From 89eee34df9a98a170af185cc4bd4f28b6816741a Mon Sep 17 00:00:00 2001 From: Chris Cheshire Date: Wed, 16 Dec 2020 11:04:46 +0000 Subject: [PATCH 01/42] seacr | Added callpeak skeletonmain.nf --- software/seacr/callpeak/functions.nf | 59 ++++++++++++++++++++++++++++ software/seacr/callpeak/main.nf | 0 software/seacr/callpeak/meta.yml | 0 3 files changed, 59 insertions(+) create mode 100644 software/seacr/callpeak/functions.nf create mode 100644 software/seacr/callpeak/main.nf create mode 100644 software/seacr/callpeak/meta.yml diff --git a/software/seacr/callpeak/functions.nf b/software/seacr/callpeak/functions.nf new file mode 100644 index 00000000..b3ac3801 --- /dev/null +++ b/software/seacr/callpeak/functions.nf @@ -0,0 +1,59 @@ +/* + * ----------------------------------------------------- + * Utility functions used in nf-core DSL2 module files + * ----------------------------------------------------- + */ + +/* + * Extract name of software tool from process name using $task.process + */ +def getSoftwareName(task_process) { + return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase() +} + +/* + * Function to initialise default values and to generate a Groovy Map of available options for nf-core modules + */ +def initOptions(Map args) { + def Map options = [:] + options.args = args.args ?: '' + options.args2 = args.args2 ?: '' + options.publish_by_id = args.publish_by_id ?: false + options.publish_dir = args.publish_dir ?: '' + options.publish_files = args.publish_files + options.suffix = args.suffix ?: '' + return options +} + +/* + * Tidy up and join elements of a list to return a path string + */ +def getPathFromList(path_list) { + def paths = path_list.findAll { item -> !item?.trim().isEmpty() } // Remove empty entries + paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes + return paths.join('/') +} + +/* + * Function to save/publish module results + */ +def saveFiles(Map args) { + if (!args.filename.endsWith('.version.txt')) { + def ioptions = initOptions(args.options) + def path_list = [ ioptions.publish_dir ?: args.publish_dir ] + if (ioptions.publish_by_id) { + path_list.add(args.publish_id) + } + if (ioptions.publish_files instanceof Map) { + for (ext in ioptions.publish_files) { + if (args.filename.endsWith(ext.key)) { + def ext_list = path_list.collect() + ext_list.add(ext.value) + return "${getPathFromList(ext_list)}/$args.filename" + } + } + } else if (ioptions.publish_files == null) { + return "${getPathFromList(path_list)}/$args.filename" + } + } +} diff --git a/software/seacr/callpeak/main.nf b/software/seacr/callpeak/main.nf new file mode 100644 index 00000000..e69de29b diff --git a/software/seacr/callpeak/meta.yml b/software/seacr/callpeak/meta.yml new file mode 100644 index 00000000..e69de29b From 3ff2b558e026840044ad7e446c30342a39ca9b7e Mon Sep 17 00:00:00 2001 From: Chris Cheshire Date: Wed, 16 Dec 2020 11:04:46 +0000 Subject: [PATCH 02/42] seacr | Added callpeak skeleton --- software/seacr/callpeak/functions.nf | 59 ++++++++++++++++++++++++++++ software/seacr/callpeak/main.nf | 0 software/seacr/callpeak/meta.yml | 0 3 files changed, 59 insertions(+) create mode 100644 software/seacr/callpeak/functions.nf create mode 100644 software/seacr/callpeak/main.nf create mode 100644 software/seacr/callpeak/meta.yml diff --git a/software/seacr/callpeak/functions.nf b/software/seacr/callpeak/functions.nf new file mode 100644 index 00000000..b3ac3801 --- /dev/null +++ b/software/seacr/callpeak/functions.nf @@ -0,0 +1,59 @@ +/* + * ----------------------------------------------------- + * Utility functions used in nf-core DSL2 module files + * ----------------------------------------------------- + */ + +/* + * Extract name of software tool from process name using $task.process + */ +def getSoftwareName(task_process) { + return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase() +} + +/* + * Function to initialise default values and to generate a Groovy Map of available options for nf-core modules + */ +def initOptions(Map args) { + def Map options = [:] + options.args = args.args ?: '' + options.args2 = args.args2 ?: '' + options.publish_by_id = args.publish_by_id ?: false + options.publish_dir = args.publish_dir ?: '' + options.publish_files = args.publish_files + options.suffix = args.suffix ?: '' + return options +} + +/* + * Tidy up and join elements of a list to return a path string + */ +def getPathFromList(path_list) { + def paths = path_list.findAll { item -> !item?.trim().isEmpty() } // Remove empty entries + paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes + return paths.join('/') +} + +/* + * Function to save/publish module results + */ +def saveFiles(Map args) { + if (!args.filename.endsWith('.version.txt')) { + def ioptions = initOptions(args.options) + def path_list = [ ioptions.publish_dir ?: args.publish_dir ] + if (ioptions.publish_by_id) { + path_list.add(args.publish_id) + } + if (ioptions.publish_files instanceof Map) { + for (ext in ioptions.publish_files) { + if (args.filename.endsWith(ext.key)) { + def ext_list = path_list.collect() + ext_list.add(ext.value) + return "${getPathFromList(ext_list)}/$args.filename" + } + } + } else if (ioptions.publish_files == null) { + return "${getPathFromList(path_list)}/$args.filename" + } + } +} diff --git a/software/seacr/callpeak/main.nf b/software/seacr/callpeak/main.nf new file mode 100644 index 00000000..e69de29b diff --git a/software/seacr/callpeak/meta.yml b/software/seacr/callpeak/meta.yml new file mode 100644 index 00000000..e69de29b From 74e7b5385f3fb1a5c37c65a3f2b6a9d45ea9f8f2 Mon Sep 17 00:00:00 2001 From: Chris Cheshire Date: Thu, 17 Dec 2020 13:54:48 +0000 Subject: [PATCH 03/42] seacr | Added main process structure --- software/seacr/callpeak/main.nf | 41 +++++++++++++++++++++++++++++++++ 1 file changed, 41 insertions(+) diff --git a/software/seacr/callpeak/main.nf b/software/seacr/callpeak/main.nf index e69de29b..3fcdf05d 100644 --- a/software/seacr/callpeak/main.nf +++ b/software/seacr/callpeak/main.nf @@ -0,0 +1,41 @@ +// Import generic module functions +include { initOptions; saveFiles; getSoftwareName } from './functions' + +params.options = [:] +def options = initOptions(params.options) + +process SEACR_CALLPEAK { + tag "$meta.id" + label 'process_medium' + publishDir "${params.outdir}", + mode: params.publish_dir_mode, + saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) } + + conda (params.enable_conda ? "bioconda::seacr=1.3" : null) + + if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) { + container "https://depot.galaxyproject.org/singularity/mulled-v2-03bfeb32fe80910c231f630d4262b83677c8c0f4:5bb5ed4307a8187a7f34730b00431de93688fa59-0" + } else { + container 'quay.io/biocontainers/mulled-v2-03bfeb32fe80910c231f630d4262b83677c8c0f4:5bb5ed4307a8187a7f34730b00431de93688fa59-0' + } + + input: + tuple