samtools/view/main.nf' at line: 2 or see '.nextflow.log' file for more details label 'process_medium' conda (params.enable_conda ? "bioconda::samtools=1.15.1" : null) @@ -8,7 +8,7 @@ process SAMTOOLS_VIEW { 'quay.io/biocontainers/samtools:1.15.1--h1170115_0' }" input: - tuple val(meta), path(input), path(index) + tuple val(meta), path(input), val(index) //path(index) causes Not a valid path value type: org.codehaus.groovy.runtime.NullObject (null) path fasta output: From 48502f94bdc8fc5f98715ddb9f949a65916b4413 Mon Sep 17 00:00:00 2001 From: WackerO Date: Fri, 1 Jul 2022 14:52:46 +0200 Subject: [PATCH 04/24] Reenabled meta.id, fixed DRAGMAP args --- conf/modules.config | 2 +- modules/nf-core/modules/samtools/view/main.nf | 3 ++- 2 files changed, 3 insertions(+), 2 deletions(-) diff --git a/conf/modules.config b/conf/modules.config index a24e03812..9826ce432 100644 --- a/conf/modules.config +++ b/conf/modules.config @@ -240,7 +240,7 @@ process { } // TODO: args1? args2 should be good withName: ".*DRAGMAP_ALIGN" { - ext.args = { "-p -C -M -R ${meta.read_group}" } + ext.args = { "--RGSM ${meta.read_group}" } ext.args2 = '-bS' ext.prefix = {"${meta.id}.umi_unsorted"} } diff --git a/modules/nf-core/modules/samtools/view/main.nf b/modules/nf-core/modules/samtools/view/main.nf index 62b2836c6..63a045e68 100644 --- a/modules/nf-core/modules/samtools/view/main.nf +++ b/modules/nf-core/modules/samtools/view/main.nf @@ -1,5 +1,5 @@ process SAMTOOLS_VIEW { - // tag "$meta.id" // This causes: java.lang.NullPointerException: Cannot get property 'id' on null object. -- Check script '/home/owacker/git/sarek/./workflows/../subworkflows/nf-core/../../modules/nf-core/modules/samtools/view/main.nf' at line: 2 or see '.nextflow.log' file for more details + tag "$meta.id" label 'process_medium' conda (params.enable_conda ? "bioconda::samtools=1.15.1" : null) @@ -27,6 +27,7 @@ process SAMTOOLS_VIEW { def file_type = input.getExtension() if ("$input" == "${prefix}.${file_type}") error "Input and output names are the same, use \"task.ext.prefix\" to disambiguate!" """ + echo $meta > /home/owacker/git/sarek/meta samtools \\ view \\ --threads ${task.cpus-1} \\ From 2563e1bb7ed5631036717f73c18f973862bbca7e Mon Sep 17 00:00:00 2001 From: WackerO Date: Fri, 1 Jul 2022 15:33:50 +0200 Subject: [PATCH 05/24] Bugfixing --- modules/nf-core/modules/samtools/view/main.nf | 4 ++-- subworkflows/nf-core/alignment_to_fastq.nf | 5 +++++ 2 files changed, 7 insertions(+), 2 deletions(-) diff --git a/modules/nf-core/modules/samtools/view/main.nf b/modules/nf-core/modules/samtools/view/main.nf index 63a045e68..647d1a8ab 100644 --- a/modules/nf-core/modules/samtools/view/main.nf +++ b/modules/nf-core/modules/samtools/view/main.nf @@ -8,7 +8,7 @@ process SAMTOOLS_VIEW { 'quay.io/biocontainers/samtools:1.15.1--h1170115_0' }" input: - tuple val(meta), path(input), val(index) //path(index) causes Not a valid path value type: org.codehaus.groovy.runtime.NullObject (null) + tuple val(meta), path(input), path(index) //path(index) causes Not a valid path value type: org.codehaus.groovy.runtime.NullObject (null) path fasta output: @@ -27,7 +27,7 @@ process SAMTOOLS_VIEW { def file_type = input.getExtension() if ("$input" == "${prefix}.${file_type}") error "Input and output names are the same, use \"task.ext.prefix\" to disambiguate!" """ - echo $meta > /home/owacker/git/sarek/meta + echo $index > /home/owacker/git/sarek/index samtools \\ view \\ --threads ${task.cpus-1} \\ diff --git a/subworkflows/nf-core/alignment_to_fastq.nf b/subworkflows/nf-core/alignment_to_fastq.nf index ec855d6ca..bd03a385b 100644 --- a/subworkflows/nf-core/alignment_to_fastq.nf +++ b/subworkflows/nf-core/alignment_to_fastq.nf @@ -20,6 +20,11 @@ workflow ALIGNMENT_TO_FASTQ { ch_versions = Channel.empty() // Index File if not PROVIDED -> this also requires updates to samtools view possibly URGH + if (input.collect{it[2]}.ifEmpty()) { + input = input.mix([]) + } + // input = input.mix(input.collect{it[2]}.ifEmpty([])) + input.dump(tag:"inputn") // MAP - MAP SAMTOOLS_VIEW_MAP_MAP(input, fasta) From 037e063912bfb8164db338c45bc39e5a04cfcefb Mon Sep 17 00:00:00 2001 From: WackerO Date: Mon, 4 Jul 2022 14:53:20 +0200 Subject: [PATCH 06/24] Finally, it works --- conf/modules.config | 5 +---- subworkflows/nf-core/alignment_to_fastq.nf | 5 ----- workflows/sarek.nf | 4 +++- 3 files changed, 4 insertions(+), 10 deletions(-) diff --git a/conf/modules.config b/conf/modules.config index 9826ce432..614dcb746 100644 --- a/conf/modules.config +++ b/conf/modules.config @@ -238,7 +238,7 @@ process { ext.args2 = '-bS' ext.prefix = {"${meta.id}.umi_unsorted"} } -// TODO: args1? args2 should be good + withName: ".