From 90c67794bfe33cd82954ca482979d5e8d5d3fc12 Mon Sep 17 00:00:00 2001 From: Chris Cheshire Date: Thu, 12 May 2022 10:01:33 +0100 Subject: [PATCH 1/9] Added extra tests but error with collection --- modules/bowtie2/align/main.nf | 1 - tests/modules/bowtie2/align/main.nf | 29 +++++++++++ tests/modules/bowtie2/align/nextflow.config | 1 + tests/modules/bowtie2/align/test.yml | 56 +++++++++++++++------ 4 files changed, 71 insertions(+), 16 deletions(-) diff --git a/modules/bowtie2/align/main.nf b/modules/bowtie2/align/main.nf index 38242fcb..e4bb4327 100644 --- a/modules/bowtie2/align/main.nf +++ b/modules/bowtie2/align/main.nf @@ -69,4 +69,3 @@ process BOWTIE2_ALIGN { END_VERSIONS """ } - diff --git a/tests/modules/bowtie2/align/main.nf b/tests/modules/bowtie2/align/main.nf index f91394ff..42e2306a 100644 --- a/tests/modules/bowtie2/align/main.nf +++ b/tests/modules/bowtie2/align/main.nf @@ -30,6 +30,35 @@ workflow test_bowtie2_align_paired_end { fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) save_unaligned = false + BOWTIE2_BUILD ( fasta ) + BOWTIE2_ALIGN ( input, BOWTIE2_BUILD.out.index, save_unaligned ) +} + +workflow test_bowtie2_align_single_end_large_index { + input = [ + [ id:'test', single_end:true ], // meta map + [ + file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true) + ] + ] + fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) + save_unaligned = false + + BOWTIE2_BUILD ( fasta ) + BOWTIE2_ALIGN ( input, BOWTIE2_BUILD.out.index, save_unaligned ) +} + +workflow test_bowtie2_align_paired_end_large_index { + input = [ + [ id:'test', single_end:false ], // meta map + [ + file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true), + file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true) + ] + ] + fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) + save_unaligned = false + BOWTIE2_BUILD ( fasta ) BOWTIE2_ALIGN ( input, BOWTIE2_BUILD.out.index, save_unaligned ) } \ No newline at end of file diff --git a/tests/modules/bowtie2/align/nextflow.config b/tests/modules/bowtie2/align/nextflow.config index b4640de7..08f7bed0 100644 --- a/tests/modules/bowtie2/align/nextflow.config +++ b/tests/modules/bowtie2/align/nextflow.config @@ -5,6 +5,7 @@ params { process { publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" } + } if (params.force_large_index) { diff --git a/tests/modules/bowtie2/align/test.yml b/tests/modules/bowtie2/align/test.yml index ef05d70d..8a33c928 100644 --- a/tests/modules/bowtie2/align/test.yml +++ b/tests/modules/bowtie2/align/test.yml @@ -1,21 +1,47 @@ - name: bowtie2 align test_bowtie2_align_single_end command: nextflow run ./tests/modules/bowtie2/align -entry test_bowtie2_align_single_end -c ./tests/config/nextflow.config -c ./tests/modules/bowtie2/align/nextflow.config tags: - - bowtie2/align - bowtie2 + - bowtie2/align files: - - path: output/bowtie2/test.bam - - path: output/bowtie2/test.bowtie2.log - md5sum: 7b8a9e61b7646da1089b041333c41a87 - - path: output/bowtie2/versions.yml + - path: ./output/bowtie2/test.bam + # - path: output/bowtie2/test.bowtie2.log + # md5sum: 7b8a9e61b7646da1089b041333c41a87 + # - path: output/bowtie2/versions.yml + # md5sum: 24621c58884fe90c2255ccd1fe4352ae -- name: bowtie2 align test_bowtie2_align_paired_end - command: nextflow run ./tests/modules/bowtie2/align -entry test_bowtie2_align_paired_end -c ./tests/config/nextflow.config -c ./tests/modules/bowtie2/align/nextflow.config - tags: - - bowtie2/align - - bowtie2 - files: - - path: output/bowtie2/test.bam - - path: output/bowtie2/test.bowtie2.log - md5sum: bd89ce1b28c93bf822bae391ffcedd19 - - path: output/bowtie2/versions.yml +# - name: bowtie2 align test_bowtie2_align_paired_end +# command: nextflow run tests/modules/bowtie2/align -entry test_bowtie2_align_paired_end -c tests/config/nextflow.config -c tests/modules/bowtie2/align/nextflow.config +# tags: +# - bowtie2 +# - bowtie2/align +# files: +# - path: output/bowtie2/test.bam +# - path: output/bowtie2/test.bowtie2.log +# md5sum: bd89ce1b28c93bf822bae391ffcedd19 +# - path: output/bowtie2/versions.yml +# md5sum: f9712ca6d75393ad5c1781a2dcf82d32 + +# - name: bowtie2 align test_bowtie2_align_single_end_large_index +# command: nextflow run tests/modules/bowtie2/align -entry test_bowtie2_align_single_end_large_index -c tests/config/nextflow.config -c tests/modules/bowtie2/align/nextflow.config --force_large_index +# tags: +# - bowtie2 +# - bowtie2/align +# files: +# - path: output/bowtie2/test.bam +# - path: output/bowtie2/test.bowtie2.log +# md5sum: 7b8a9e61b7646da1089b041333c41a87 +# - path: output/bowtie2/versions.yml +# md5sum: bf0537964a85ce9461ae1b0e2f260211 + +# - name: bowtie2 align test_bowtie2_align_paired_end_large_index +# command: nextflow run tests/modules/bowtie2/align -entry test_bowtie2_align_paired_end_large_index -c tests/config/nextflow.config -c tests/modules/bowtie2/align/nextflow.config --force_large_index +# tags: +# - bowtie2 +# - bowtie2/align +# files: +# - path: output/bowtie2/test.bam +# - path: output/bowtie2/test.bowtie2.log +# md5sum: bd89ce1b28c93bf822bae391ffcedd19 +# - path: output/bowtie2/versions.yml +# md5sum: c0a88953500eaf46de7ff378a7de4a37 From d816f2bc5d5338526919d7e1eea42ca6143513fb Mon Sep 17 00:00:00 2001 From: Chris Cheshire Date: Fri, 13 May 2022 12:01:16 +0100 Subject: [PATCH 2/9] Reactivated all tests --- tests/modules/bowtie2/align/test.yml | 70 +++++++++++++--------------- 1 file changed, 33 insertions(+), 37 deletions(-) diff --git a/tests/modules/bowtie2/align/test.yml b/tests/modules/bowtie2/align/test.yml index 8a33c928..56a8bf53 100644 --- a/tests/modules/bowtie2/align/test.yml +++ b/tests/modules/bowtie2/align/test.yml @@ -5,43 +5,39 @@ - bowtie2/align files: - path: ./output/bowtie2/test.bam - # - path: output/bowtie2/test.bowtie2.log - # md5sum: 7b8a9e61b7646da1089b041333c41a87 - # - path: output/bowtie2/versions.yml - # md5sum: 24621c58884fe90c2255ccd1fe4352ae + - path: ./output/bowtie2/test.bowtie2.log + - path: ./output/bowtie2/versions.yml + md5sum: 24621c58884fe90c2255ccd1fe4352ae -# - name: bowtie2 align test_bowtie2_align_paired_end -# command: nextflow run tests/modules/bowtie2/align -entry test_bowtie2_align_paired_end -c tests/config/nextflow.config -c tests/modules/bowtie2/align/nextflow.config -# tags: -# - bowtie2 -# - bowtie2/align -# files: -# - path: output/bowtie2/test.bam -# - path: output/bowtie2/test.bowtie2.log -# md5sum: bd89ce1b28c93bf822bae391ffcedd19 -# - path: output/bowtie2/versions.yml -# md5sum: f9712ca6d75393ad5c1781a2dcf82d32 +- name: bowtie2 align test_bowtie2_align_paired_end + command: nextflow run