val(meta), path(bedgraph), path(ctrlbedgraph) + + output: + tuple val(meta), path("*.bed"), emit: bed + path "*.version.txt" , emit: version + + script: + def software = getSoftwareName(task.process) + def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}" + """ + SEACR_1.3.sh \\ + $bedgraph \\ + $ctrlbedgraph \\ + $options.args \\ + $prefix + + echo 1.3' > ${software}.version.txt + """ +} From a964d98d7fe2c9047bf6052ab9c683a5abd525f8 Mon Sep 17 00:00:00 2001 From: Chris Cheshire Date: Thu, 17 Dec 2020 13:55:58 +0000 Subject: [PATCH 04/42] seacr | Added test data --- tests/data/bedgraph/IgG_1_to_chr20.bedgraph | 10234 +++++++++ tests/data/bedgraph/IgG_2_to_chr20.bedgraph | 6879 ++++++ .../data/bedgraph/K27me3_1_to_chr20.bedgraph | 12451 ++++++++++ .../data/bedgraph/K27me3_2_to_chr20.bedgraph | 18871 ++++++++++++++++ 4 files changed, 48435 insertions(+) create mode 100644 tests/data/bedgraph/IgG_1_to_chr20.bedgraph create mode 100644 tests/data/bedgraph/IgG_2_to_chr20.bedgraph create mode 100644 tests/data/bedgraph/K27me3_1_to_chr20.bedgraph create mode 100644 tests/data/bedgraph/K27me3_2_to_chr20.bedgraph diff --git a/tests/data/bedgraph/IgG_1_to_chr20.bedgraph 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64300529 64300547 2 +chr20 64300547 64300647 1 +chr20 64301105 64301530 1 +chr20 64301794 64301839 1 +chr20 64301891 64302096 1 +chr20 64303315 64303437 1 +chr20 64303542 64303754 1 +chr20 64305179 64305388 1 +chr20 64305437 64305640 1 +chr20 64306044 64306211 1 +chr20 64306394 64306674 1 +chr20 64308558 64308794 1 +chr20 64309474 64309644 1 +chr20 64311291 64311449 1 +chr20 64312156 64312320 1 +chr20 64317219 64317292 1 +chr20 64317502 64317569 1 +chr20 64318772 64319009 1 +chr20 64319031 64319426 1 +chr20 64320226 64320302 1 +chr20 64322070 64322281 1 +chr20 64324086 64324294 1 +chr20 64325070 64325126 1 +chr20 64326421 64326668 1 +chr20 64330211 64330377 1 +chr20 64331721 64331776 1 +chr20 64332986 64333145 1 +chr20 64333543 64333582 1 +chr20 64333696 64333876 1 +chr20 64333978 64334003 1 From 4e55bdcf8432b36f67425d62d60c91bfaa6f80e4 Mon Sep 17 00:00:00 2001 From: Chris Cheshire Date: Thu, 17 Dec 2020 14:20:02 +0000 Subject: [PATCH 05/42] seacr | removed test files --- tests/data/bedgraph/IgG_2_to_chr20.bedgraph | 6879 ------ .../data/bedgraph/K27me3_2_to_chr20.bedgraph | 18871 ---------------- 2 files changed, 25750 deletions(-) delete mode 100644 tests/data/bedgraph/IgG_2_to_chr20.bedgraph delete mode 100644 tests/data/bedgraph/K27me3_2_to_chr20.bedgraph diff --git a/tests/data/bedgraph/IgG_2_to_chr20.bedgraph b/tests/data/bedgraph/IgG_2_to_chr20.bedgraph deleted file mode 100644 index d3ed1a15..00000000 --- a/tests/data/bedgraph/IgG_2_to_chr20.bedgraph +++ /dev/null @@ -1,6879 +0,0 @@ -chr20 73727 73778 1 -chr20 91394 91867 1 -chr20 105695 106077 1 -chr20 113055 113100 1 -chr20 186287 186506 1 -chr20 202498 202857 1 -chr20 203511 203585 1 -chr20 204073 204180 1 -chr20 206279 206599 1 -chr20 214906 214990 1 -chr20 215766 215963 1 -chr20 233447 233525 1 -chr20 248723 248824 1 -chr20 278935 278976 1 -chr20 279089 279126 1 -chr20 294970 295447 1 -chr20 297365 297514 1 -chr20 306586 306652 1 -chr20 314411 314598 1 -chr20 325463 325770 1 -chr20 360452 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64326421 64326668 1 -chr20 64330211 64330377 1 -chr20 64331721 64331776 1 -chr20 64332986 64333145 1 -chr20 64333543 64333582 1 -chr20 64333696 64333876 1 -chr20 64333978 64334003 1 From