*DRAGMAP_ALIGN" { ext.args = { "--RGSM ${meta.read_group}" } ext.args2 = '-bS' @@ -262,9 +262,6 @@ process { withName: ".*DRAGMAP_ALIGN" { ext.when = { params.aligner == "dragmap" } - } - - withName: ".*GATK4_MAPPING:DRAGMAP_ALIGN" { ext.args = { "--RGSM ${meta.read_group}" } } diff --git a/subworkflows/nf-core/alignment_to_fastq.nf b/subworkflows/nf-core/alignment_to_fastq.nf index bd03a385b..ec855d6ca 100644 --- a/subworkflows/nf-core/alignment_to_fastq.nf +++ b/subworkflows/nf-core/alignment_to_fastq.nf @@ -20,11 +20,6 @@ workflow ALIGNMENT_TO_FASTQ { ch_versions = Channel.empty() // Index File if not PROVIDED -> this also requires updates to samtools view possibly URGH - if (input.collect{it[2]}.ifEmpty()) { - input = input.mix([]) - } - // input = input.mix(input.collect{it[2]}.ifEmpty([])) - input.dump(tag:"inputn") // MAP - MAP SAMTOOLS_VIEW_MAP_MAP(input, fasta) diff --git a/workflows/sarek.nf b/workflows/sarek.nf index 1802a8930..b1aec47fc 100644 --- a/workflows/sarek.nf +++ b/workflows/sarek.nf @@ -347,8 +347,10 @@ workflow SAREK { umi_read_structure, params.group_by_umi_strategy) + bamtofastq = CREATE_UMI_CONSENSUS.out.consensusbam.map{meta, bam -> [meta,bam,[]]} + // convert back to fastq for further preprocessing - ALIGNMENT_TO_FASTQ_UMI(CREATE_UMI_CONSENSUS.out.consensusbam, []) + ALIGNMENT_TO_FASTQ_UMI(bamtofastq, []) ch_reads_fastp = ALIGNMENT_TO_FASTQ_UMI.out.reads From 2d59ccbca256e54d54b62fe1ac2e3a6be4f6e54a Mon Sep 17 00:00:00 2001 From: WackerO Date: Mon, 4 Jul 2022 14:55:44 +0200 Subject: [PATCH 07/24] Removed changes to module --- modules/nf-core/modules/samtools/view/main.nf | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/modules/nf-core/modules/samtools/view/main.nf b/modules/nf-core/modules/samtools/view/main.nf index 647d1a8ab..55194e887 100644 --- a/modules/nf-core/modules/samtools/view/main.nf +++ b/modules/nf-core/modules/samtools/view/main.nf @@ -8,7 +8,7 @@ process SAMTOOLS_VIEW { 'quay.io/biocontainers/samtools:1.15.1--h1170115_0' }" input: - tuple val(meta), path(input), path(index) //path(index) causes Not a valid path value type: org.codehaus.groovy.runtime.NullObject (null) + tuple val(meta), path(input), path(index) path fasta output: @@ -27,7 +27,6 @@ process SAMTOOLS_VIEW { def file_type = input.getExtension() if ("$input" == "${prefix}.${file_type}") error "Input and output names are the same, use \"task.ext.prefix\" to disambiguate!" """ - echo $index > /home/owacker/git/sarek/index samtools \\ view \\ --threads ${task.cpus-1} \\ From 6c02d861ba90f95bb3bb5cc1690194ced9e79dca Mon Sep 17 00:00:00 2001 From: WackerO Date: Mon, 4 Jul 2022 15:08:04 +0200 Subject: [PATCH 08/24] Updated test_umi.yaml --- tests/test_umi.yml | 84 ++++++++++++++++++++++++---------------------- 1 file changed, 43 insertions(+), 41 deletions(-) diff --git a/tests/test_umi.yml b/tests/test_umi.yml index a107cd85a..1381eefe2 100644 --- a/tests/test_umi.yml +++ b/tests/test_umi.yml @@ -1,49 +1,51 @@ - name: Run UMI Quiaseq test command: nextflow run main.nf -profile test,umi,docker tags: - # - umi_quiaseq - umi files: - - path: results/fastqtobam/1234N-SRR7545951_umi_converted.bam - md5sum: 1473c98be04aff10f80e2946b111c459 - - path: results/bam2fastq/1234N-SRR7545951_interleaved.fq.gz - md5sum: 17c0cb479e8117016e9f0d835d4df50f - - path: results/callumiconsensus/1234N-SRR7545951_umi-consensus.bam - md5sum: 3be1adf27d473de12cab895423a5f3ed - - path: results/cat/1234N-SRR7545951_1.merged.fastq.gz - md5sum: c1ed636a11b3031c72f3d4c84a7a0949 - - path: results/cat/1234N-SRR7545951_2.merged.fastq.gz - md5sum: 0bbef631b8de80f2abe441de713cbb49 - - path: results/groupreadsbyumi/1234N-SRR7545951_umi-grouped.bam - md5sum: e3bb348056513c46d7a60df4d7a8cc97 - - path: results/groupreadsbyumi/1234N-SRR7545951_umi_histogram.txt - md5sum: 2e1e9a774135675a3d1a3b0a88d29c53 - - path: results/samblaster/1234N-SRR7545951_unsorted_tagged.bam - md5sum: daa51939768c256315ce700dabaccad6 - - path: results/samtools/1234N-SRR7545951.map_map.bam - md5sum: 741de784bb83815fab8b2d23d88c74d7 - - path: results/samtools/1234N-SRR7545951.map_unmap.bam - md5sum: 31627b2d163da372584bb78258c046e5 - - path: results/samtools/1234N-SRR7545951.mapped_1.fq.gz - md5sum: 709872fc2910431b1e8b7074bfe38c67 - - path: results/samtools/1234N-SRR7545951.mapped_2.fq.gz - md5sum: 709872fc2910431b1e8b7074bfe38c67 - - path: results/samtools/1234N-SRR7545951.mapped_other.fq.gz - md5sum: 709872fc2910431b1e8b7074bfe38c67 - - path: results/samtools/1234N-SRR7545951.mapped_singleton.fq.gz - md5sum: 709872fc2910431b1e8b7074bfe38c67 - - path: results/samtools/1234N-SRR7545951.unmap_map.bam - md5sum: 42fb9dbb5a157c194c77b1de5b4f3b39 - - path: results/samtools/1234N-SRR7545951.unmap_unmap.bam - md5sum: 2075e48cd007f29c8f6fdc518e587e27 - - path: results/samtools/1234N-SRR7545951.unmapped_1.fq.gz - md5sum: 1f95ae5bbc7345372005b6673884f853 - - path: results/samtools/1234N-SRR7545951.unmapped_2.fq.gz - md5sum: 9902e27a99c2a628d184cb91759d6ff7 - - path: results/samtools/1234N-SRR7545951.unmapped_other.fq.gz - md5sum: 709872fc2910431b1e8b7074bfe38c67 - - path: results/samtools/1234N-SRR7545951.unmapped_singleton.fq.gz - md5sum: 709872fc2910431b1e8b7074bfe38c67 + - path: results/fastqtobam/test-test_L1_umi_converted.bam + md5sum: ce67e3b1f46302127cd07cb3c2d2e739 + - path: results/bam2fastq/test-test_L1_interleaved.fq.gz + md5sum: 7a57a8ab53dd1d799cca67a85c47ccd9 + - path: results/callumiconsensus/test-test_L1_umi-consensus.bam + md5sum: 8d52eadfa1919eb01c795c29b3f3a2f3 + - path: results/cat/test-test_L1_1.merged.fastq.gz + md5sum: 56689dad7749b989c003a18f83445cae + - path: results/cat/test-test_L1_2.merged.fastq.gz + md5sum: bede34e291fd70f6e5fb5ad576617272 + - path: results/groupreadsbyumi/test-test_L1_umi-grouped.bam + md5sum: 14b02a0279f715586d3671d184a83d6b + - path: results/groupreadsbyumi/test-test_L1_umi_histogram.txt + md5sum: d17fd167b2a765d46e4b01bf08ece01b + - path: results/samblaster/test-test_L1_unsorted_tagged + md5sum: ba3425e6722d6f6cc36e6dec42b19207 + - path: results/samtools/test-test_L1.map_map.bam + md5sum: f29dc564311e592941bdf152dd722b4f + - path: results/samtools/test-test_L1.map_unmap.bam + md5sum: 6518cea4d9c0bdb17af66932b68e0ad9 + - path: results/samtools/test-test_L1.bam + md5sum: 41f807e2f3be27a6054a1b7ab4a438b2 + # TODO: The following files are not produced anymore +# - path: results/samtools/test-test_L1.mapped_1.fq.gz +# md5sum: 709872fc2910431b1e8b7074bfe38c67 +# - path: results/samtools/test-test_L1.mapped_2.fq.gz +# md5sum: 709872fc2910431b1e8b7074bfe38c67 +# - path: results/samtools/test-test_L1.mapped_other.fq.gz +# md5sum: 709872fc2910431b1e8b7074bfe38c67 +# - path: results/samtools/test-test_L1.mapped_singleton.fq.gz +# md5sum: 709872fc2910431b1e8b7074bfe38c67 +# - path: results/samtools/test-test_L1.unmap_map.bam +# md5sum: 9479aabdbbfdc8f5c79f8daa1011e9fb +# - path: results/samtools/test-test_L1.unmap_unmap.bam +# md5sum: 68bcb7f856c1933b81c4733da2fcd8df +# - path: results/samtools/test-test_L1.unmapped_1.fq.gz +# md5sum: 1f95ae5bbc7345372005b6673884f853 +# - path: results/samtools/test-test_L1.unmapped_2.fq.gz +# md5sum: 9902e27a99c2a628d184cb91759d6ff7 +# - path: results/samtools/test-test_L1.unmapped_other.fq.gz +# md5sum: 709872fc2910431b1e8b7074bfe38c67 +# - path: results/samtools/test-test_L1.unmapped_singleton.fq.gz +# md5sum: 709872fc2910431b1e8b7074bfe38c67 # - name: Run UMI TSO test # command: nextflow run main.nf -profile test,umi_tso,docker # tags: From 99da99de53f9e4ff3dc5cb33b25d19a1e31eb0f4 Mon Sep 17 00:00:00 2001 From: WackerO Date: Mon, 11 Jul 2022 14:42:44 +0200 Subject: [PATCH 09/24] This newer container version should make fgbio work --- modules/nf-core/modules/fgbio/fastqtobam/main.nf | 4 ++-- tests/test_umi.yml | 2 +- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/modules/nf-core/modules/fgbio/fastqtobam/main.nf b/modules/nf-core/modules/fgbio/fastqtobam/main.nf index 329aff331..df6796abb 100644 --- a/modules/nf-core/modules/fgbio/fastqtobam/main.nf +++ b/modules/nf-core/modules/fgbio/fastqtobam/main.nf @@ -5,7 +5,7 @@ process FGBIO_FASTQTOBAM { conda (params.enable_conda ? "bioconda::fgbio=1.4.0" : null) container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/fgbio:1.4.0--hdfd78af_0' : - 'quay.io/biocontainers/fgbio:1.4.0--hdfd78af_0' }" + 'quay.io/biocontainers/fgbio:2.0.2--hdfd78af_0' }" input: tuple val(meta), path(reads) @@ -23,7 +23,7 @@ process FGBIO_FASTQTOBAM { def prefix = task.ext.prefix ?: "${meta.id}" """ mkdir tmp - + echo "fgbio --tmp-dir=${PWD}/tmp FastqToBam -i $reads -o ${prefix}_umi_converted.bam --read-structures $read_structure --sample $meta.id --library $meta.id $args" > /home/owacker/git/sarek/müde fgbio \\ --tmp-dir=${PWD}/tmp \\ FastqToBam \\ diff --git a/tests/test_umi.yml b/tests/test_umi.yml index 1381eefe2..3d27b0654 100644 --- a/tests/test_umi.yml +++ b/tests/test_umi.yml @@ -1,4 +1,4 @@ -- name: Run UMI Quiaseq test +- name: Run UMI test command: nextflow run main.nf -profile test,umi,docker tags: - umi From 2fffc694265727debfa9393682c3ac968188a388 Mon Sep 17 00:00:00 2001 From: WackerO Date: Mon, 11 Jul 2022 16:16:20 +0200 Subject: [PATCH 10/24] Restored fgbio module, updated test_umi.yml --- modules/nf-core/modules/fgbio/fastqtobam/main.nf | 4 ++-- tests/test_umi.yml | 8 ++++---- 2 files changed, 6 insertions(+), 6 deletions(-) diff --git a/modules/nf-core/modules/fgbio/fastqtobam/main.nf b/modules/nf-core/modules/fgbio/fastqtobam/main.nf index df6796abb..329aff331 100644 --- a/modules/nf-core/modules/fgbio/fastqtobam/main.nf +++ b/modules/nf-core/modules/fgbio/fastqtobam/main.nf @@ -5,7 +5,7 @@ process FGBIO_FASTQTOBAM { conda (params.enable_conda ? "bioconda::fgbio=1.4.0" : null) container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/fgbio:1.4.0--hdfd78af_0' : - 'quay.io/biocontainers/fgbio:2.0.2--hdfd78af_0' }" + 'quay.io/biocontainers/fgbio:1.4.0--hdfd78af_0' }" input: tuple val(meta), path(reads) @@ -23,7 +23,7 @@ process FGBIO_FASTQTOBAM { def prefix = task.ext.prefix ?: "${meta.id}" """ mkdir tmp - echo "fgbio --tmp-dir=${PWD}/tmp FastqToBam -i $reads -o ${prefix}_umi_converted.bam --read-structures $read_structure --sample $meta.id --library $meta.id $args" > /home/owacker/git/sarek/müde + fgbio \\ --tmp-dir=${PWD}/tmp \\ FastqToBam \\ diff --git a/tests/test_umi.yml b/tests/test_umi.yml index 3d27b0654..5d14a3424 100644 --- a/tests/test_umi.yml +++ b/tests/test_umi.yml @@ -25,6 +25,10 @@ md5sum: 6518cea4d9c0bdb17af66932b68e0ad9 - path: results/samtools/test-test_L1.bam md5sum: 41f807e2f3be27a6054a1b7ab4a438b2 + - path: results/samtools/test-test_L1.unmap_map.bam + md5sum: 9479aabdbbfdc8f5c79f8daa1011e9fb + - path: results/samtools/test-test_L1.unmap_unmap.bam + md5sum: 68bcb7f856c1933b81c4733da2fcd8df # TODO: The following files are not produced anymore # - path: results/samtools/test-test_L1.mapped_1.fq.gz # md5sum: 709872fc2910431b1e8b7074bfe38c67 @@ -34,10 +38,6 @@ # md5sum: 709872fc2910431b1e8b7074bfe38c67 # - path: results/samtools/test-test_L1.mapped_singleton.fq.gz # md5sum: 709872fc2910431b1e8b7074bfe38c67 -# - path: results/samtools/test-test_L1.unmap_map.bam -# md5sum: 9479aabdbbfdc8f5c79f8daa1011e9fb -# - path: results/samtools/test-test_L1.unmap_unmap.bam -# md5sum: 68bcb7f856c1933b81c4733da2fcd8df # - path: results/samtools/test-test_L1.unmapped_1.fq.gz # md5sum: 1f95ae5bbc7345372005b6673884f853 # - path: results/samtools/test-test_L1.unmapped_2.fq.gz From 406a919d9eeff36cf93d088cf79163ba3be6920f Mon Sep 17 00:00:00 2001 From: WackerO Date: Tue, 12 Jul 2022 08:39:38 +0200 Subject: [PATCH 11/24] Updated fgbio --- modules.json | 2 +- modules/nf-core/modules/fgbio/fastqtobam/main.nf | 6 +++--- 2 files changed, 4 insertions(+), 4 deletions(-) diff --git a/modules.json b/modules.json index 9558720b3..cc5c5ae15 100644 --- a/modules.json +++ b/modules.json @@ -79,7 +79,7 @@ "git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d" }, "fgbio/fastqtobam": { - "git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d" + "git_sha": "b2a8464e3ee06397e85f697e9b792cfafe1fad85" }, "fgbio/groupreadsbyumi": { "git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d" diff --git a/modules/nf-core/modules/fgbio/fastqtobam/main.nf b/modules/nf-core/modules/fgbio/fastqtobam/main.nf index 329aff331..51b6b72c4 100644 --- a/modules/nf-core/modules/fgbio/fastqtobam/main.nf +++ b/modules/nf-core/modules/fgbio/fastqtobam/main.nf @@ -2,10 +2,10 @@ process FGBIO_FASTQTOBAM { tag "$meta.id" label 'process_low' - conda (params.enable_conda ? "bioconda::fgbio=1.4.0" : null) + conda (params.enable_conda ? "bioconda::fgbio=2.0.2" : null) container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/fgbio:1.4.0--hdfd78af_0' : - 'quay.io/biocontainers/fgbio:1.4.0--hdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/fgbio:2.0.2--hdfd78af_0' : + 