tests/modules/bowtie2/align -entry test_bowtie2_align_paired_end -c tests/config/nextflow.config -c tests/modules/bowtie2/align/nextflow.config + tags: + - bowtie2 + - bowtie2/align + files: + - path: ./output/bowtie2/test.bam + - path: ./output/bowtie2/test.bowtie2.log + - path: ./output/bowtie2/versions.yml + md5sum: f9712ca6d75393ad5c1781a2dcf82d32 -# - name: bowtie2 align test_bowtie2_align_single_end_large_index -# command: nextflow run tests/modules/bowtie2/align -entry test_bowtie2_align_single_end_large_index -c tests/config/nextflow.config -c tests/modules/bowtie2/align/nextflow.config --force_large_index -# tags: -# - bowtie2 -# - bowtie2/align -# files: -# - path: output/bowtie2/test.bam -# - path: output/bowtie2/test.bowtie2.log -# md5sum: 7b8a9e61b7646da1089b041333c41a87 -# - path: output/bowtie2/versions.yml -# md5sum: bf0537964a85ce9461ae1b0e2f260211 +- name: bowtie2 align test_bowtie2_align_single_end_large_index + command: nextflow run tests/modules/bowtie2/align -entry test_bowtie2_align_single_end_large_index -c tests/config/nextflow.config -c tests/modules/bowtie2/align/nextflow.config --force_large_index + tags: + - bowtie2 + - bowtie2/align + files: + - path: ./output/bowtie2/test.bam + - path: ./output/bowtie2/test.bowtie2.log + - path: ./output/bowtie2/versions.yml + md5sum: bf0537964a85ce9461ae1b0e2f260211 -# - name: bowtie2 align test_bowtie2_align_paired_end_large_index -# command: nextflow run tests/modules/bowtie2/align -entry test_bowtie2_align_paired_end_large_index -c tests/config/nextflow.config -c tests/modules/bowtie2/align/nextflow.config --force_large_index -# tags: -# - bowtie2 -# - bowtie2/align -# files: -# - path: output/bowtie2/test.bam -# - path: output/bowtie2/test.bowtie2.log -# md5sum: bd89ce1b28c93bf822bae391ffcedd19 -# - path: output/bowtie2/versions.yml -# md5sum: c0a88953500eaf46de7ff378a7de4a37 +- name: bowtie2 align test_bowtie2_align_paired_end_large_index + command: nextflow run tests/modules/bowtie2/align -entry test_bowtie2_align_paired_end_large_index -c tests/config/nextflow.config -c tests/modules/bowtie2/align/nextflow.config --force_large_index + tags: + - bowtie2 + - bowtie2/align + files: + - path: ./output/bowtie2/test.bam + - path: ./output/bowtie2/test.bowtie2.log + - path: ./output/bowtie2/versions.yml + md5sum: c0a88953500eaf46de7ff378a7de4a37 From ea55129ba3e3cef1a38df236c95d3d4daca63265 Mon Sep 17 00:00:00 2001 From: Chris Cheshire Date: Fri, 13 May 2022 12:20:41 +0100 Subject: [PATCH 3/9] Removed version file checksums --- tests/modules/bowtie2/align/test.yml | 4 ---- 1 file changed, 4 deletions(-) diff --git a/tests/modules/bowtie2/align/test.yml b/tests/modules/bowtie2/align/test.yml index 56a8bf53..103d65e9 100644 --- a/tests/modules/bowtie2/align/test.yml +++ b/tests/modules/bowtie2/align/test.yml @@ -7,7 +7,6 @@ - path: ./output/bowtie2/test.bam - path: ./output/bowtie2/test.bowtie2.log - path: ./output/bowtie2/versions.yml - md5sum: 24621c58884fe90c2255ccd1fe4352ae - name: bowtie2 align test_bowtie2_align_paired_end command: nextflow run tests/modules/bowtie2/align -entry test_bowtie2_align_paired_end -c tests/config/nextflow.config -c tests/modules/bowtie2/align/nextflow.config @@ -18,7 +17,6 @@ - path: ./output/bowtie2/test.bam - path: ./output/bowtie2/test.bowtie2.log - path: ./output/bowtie2/versions.yml - md5sum: f9712ca6d75393ad5c1781a2dcf82d32 - name: bowtie2 align test_bowtie2_align_single_end_large_index command: nextflow run tests/modules/bowtie2/align -entry test_bowtie2_align_single_end_large_index -c tests/config/nextflow.config -c tests/modules/bowtie2/align/nextflow.config --force_large_index @@ -29,7 +27,6 @@ - path: ./output/bowtie2/test.bam - path: ./output/bowtie2/test.bowtie2.log - path: ./output/bowtie2/versions.yml - md5sum: bf0537964a85ce9461ae1b0e2f260211 - name: bowtie2 align test_bowtie2_align_paired_end_large_index command: nextflow run tests/modules/bowtie2/align -entry test_bowtie2_align_paired_end_large_index -c tests/config/nextflow.config -c tests/modules/bowtie2/align/nextflow.config --force_large_index @@ -40,4 +37,3 @@ - path: ./output/bowtie2/test.bam - path: ./output/bowtie2/test.bowtie2.log - path: ./output/bowtie2/versions.yml - md5sum: c0a88953500eaf46de7ff378a7de4a37 From 8a17b6dd0e247746cee97e7dc6fa0761534f13ec Mon Sep 17 00:00:00 2001 From: Nicolas Vannieuwkerke Date: Fri, 13 May 2022 13:46:34 +0200 Subject: [PATCH 4/9] added gatk4/splitintervals --- modules/gatk4/splitintervals/main.nf | 47 +++++++++++++++++++ modules/gatk4/splitintervals/meta.yml | 41 ++++++++++++++++ tests/config/pytest_modules.yml | 12 +++-- tests/modules/gatk4/splitintervals/main.nf | 33 +++++++++++++ .../gatk4/splitintervals/nextflow.config | 9 ++++ tests/modules/gatk4/splitintervals/test.yml | 25 ++++++++++ 6 files changed, 163 insertions(+), 4 deletions(-) create mode 100644 modules/gatk4/splitintervals/main.nf create mode 100644 modules/gatk4/splitintervals/meta.yml create mode 100644 tests/modules/gatk4/splitintervals/main.nf create mode 100644 tests/modules/gatk4/splitintervals/nextflow.config create mode 100644 tests/modules/gatk4/splitintervals/test.yml diff --git a/modules/gatk4/splitintervals/main.nf b/modules/gatk4/splitintervals/main.nf new file mode 100644 index 00000000..d9407b95 --- /dev/null +++ b/modules/gatk4/splitintervals/main.nf @@ -0,0 +1,47 @@ +process GATK4_SPLITINTERVALS { + tag "$meta.id" + label 'process_low' + + conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null) + container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + 'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0': + 'quay.io/biocontainers/gatk4:4.2.6.1--hdfd78af_0' }" + + input: + tuple val(meta), path(intervals) + path(fasta) + path(fasta_fai) + path(fasta_dict) + + output: + tuple val(meta), path("**.interval_list"), emit: split_intervals + path "versions.yml" , emit: versions + + when: + task.ext.when == null || task.ext.when + + script: + def args = task.ext.args ?: '' + def prefix = task.ext.prefix ?: "${meta.id}" + def reference = fasta ? "--reference $fasta" : "" + + def avail_mem = 3 + if (!task.memory) { + log.info '[GATK IntervalListToBed] Available memory not known - defaulting to 3GB. Specify process memory requirements to change this.' + } else { + avail_mem = task.memory.giga + } + + """ + gatk --java-options "-Xmx${avail_mem}g" SplitIntervals \\ + --output ${prefix} \\ + --intervals $intervals \\ + $reference \\ + $args + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + gatk4: \$(echo \$(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//') + END_VERSIONS + """ +} diff --git