b24834dfce788212f29268651321215282545983 Mon Sep 17 00:00:00 2001 From: Chris Cheshire Date: Thu, 17 Dec 2020 14:20:24 +0000 Subject: [PATCH 06/42] seacr | local testing implimented --- software/seacr/callpeak/main.nf | 2 +- tests/software/seacr/main.nf | 20 +++++++++++++++ tests/software/seacr/test.yml | 44 +++++++++++++++++++++++++++++++++ 3 files changed, 65 insertions(+), 1 deletion(-) create mode 100644 tests/software/seacr/main.nf create mode 100644 tests/software/seacr/test.yml diff --git a/software/seacr/callpeak/main.nf b/software/seacr/callpeak/main.nf index 3fcdf05d..289b0151 100644 --- a/software/seacr/callpeak/main.nf +++ b/software/seacr/callpeak/main.nf @@ -36,6 +36,6 @@ process SEACR_CALLPEAK { $options.args \\ $prefix - echo 1.3' > ${software}.version.txt + echo 1.3 > ${software}.version.txt """ } diff --git a/tests/software/seacr/main.nf b/tests/software/seacr/main.nf new file mode 100644 index 00000000..7e3c4164 --- /dev/null +++ b/tests/software/seacr/main.nf @@ -0,0 +1,20 @@ +#!/usr/bin/env nextflow + +nextflow.enable.dsl = 2 + +include { SEACR_CALLPEAK } from '../../../software/seacr/callpeak/main.nf' addParams( options: [ args:'norm stringent' ] ) + +workflow test_seacr_callpeak { + + def input = [] + input = [[ id:'test_1'], + file("${launchDir}/tests/data/bedgraph/K27me3_1_to_chr20.bedgraph", checkIfExists: true), + file("${launchDir}/tests/data/bedgraph/IgG_1_to_chr20.bedgraph", checkIfExists: true) ] + + SEACR_CALLPEAK ( input ) +} + +// For local testing +workflow { + test_seacr_callpeak() +} \ No newline at end of file diff --git a/tests/software/seacr/test.yml b/tests/software/seacr/test.yml new file mode 100644 index 00000000..e9ec7ad7 --- /dev/null +++ b/tests/software/seacr/test.yml @@ -0,0 +1,44 @@ +- name: Run samtools call peak test workflow + command: nextflow run ./tests/software/samtools/ -profile docker -entry test_samtools_flagstat -c tests/config/nextflow.config + tags: + - samtools + - samtools_flagstat + files: + - path: output/samtools/test.paired_end.sorted.bam.flagstat + md5sum: 80590621c74f5ee43ada20d010a3837f + +- name: Run samtools idxstats test workflow + command: nextflow run ./tests/software/samtools/ -profile docker -entry test_samtools_idxstats -c tests/config/nextflow.config + tags: + - samtools + - samtools_idxstats + files: + - path: output/samtools/test.paired_end.sorted.bam.idxstats + md5sum: 3bee8b7d55e412da2b3816c5a18d60d5 + +- name: Run samtools index test workflow + command: nextflow run ./tests/software/samtools/ -profile docker -entry test_samtools_index -c tests/config/nextflow.config + tags: + - samtools + - samtools_index + files: + - path: output/samtools/test.paired_end.sorted.bam.bai + md5sum: 67338c2995eae82c849830ca55aa7bd1 + +- name: Run samtools sort test workflow + command: nextflow run ./tests/software/samtools/ -profile docker -entry test_samtools_sort -c tests/config/nextflow.config + tags: + - samtools + - samtools_sort + files: + - path: output/samtools/test.bam + md5sum: a41bfadacd2eeef1d31e05c135cc4f4e + +- name: Run samtools stats test workflow + command: nextflow run ./tests/software/samtools/ -profile docker -entry test_samtools_stats -c tests/config/nextflow.config + tags: + - samtools + - samtools_stats + files: + - path: output/samtools/test.paired_end.sorted.bam.stats + md5sum: 06c183864d6e47ab89b0650cae831a93 From 1aa7ed187a4a22ee92e3a0f42de2beccf748eab3 Mon Sep 17 00:00:00 2001 From: Chris Cheshire