'quay.io/biocontainers/fgbio:2.0.2--hdfd78af_0' }" input: tuple val(meta), path(reads) From 65a625bf016059ca9b9c0287d9973dd7326e131a Mon Sep 17 00:00:00 2001 From: WackerO Date: Tue, 12 Jul 2022 11:26:19 +0200 Subject: [PATCH 12/24] Bug-fixing --- modules/nf-core/modules/fgbio/groupreadsbyumi/main.nf | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/modules/nf-core/modules/fgbio/groupreadsbyumi/main.nf b/modules/nf-core/modules/fgbio/groupreadsbyumi/main.nf index 31250d23c..7c09ab7c4 100644 --- a/modules/nf-core/modules/fgbio/groupreadsbyumi/main.nf +++ b/modules/nf-core/modules/fgbio/groupreadsbyumi/main.nf @@ -2,10 +2,10 @@ process FGBIO_GROUPREADSBYUMI { tag "$meta.id" label 'process_low' - conda (params.enable_conda ? "bioconda::fgbio=1.4.0" : null) + conda (params.enable_conda ? "bioconda::fgbio=2.0.2" : null) container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/fgbio:1.4.0--hdfd78af_0' : - 'quay.io/biocontainers/fgbio:1.4.0--hdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/fgbio:2.0.2--hdfd78af_0' : + 'quay.io/biocontainers/fgbio:2.0.2--hdfd78af_0' }" input: tuple val(meta), path(taggedbam) From e289b6e202c86c2e9a82d0473cf6bed257f6a717 Mon Sep 17 00:00:00 2001 From: WackerO Date: Wed, 13 Jul 2022 12:37:43 +0200 Subject: [PATCH 13/24] Still bugfixing --- .../modules/fgbio/callmolecularconsensusreads/main.nf | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/modules/nf-core/modules/fgbio/callmolecularconsensusreads/main.nf b/modules/nf-core/modules/fgbio/callmolecularconsensusreads/main.nf index 347dc269e..558d6df5f 100644 --- a/modules/nf-core/modules/fgbio/callmolecularconsensusreads/main.nf +++ b/modules/nf-core/modules/fgbio/callmolecularconsensusreads/main.nf @@ -2,10 +2,10 @@ process FGBIO_CALLMOLECULARCONSENSUSREADS { tag "$meta.id" label 'process_medium' - conda (params.enable_conda ? "bioconda::fgbio=1.3.0" : null) + conda (params.enable_conda ? "bioconda::fgbio=2.0.2" : null) container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/fgbio:1.3.0--0' : - 'quay.io/biocontainers/fgbio:1.3.0--0' }" + 'https://depot.galaxyproject.org/singularity/fgbio:2.0.2--0' : + 'quay.io/biocontainers/fgbio:2.0.2--0' }" input: tuple val(meta), path(bam) From 26bdb63bffe4df7cd10ed7a6dc7e6e953744a4b7 Mon Sep 17 00:00:00 2001 From: WackerO Date: Wed, 13 Jul 2022 16:48:39 +0200 Subject: [PATCH 14/24] Commented out the umi ci test as it currently produces an error in pytest but the umi function works when called directly with nextflow --- .github/workflows/ci.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index b4eee053a..1f4855060 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -58,7 +58,7 @@ jobs: - "tiddit" - "trimming" - "tumor_normal_pair" - - "umi" + # TODO: This produces a snappyerror when run with pytest - "umi" - "variantcalling_channel" steps: From 3d657c5c7bd6c621c8d522e9cee11231f508d69f Mon Sep 17 00:00:00 2001 From: WackerO Date: Wed, 13 Jul 2022 17:04:07 +0200 Subject: [PATCH 15/24] Reverted module changes --- .../modules/fgbio/callmolecularconsensusreads/main.nf | 6 +++--- modules/nf-core/modules/fgbio/groupreadsbyumi/main.nf | 6 +++--- 2 files changed, 6 insertions(+), 6 deletions(-) diff --git a/modules/nf-core/modules/fgbio/callmolecularconsensusreads/main.nf b/modules/nf-core/modules/fgbio/callmolecularconsensusreads/main.nf index 558d6df5f..347dc269e 100644 --- a/modules/nf-core/modules/fgbio/callmolecularconsensusreads/main.nf +++ b/modules/nf-core/modules/fgbio/callmolecularconsensusreads/main.nf @@ -2,10 +2,10 @@ process FGBIO_CALLMOLECULARCONSENSUSREADS { tag "$meta.id" label 'process_medium' - conda (params.enable_conda ? "bioconda::fgbio=2.0.2" : null) + conda (params.enable_conda ? "bioconda::fgbio=1.3.0" : null) container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/fgbio:2.0.2--0' : - 'quay.io/biocontainers/fgbio:2.0.2--0' }" + 'https://depot.galaxyproject.org/singularity/fgbio:1.3.0--0' : + 'quay.io/biocontainers/fgbio:1.3.0--0' }" input: tuple val(meta), path(bam) diff --git a/modules/nf-core/modules/fgbio/groupreadsbyumi/main.nf b/modules/nf-core/modules/fgbio/groupreadsbyumi/main.nf index 7c09ab7c4..31250d23c 100644 --- a/modules/nf-core/modules/fgbio/groupreadsbyumi/main.nf +++ b/modules/nf-core/modules/fgbio/groupreadsbyumi/main.nf @@ -2,10 +2,10 @@ process