a/modules/gatk4/splitintervals/meta.yml b/modules/gatk4/splitintervals/meta.yml new file mode 100644 index 00000000..6cf7cedc --- /dev/null +++ b/modules/gatk4/splitintervals/meta.yml @@ -0,0 +1,41 @@ +name: gatk4_splitintervals +keywords: + - interval + - bed +tools: + - gatk4: + description: Genome Analysis Toolkit (GATK4) + homepage: https://gatk.broadinstitute.org/hc/en-us + documentation: https://gatk.broadinstitute.org/hc/en-us/categories/360002369672s + tool_dev_url: https://github.com/broadinstitute/gatk + doi: "10.1158/1538-7445.AM2017-3590" + licence: ["BSD-3-clause"] + +input: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - interval: + type: file + description: Interval list or BED + pattern: "*.{interval,interval_list,bed}" + +output: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - bed: + type: file + description: A list of scattered interval lists + pattern: "*.interval_list" + - versions: + type: file + description: File containing software versions + pattern: "versions.yml" + +authors: + - "@nvnieuwk" diff --git a/tests/config/pytest_modules.yml b/tests/config/pytest_modules.yml index 428c3652..bfd8554a 100644 --- a/tests/config/pytest_modules.yml +++ b/tests/config/pytest_modules.yml @@ -819,6 +819,10 @@ gatk4/selectvariants: - modules/gatk4/selectvariants/** - tests/modules/gatk4/selectvariants/** +gatk4/splitintervals: + - modules/gatk4/splitintervals/** + - tests/modules/gatk4/splitintervals/** + gatk4/splitncigarreads: - modules/gatk4/splitncigarreads/** - tests/modules/gatk4/splitncigarreads/** @@ -1647,14 +1651,14 @@ samtools/bam2fq: - modules/samtools/bam2fq/** - tests/modules/samtools/bam2fq/** -samtools/convert: - - modules/samtools/convert/** - - tests/modules/samtools/convert/** - samtools/collatefastq: - modules/samtools/collatefastq/** - tests/modules/samtools/collatefastq/** +samtools/convert: + - modules/samtools/convert/** + - tests/modules/samtools/convert/** + samtools/depth: - modules/samtools/depth/** - tests/modules/samtools/depth/** diff --git a/tests/modules/gatk4/splitintervals/main.nf b/tests/modules/gatk4/splitintervals/main.nf new file mode 100644 index 00000000..f507ece5 --- /dev/null +++ b/tests/modules/gatk4/splitintervals/main.nf @@ -0,0 +1,33 @@ +#!/usr/bin/env nextflow + +nextflow.enable.dsl = 2 + +include { GATK4_SPLITINTERVALS } from '../../../../modules/gatk4/splitintervals/main.nf' + +workflow test_gatk4_splitintervals_bed { + + input = [ + [ id:'test' ], // meta map + file(params.test_data['homo_sapiens']['genome']['genome_multi_interval_bed'], checkIfExists: true) + ] + + fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true) + fasta_fai = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true) + fasta_dict = file(params.test_data['homo_sapiens']['genome']['genome_dict'], checkIfExists: true) + + GATK4_SPLITINTERVALS ( input, fasta, fasta_fai, fasta_dict) +} + +workflow test_gatk4_splitintervals_intervals { + + input = [ + [ id:'test' ], // meta map + file(params.test_data['homo_sapiens']['genome']['genome_interval_list'], checkIfExists: true) + ] + + fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true) + fasta_fai = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true) + fasta_dict = file(params.test_data['homo_sapiens']['genome']['genome_dict'], checkIfExists: true) + + GATK4_SPLITINTERVALS ( input, fasta, fasta_fai, fasta_dict) +} \ No newline at end of file diff --git a/tests/modules/gatk4/splitintervals/nextflow.config b/tests/modules/gatk4/splitintervals/nextflow.config new file mode 100644 index 00000000..10fda96c --- /dev/null +++ b/tests/modules/gatk4/splitintervals/nextflow.config @@ -0,0 +1,9 @@ +process { + + publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" } + + + withName: GATK4_SPLITINTERVALS { + ext.args = "--scatter-count 2" + } +} \ No newline at end of file diff --git a/tests/modules/gatk4/splitintervals/test.yml b/tests/modules/gatk4/splitintervals/test.yml new file mode 100644 index 00000000..dc0ea6ba --- /dev/null +++ b/tests/modules/gatk4/splitintervals/test.yml @@ -0,0 +1,25 @@ +- name: gatk4 splitintervals test_gatk4_splitintervals_bed + command: nextflow run tests/modules/gatk4/splitintervals -entry test_gatk4_splitintervals_bed -c tests/config/nextflow.config + tags: + - gatk4/splitintervals + - gatk4 + files: + - path: output/gatk4/test/0000-scattered.interval_list + md5sum: c8d6b19e7a92535b6ce9608eae558faa + - path: output/gatk4/test/0001-scattered.interval_list + md5sum: b1877ad96aec308906594c50ebbe3ded + - path: output/gatk4/versions.yml + md5sum: c7b9068d84e0e05412f50e86d5b87078 + +- name: gatk4 splitintervals test_gatk4_splitintervals_intervals + command: nextflow run tests/modules/gatk4/splitintervals -entry test_gatk4_splitintervals_intervals -c tests/config/nextflow.config + tags: + - gatk4/splitintervals + - gatk4 + files: + - path: output/gatk4/test/0000-scattered.interval_list + md5sum: ebd6b34a335efc6732ff541936c6d2d5 + - path: output/gatk4/test/0001-scattered.interval_list + md5sum: 9459b0e124fa84ec1e64ac4615bc9af7 + - path: output/gatk4/versions.yml + md5sum: 4eec8245944ad3be4cc22403c6ffb877 From 9d53577282ecb9d683ba93f9741dd4e721b2fcba Mon Sep 17 00:00:00 2001 From: Nicolas Vannieuwkerke Date: Fri, 13 May 2022 13:48:33 +0200 Subject: [PATCH 5/9] linting --- modules/gatk4/splitintervals/main.nf | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/modules/gatk4/splitintervals/main.nf b/modules/gatk4/splitintervals/main.nf index d9407b95..d575191f 100644 --- a/modules/gatk4/splitintervals/main.nf +++ b/modules/gatk4/splitintervals/main.nf @@ -37,7 +37,7 @@ process GATK4_SPLITINTERVALS { --output ${prefix} \\ --intervals $intervals \\ $reference \\ - $args + $args cat <<-END_VERSIONS > versions.yml "${task.process}": From d1f824ae66f432301bf1325ab8fa48825aa43bac Mon Sep 17 00:00:00 2001 From: Nicolas Vannieuwkerke Date: Fri, 13 May 2022 14:21:48 +0200 Subject: [PATCH 6/9] updated meta.yml --- modules/gatk4/splitintervals/main.nf | 2 +- modules/gatk4/splitintervals/meta.yml | 12 ++++++++++++ 2 files changed, 13 insertions(+), 1 deletion(-) diff --git a/modules/gatk4/splitintervals/main.nf b/modules/gatk4/splitintervals/main.nf index d575191f..adb72dfb 100644 --- a/modules/gatk4/splitintervals/main.nf +++ b/modules/gatk4/splitintervals/main.nf @@ -11,7 +11,7 @@ process GATK4_SPLITINTERVALS { tuple val(meta), path(intervals) path(fasta) path(fasta_fai) - path(fasta_dict) + path(dict) output: tuple val(meta), path("**.interval_list"), emit: split_intervals diff --git a/modules/gatk4/splitintervals/meta.yml b/modules/gatk4/splitintervals/meta.yml index 6cf7cedc..ba557544 100644 --- a/modules/gatk4/splitintervals/meta.yml +++ b/modules/gatk4/splitintervals/meta.yml @@ -21,6 +21,18 @@ input: type: file description: Interval list or BED pattern: "*.