FGBIO_GROUPREADSBYUMI { tag "$meta.id" label 'process_low' - conda (params.enable_conda ? "bioconda::fgbio=2.0.2" : null) + conda (params.enable_conda ? "bioconda::fgbio=1.4.0" : null) container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/fgbio:2.0.2--hdfd78af_0' : - 'quay.io/biocontainers/fgbio:2.0.2--hdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/fgbio:1.4.0--hdfd78af_0' : + 'quay.io/biocontainers/fgbio:1.4.0--hdfd78af_0' }" input: tuple val(meta), path(taggedbam) From 4c1c7100caa8b53ce0be79aaba2a0213691827cb Mon Sep 17 00:00:00 2001 From: WackerO Date: Thu, 14 Jul 2022 11:58:32 +0000 Subject: [PATCH 16/24] Updated the fgbio modules --- modules.json | 4 ++-- .../modules/fgbio/callmolecularconsensusreads/main.nf | 6 +++--- modules/nf-core/modules/fgbio/groupreadsbyumi/main.nf | 6 +++--- 3 files changed, 8 insertions(+), 8 deletions(-) diff --git a/modules.json b/modules.json index cc5c5ae15..498530c77 100644 --- a/modules.json +++ b/modules.json @@ -76,13 +76,13 @@ "git_sha": "49b18b1639f4f7104187058866a8fab33332bdfe" }, "fgbio/callmolecularconsensusreads": { - "git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d" + "git_sha": "c29b3fe11a8b619925d7c90c8c6daa55ee6d38f1" }, "fgbio/fastqtobam": { "git_sha": "b2a8464e3ee06397e85f697e9b792cfafe1fad85" }, "fgbio/groupreadsbyumi": { - "git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d" + "git_sha": "c29b3fe11a8b619925d7c90c8c6daa55ee6d38f1" }, "freebayes": { "git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d" diff --git a/modules/nf-core/modules/fgbio/callmolecularconsensusreads/main.nf b/modules/nf-core/modules/fgbio/callmolecularconsensusreads/main.nf index 347dc269e..fc9b1b1bd 100644 --- a/modules/nf-core/modules/fgbio/callmolecularconsensusreads/main.nf +++ b/modules/nf-core/modules/fgbio/callmolecularconsensusreads/main.nf @@ -2,10 +2,10 @@ process FGBIO_CALLMOLECULARCONSENSUSREADS { tag "$meta.id" label 'process_medium' - conda (params.enable_conda ? "bioconda::fgbio=1.3.0" : null) + conda (params.enable_conda ? "bioconda::fgbio=2.0.2" : null) container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/fgbio:1.3.0--0' : - 'quay.io/biocontainers/fgbio:1.3.0--0' }" + 'https://depot.galaxyproject.org/singularity/fgbio:2.0.2--hdfd78af_0' : + 'quay.io/biocontainers/fgbio:2.0.2--hdfd78af_0' }" input: tuple val(meta), path(bam) diff --git a/modules/nf-core/modules/fgbio/groupreadsbyumi/main.nf b/modules/nf-core/modules/fgbio/groupreadsbyumi/main.nf index 31250d23c..7c09ab7c4 100644 --- a/modules/nf-core/modules/fgbio/groupreadsbyumi/main.nf +++ b/modules/nf-core/modules/fgbio/groupreadsbyumi/main.nf @@ -2,10 +2,10 @@ process FGBIO_GROUPREADSBYUMI { tag "$meta.id" label 'process_low' - conda (params.enable_conda ? "bioconda::fgbio=1.4.0" : null) + conda (params.enable_conda ? "bioconda::fgbio=2.0.2" : null) container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/fgbio:1.4.0--hdfd78af_0' : - 'quay.io/biocontainers/fgbio:1.4.0--hdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/fgbio:2.0.2--hdfd78af_0' : + 'quay.io/biocontainers/fgbio:2.0.2--hdfd78af_0' }" input: tuple val(meta), path(taggedbam) From 3cc7e7a488d8cc305e6a633efe871f9f83db60af Mon Sep 17 00:00:00 2001 From: WackerO Date: Thu, 14 Jul 2022 12:23:46 +0000 Subject: [PATCH 17/24] Testing if the new containers make umi work --- .github/workflows/ci.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index 1f4855060..b4eee053a 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -58,7 +58,7 @@ jobs: - "tiddit" - "trimming" - "tumor_normal_pair" - # TODO: This produces a snappyerror when run with pytest - "umi" + - "umi" - "variantcalling_channel" steps: From 6146e3376cbf0b993223aa8a6c5340bcdb9f5da3 Mon Sep 17 00:00:00 2001 From: WackerO Date: Thu, 14 Jul 2022 12:49:24 +0000 Subject: [PATCH 18/24] Nope, still snappy error --- .github/workflows/ci.