{interval,interval_list,bed}" + - fasta: + type: file + description: Reference FASTA + pattern: "*.{fa,fasta}" + - fasta_fai: + type: file + description: Reference FASTA index + pattern: "*.fai" + - dict: + type: file + description: Reference sequence dictionary + pattern: "*.dict" output: - meta: From 1c2a99142928c6ba2d32226168e6755263784474 Mon Sep 17 00:00:00 2001 From: Nicolas Vannieuwkerke Date: Fri, 13 May 2022 14:25:53 +0200 Subject: [PATCH 7/9] fixed memory warning --- modules/gatk4/splitintervals/main.nf | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/modules/gatk4/splitintervals/main.nf b/modules/gatk4/splitintervals/main.nf index adb72dfb..3ab5a71b 100644 --- a/modules/gatk4/splitintervals/main.nf +++ b/modules/gatk4/splitintervals/main.nf @@ -27,7 +27,7 @@ process GATK4_SPLITINTERVALS { def avail_mem = 3 if (!task.memory) { - log.info '[GATK IntervalListToBed] Available memory not known - defaulting to 3GB. Specify process memory requirements to change this.' + log.info '[GATK SplitIntervals] Available memory not known - defaulting to 3GB. Specify process memory requirements to change this.' } else { avail_mem = task.memory.giga } From a72f06dfe8ce6f29d90f3f952bf5700019ff4d14 Mon Sep 17 00:00:00 2001 From: Nicolas Vannieuwkerke Date: Fri, 13 May 2022 14:27:59 +0200 Subject: [PATCH 8/9] removed versions checksum --- tests/modules/gatk4/splitintervals/test.yml | 2 -- 1 file changed, 2 deletions(-) diff --git a/tests/modules/gatk4/splitintervals/test.yml b/tests/modules/gatk4/splitintervals/test.yml index dc0ea6ba..741c6bec 100644 --- a/tests/modules/gatk4/splitintervals/test.yml +++ b/tests/modules/gatk4/splitintervals/test.yml @@ -9,7 +9,6 @@ - path: output/gatk4/test/0001-scattered.interval_list md5sum: b1877ad96aec308906594c50ebbe3ded - path: output/gatk4/versions.yml - md5sum: c7b9068d84e0e05412f50e86d5b87078 - name: gatk4 splitintervals test_gatk4_splitintervals_intervals command: nextflow run tests/modules/gatk4/splitintervals -entry test_gatk4_splitintervals_intervals -c tests/config/nextflow.config @@ -22,4 +21,3 @@ - path: output/gatk4/test/0001-scattered.interval_list md5sum: 9459b0e124fa84ec1e64ac4615bc9af7 - path: output/gatk4/versions.yml - md5sum: 4eec8245944ad3be4cc22403c6ffb877 From 6427eeeca04790574303b13ba473594fdf725821 Mon Sep 17 00:00:00 2001 From: Nicolas Vannieuwkerke Date: Fri, 13 May 2022 14:35:22 +0200 Subject: [PATCH 9/9] added tmp-dir + alignment correction --- modules/gatk4/splitintervals/main.nf | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/modules/gatk4/splitintervals/main.nf b/modules/gatk4/splitintervals/main.nf index 3ab5a71b..9df66c21 100644 --- a/modules/gatk4/splitintervals/main.nf +++ b/modules/gatk4/splitintervals/main.nf @@ -15,7 +15,7 @@ process GATK4_SPLITINTERVALS { output: tuple val(meta), path("**.interval_list"), emit: split_intervals - path "versions.yml" , emit: versions + path "versions.yml" , emit: versions when: task.ext.when == null || task.ext.when @@ -37,6 +37,7 @@ process GATK4_SPLITINTERVALS { --output ${prefix} \\ --intervals $intervals \\ $reference \\ + --tmp-dir . \\ $args cat <<-END_VERSIONS > versions.yml