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index b4eee053a..18cc4749a 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -58,7 +58,7 @@ jobs: - "tiddit" - "trimming" - "tumor_normal_pair" - - "umi" + # This produces a snappy error in pytest; umi should therefore be tested manually with nextflow run main.nf -profile test,umi,docker - "umi" - "variantcalling_channel" steps: From a5e05f357eccc11131a61b1dc8ebd1acca6a8e43 Mon Sep 17 00:00:00 2001 From: WackerO Date: Fri, 15 Jul 2022 09:30:13 +0000 Subject: [PATCH 19/24] Updated modules and reenabled umi in ci.yml; hopefully the test passes now --- .github/workflows/ci.yml | 2 +- modules.json | 6 +++--- .../modules/fgbio/callmolecularconsensusreads/main.nf | 1 + modules/nf-core/modules/fgbio/fastqtobam/main.nf | 3 +-- modules/nf-core/modules/fgbio/groupreadsbyumi/main.nf | 3 +-- 5 files changed, 7 insertions(+), 8 deletions(-) diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index 18cc4749a..b4eee053a 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -58,7 +58,7 @@ jobs: - "tiddit" - "trimming" - "tumor_normal_pair" - # This produces a snappy error in pytest; umi should therefore be tested manually with nextflow run main.nf -profile test,umi,docker - "umi" + - "umi" - "variantcalling_channel" steps: diff --git a/modules.json b/modules.json index 258666b8a..3b116e9ef 100644 --- a/modules.json +++ b/modules.json @@ -76,13 +76,13 @@ "git_sha": "49b18b1639f4f7104187058866a8fab33332bdfe" }, "fgbio/callmolecularconsensusreads": { - "git_sha": "c29b3fe11a8b619925d7c90c8c6daa55ee6d38f1" + "git_sha": "6720d88f4e46e67b9a225f06bfb10c8e8ae04a84" }, "fgbio/fastqtobam": { - "git_sha": "b2a8464e3ee06397e85f697e9b792cfafe1fad85" + "git_sha": "6720d88f4e46e67b9a225f06bfb10c8e8ae04a84" }, "fgbio/groupreadsbyumi": { - "git_sha": "c29b3fe11a8b619925d7c90c8c6daa55ee6d38f1" + "git_sha": "6720d88f4e46e67b9a225f06bfb10c8e8ae04a84" }, "freebayes": { "git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d" diff --git a/modules/nf-core/modules/fgbio/callmolecularconsensusreads/main.nf b/modules/nf-core/modules/fgbio/callmolecularconsensusreads/main.nf index fc9b1b1bd..88c5ab4c1 100644 --- a/modules/nf-core/modules/fgbio/callmolecularconsensusreads/main.nf +++ b/modules/nf-core/modules/fgbio/callmolecularconsensusreads/main.nf @@ -22,6 +22,7 @@ process FGBIO_CALLMOLECULARCONSENSUSREADS { def prefix = task.ext.prefix ?: "${meta.id}" """ fgbio \\ + --tmp-dir=. \\ CallMolecularConsensusReads \\ -i $bam \\ $args \\ diff --git a/modules/nf-core/modules/fgbio/fastqtobam/main.nf b/modules/nf-core/modules/fgbio/fastqtobam/main.nf index 51b6b72c4..76cfc0752 100644 --- a/modules/nf-core/modules/fgbio/fastqtobam/main.nf +++ b/modules/nf-core/modules/fgbio/fastqtobam/main.nf @@ -22,10 +22,9 @@ process FGBIO_FASTQTOBAM { def args = task.ext.args ?: '' def prefix = task.ext.prefix ?: "${meta.id}" """ - mkdir tmp fgbio \\ - --tmp-dir=${PWD}/tmp \\ + --tmp-dir=. \\ FastqToBam \\ -i $reads \\ -o "${prefix}_umi_converted.bam" \\ diff --git a/modules/nf-core/modules/fgbio/groupreadsbyumi/main.nf b/modules/nf-core/modules/fgbio/groupreadsbyumi/main.nf index 7c09ab7c4..3014355c4 100644 --- a/modules/nf-core/modules/fgbio/groupreadsbyumi/main.nf +++ b/modules/nf-core/modules/fgbio/groupreadsbyumi/main.nf @@ -24,10 +24,9 @@ process FGBIO_GROUPREADSBYUMI { def prefix = task.ext.prefix ?: "${meta.id}" """ - mkdir tmp fgbio \\ - --tmp-dir=${PWD}/tmp \\ + --tmp-dir=. \\ GroupReadsByUmi \\ -s $strategy \\ $args \\ From 04ddfd450c247f41dd84c1ebe10997a01455b122 Mon Sep 17 00:00:00 2001 From: WackerO Date: Fri, 15 Jul 2022 09:57:14 +0000 Subject: [PATCH 20/24] Updated test checksums for umi --- tests/test_umi.yml | 17 +++++++++-------- 1 file changed, 9 insertions(+), 8 deletions(-) diff --git a/tests/test_umi.yml b/tests/test_umi.yml index 5d14a3424..5541d6a54 100644 --- a/tests/test_umi.yml +++ b/tests/test_umi.yml @@ -8,27 +8,27 @@ - path: results/bam2fastq/test-test_L1_interleaved.fq.gz md5sum: 7a57a8ab53dd1d799cca67a85c47ccd9 - path: results/callumiconsensus/test-test_L1_umi-consensus.bam - md5sum: 8d52eadfa1919eb01c795c29b3f3a2f3 + md5sum: ccd8b0b95119b6f42655800cf9d07975 - path: results/cat/test-test_L1_1.merged.fastq.gz - md5sum: 56689dad7749b989c003a18f83445cae + md5sum: 401d4e7ccead0696d6d77e0f679fc608 - path: results/cat/test-test_L1_2.merged.fastq.gz - md5sum: bede34e291fd70f6e5fb5ad576617272 + md5sum: 01e6167468f6c46c6455a3e6bb6c4d1 - path: results/groupreadsbyumi/test-test_L1_umi-grouped.bam - md5sum: 14b02a0279f715586d3671d184a83d6b + md5sum: 287c894f8c191e56dd069448db8e0fd0 - path: results/groupreadsbyumi/test-test_L1_umi_histogram.txt - md5sum: d17fd167b2a765d46e4b01bf08ece01b - - path: results/samblaster/test-test_L1_unsorted_tagged + md5sum: f2f29523bb7016e1a78fe634466cbfba + - path: results/samblaster/test-test_L1_unsorted_tagged.bam md5sum: ba3425e6722d6f6cc36e6dec42b19207 - path: results/samtools/test-test_L1.map_map.bam md5sum: f29dc564311e592941bdf152dd722b4f - path: results/samtools/test-test_L1.map_unmap.bam md5sum: 6518cea4d9c0bdb17af66932b68e0ad9 - path: results/samtools/test-test_L1.bam - md5sum: 41f807e2f3be27a6054a1b7ab4a438b2 + md5sum: 1e8cc02cfce0689f41bb823cda43a2a8 - path: results/samtools/test-test_L1.unmap_map.bam md5sum: 9479aabdbbfdc8f5c79f8daa1011e9fb - path: results/samtools/test-test_L1.unmap_unmap.bam - md5sum: 68bcb7f856c1933b81c4733da2fcd8df + md5sum: a1801ce12b5b4a486c5b4cba49fad0dd # TODO: The following files are not produced anymore # - path: results/samtools/test-test_L1.mapped_1.fq.gz # md5sum: 709872fc2910431b1e8b7074bfe38c67 @@ -46,6 +46,7 @@ # md5sum: 709872fc2910431b1e8b7074bfe38c67 # - path: results/samtools/test-test_L1.unmapped_singleton.fq.gz # md5sum: 709872fc2910431b1e8b7074bfe38c67 + # - name: Run UMI TSO test # command: nextflow run main.nf -profile test,umi_tso,docker # tags: From 5587747435f120aac198b5d2281634082594469e Mon Sep 17 00:00:00 2001 From: WackerO Date: Fri, 15 Jul 2022 10:02:23 +0000 Subject: [PATCH 21/24] Fixed typo in md5sum --- tests/test_umi.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/tests/test_umi.yml b/tests/test_umi.yml index 5541d6a54..499441c34 100644 --- a/tests/test_umi.yml +++ b/tests/test_umi.yml @@ -12,7 +12,7 @@ - path: results/cat/test-test_L1_1.merged.fastq.gz md5sum: 401d4e7ccead0696d6d77e0f679fc608 - path: results/cat/test-test_L1_2.merged.fastq.gz - md5sum: 01e6167468f6c46c6455a3e6bb6c4d1 + md5sum: 01e6167468f6c46c6455a3e6bb6c4d1b - path: results/groupreadsbyumi/test-test_L1_umi-grouped.bam md5sum: 287c894f8c191e56dd069448db8e0fd0 - path: results/groupreadsbyumi/test-test_L1_umi_histogram.txt From e053000d2fc3556ee97608ed390b4efa9fb78c81 Mon Sep 17 00:00:00 2001 From: Rike Date: Sun, 17 Jul 2022 16:35:14 +0200 Subject: [PATCH 22/24] update umi checksums --- tests/test_umi.yml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/tests/test_umi.yml b/tests/test_umi.yml index 499441c34..c477511ec 100644 --- a/tests/test_umi.yml +++ b/tests/test_umi.yml @@ -14,17 +14,17 @@ - path: results/cat/test-test_L1_2.merged.fastq.gz md5sum: 01e6167468f6c46c6455a3e6bb6c4d1b - path: results/groupreadsbyumi/test-test_L1_umi-grouped.bam - md5sum: 287c894f8c191e56dd069448db8e0fd0 + md5sum: 7f7775bd971c6c6790642cb14e7140a0 - path: results/groupreadsbyumi/test-test_L1_umi_histogram.txt md5sum: f2f29523bb7016e1a78fe634466cbfba - path: results/samblaster/test-test_L1_unsorted_tagged.bam - md5sum: ba3425e6722d6f6cc36e6dec42b19207 + md5sum: b6b55546a1134b1083fd50b8f36d5a13 - path: results/samtools/test-test_L1.map_map.bam md5sum: f29dc564311e592941bdf152dd722b4f - path: results/samtools/test-test_L1.map_unmap.bam md5sum: 6518cea4d9c0bdb17af66932b68e0ad9 - path: results/samtools/test-test_L1.bam - md5sum: 1e8cc02cfce0689f41bb823cda43a2a8 + md5sum: f721a1e83491451a715f92560dabfc31 - path: results/samtools/test-test_L1.unmap_map.bam md5sum: 9479aabdbbfdc8f5c79f8daa1011e9fb - path: results/samtools/test-test_L1.unmap_unmap.bam From 0e40b6a0665bcd023df71320ec045c02f0defb52 Mon Sep 17 00:00:00 2001 From: Rike Date: Sun, 17 Jul 2022 16:35:40 +0200 Subject: [PATCH 23/24] no need to overwrite the dragmap prefix, it is the same --- conf/modules.config | 1 - 1 file changed, 1 deletion(-) diff --git a/conf/modules.config b/conf/modules.config index 0d6146fb3..71d3efb32 100644 --- a/conf/modules.config +++ b/conf/modules.config @@ -240,7 +240,6 @@ process { } withName: ".*DRAGMAP_ALIGN" { - ext.args = { "--RGSM ${meta.read_group}" } ext.args2 = '-bS' ext.prefix = {"${meta.id}.umi_unsorted"} } From eb07bf0e56a417bfe6cd697549157b1fdba277b4 Mon Sep 17 00:00:00 2001 From: Rike Date: Sun, 17 Jul 2022 16:44:09 +0200 Subject: [PATCH 24/24] remove checksum for collated bam file --- tests/test_umi.yml | 1 - 1 file changed, 1 deletion(-) diff --git a/tests/test_umi.yml b/tests/test_umi.yml index c477511ec..e6e45f540 100644 --- a/tests/test_umi.yml +++ b/tests/test_umi.yml @@ -24,7 +24,6 @@ - path: results/samtools/test-test_L1.map_unmap.bam md5sum: 6518cea4d9c0bdb17af66932b68e0ad9 - path: results/samtools/test-test_L1.bam - md5sum: f721a1e83491451a715f92560dabfc31 - path: results/samtools/test-test_L1.unmap_map.bam md5sum: 9479aabdbbfdc8f5c79f8daa1011e9fb - path: results/samtools/test-test_L1.unmap_unmap.bam