Date: Thu, 17 Dec 2020 14:23:07 +0000 Subject: [PATCH 07/42] seacr | Updated gitignore to ignore output folder --- .gitignore | 1 + 1 file changed, 1 insertion(+) diff --git a/.gitignore b/.gitignore index 54d7a8c1..4e3815b1 100644 --- a/.gitignore +++ b/.gitignore @@ -2,5 +2,6 @@ work/ results/ test_output/ +output/ .DS_Store *.code-workspace From a57169a5dab1f84285962e1e04a9fb2108651d67 Mon Sep 17 00:00:00 2001 From: Chris Cheshire Date: Thu, 17 Dec 2020 14:23:20 +0000 Subject: [PATCH 08/42] seacr | updated test script --- tests/software/seacr/test.yml | 48 +++++------------------------------ 1 file changed, 6 insertions(+), 42 deletions(-) diff --git a/tests/software/seacr/test.yml b/tests/software/seacr/test.yml index e9ec7ad7..88568d35 100644 --- a/tests/software/seacr/test.yml +++ b/tests/software/seacr/test.yml @@ -1,44 +1,8 @@ -- name: Run samtools call peak test workflow - command: nextflow run ./tests/software/samtools/ -profile docker -entry test_samtools_flagstat -c tests/config/nextflow.config +- name: Run seacr call peak test workflow + command: nextflow run ./tests/software/seacr/ -profile docker -entry test_seacr_callpeak -c tests/config/nextflow.config tags: - - samtools - - samtools_flagstat + - seacr + - seacr_callpeak files: - - path: output/samtools/test.paired_end.sorted.bam.flagstat - md5sum: 80590621c74f5ee43ada20d010a3837f - -- name: Run samtools idxstats test workflow - command: nextflow run ./tests/software/samtools/ -profile docker -entry test_samtools_idxstats -c tests/config/nextflow.config - tags: - - samtools - - samtools_idxstats - files: - - path: output/samtools/test.paired_end.sorted.bam.idxstats - md5sum: 3bee8b7d55e412da2b3816c5a18d60d5 - -- name: Run samtools index test workflow - command: nextflow run ./tests/software/samtools/ -profile docker -entry test_samtools_index -c tests/config/nextflow.config - tags: - - samtools - - samtools_index - files: - - path: output/samtools/test.paired_end.sorted.bam.bai - md5sum: 67338c2995eae82c849830ca55aa7bd1 - -- name: Run samtools sort test workflow - command: nextflow run ./tests/software/samtools/ -profile docker -entry test_samtools_sort -c tests/config/nextflow.config - tags: - - samtools - - samtools_sort - files: - - path: output/samtools/test.bam - md5sum: a41bfadacd2eeef1d31e05c135cc4f4e - -- name: Run samtools stats test workflow - command: nextflow run ./tests/software/samtools/ -profile docker -entry test_samtools_stats -c tests/config/nextflow.config - tags: - - samtools - - samtools_stats - files: - - path: output/samtools/test.paired_end.sorted.bam.stats - md5sum: 06c183864d6e47ab89b0650cae831a93 + - path: output/seacr/test_1.stringent.bed + md5sum: 3ac70475669eb6a7b8ca89e19a08a28e \ No newline at end of file From 15e1b860f9a7cd436152a0faec2fb6626ea31839 Mon Sep 17 00:00:00 2001 From: Chris Cheshire Date: Thu, 17 Dec 2020 14:25:42 +0000 Subject: [PATCH 09/42] seacr | added github action workflow --- .github/workflows/seacr_callpeak.yml | 40 ++++++++++++++++++++++++++++ 1 file changed, 40 insertions(+) create mode 100644 .github/workflows/seacr_callpeak.yml diff --git a/.github/workflows/seacr_callpeak.yml b/.github/workflows/seacr_callpeak.yml new file mode 100644 index 00000000..8d342495 --- /dev/null +++ b/.github/workflows/seacr_callpeak.yml @@ -0,0 +1,40 @@ +name: seacr_callpeak +on: + push: + paths: + - software/seacr/callpeak/** + - .github/workflows/seacr_callpeak.yml + - tests/software/seacr/** + pull_request: + paths: + - software/seacr/callpeak/** + - .github/workflows/seacr_callpeak.yml + - tests/software/seacr/** + +jobs: + ci_test: + runs-on: ubuntu-latest + strategy: + matrix: + nxf_version: [20.11.0-edge] + env: + NXF_ANSI_LOG: false + steps: + - uses: actions/checkout@v2 + + - name: Install Nextflow + env: + NXF_VER: ${{ matrix.nxf_version }} + run: | + wget -qO- get.nextflow.io | bash + sudo mv nextflow /usr/local/bin/ + + - name: Set up Python + uses: actions/setup-python@v2 + with: + python-version: "3.x" + - name: Install dependencies + run: python -m pip install --upgrade pip pytest-workflow + + # Test the module + - run: pytest --tag samtools_flagstat --symlink --wt 2 From 4436f59a1cb1ffe53e7d13d27d99c8feb388602f Mon Sep 17 00:00:00 2001 From: Chris Cheshire Date: Thu, 17 Dec 2020 14:27:37 +0000 Subject: [PATCH 10/42] seacr | Syntax error --- .github/workflows/seacr_callpeak.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/seacr_callpeak.yml b/.github/workflows/seacr_callpeak.yml index 8d342495..3d73a43e 100644 --- a/.github/workflows/seacr_callpeak.yml +++ b/.github/workflows/seacr_callpeak.yml @@ -37,4 +37,4 @@ jobs: run: python -m pip install --upgrade pip pytest-workflow # Test the module - - run: pytest --tag samtools_flagstat --symlink --wt 2 + - run: pytest --tag seacr_callpeak --symlink --wt 2 From 9c00d1722c4ae6b8c658175f9511ce412a894053 Mon Sep 17 00:00:00 2001 From: Chris Cheshire Date: Tue, 5 Jan 2021 09:50:47 +0000 Subject: [PATCH 11/42] seacr | PR review changes --- software/seacr/callpeak/main.nf | 9 +++++---- 1 file changed, 5 insertions(+), 4 deletions(-) diff --git a/software/seacr/callpeak/main.nf b/software/seacr/callpeak/main.nf index 289b0151..19523c7f 100644 --- a/software/seacr/callpeak/main.nf +++ b/software/seacr/callpeak/main.nf @@ -4,6 +4,8 @@ include { initOptions; saveFiles; getSoftwareName } from './functions' params.options = [:] def options = initOptions(params.options) +def VERSION = '1.3' + process SEACR_CALLPEAK { tag "$meta.id" label 'process_medium' @@ -11,8 +13,7 @@ process SEACR_CALLPEAK { mode: params.publish_dir_mode, saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) } - conda (params.enable_conda ? "bioconda::seacr=1.3" : null) - + conda (params.enable_conda ? "bioconda::seacr=1.3 conda-forge::r-base=4.0.2 bioconda::bedtools=2.29.2" : null) if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) { container "https://depot.galaxyproject.org/singularity/mulled-v2-03bfeb32fe80910c231f630d4262b83677c8c0f4:5bb5ed4307a8187a7f34730b00431de93688fa59-0" } else { @@ -30,12 +31,12 @@ process SEACR_CALLPEAK { def software = getSoftwareName(task.process) def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}" """ - SEACR_1.3.sh \\ + SEACR_1.3.sh \\ $bedgraph \\ $ctrlbedgraph \\ $options.args \\ $prefix - echo 1.3 > ${software}.version.txt + echo $VERSION > ${software}.version.txt """ } From 37840b3855ce8eccc640103b304700f39e0a8793 Mon Sep 17 00:00:00 2001 From: Chris Cheshire Date: Tue, 5 Jan 2021 09:54:32 +0000 Subject: [PATCH 12/42] seacr | updated trailing whitespace --- software/seacr/callpeak/main.nf | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/software/seacr/callpeak/main.nf b/software/seacr/callpeak/main.nf index 19523c7f..7931e31a 100644 --- a/software/seacr/callpeak/main.nf +++ b/software/seacr/callpeak/main.nf @@ -19,10 +19,10 @@ process SEACR_CALLPEAK { } else { container 'quay.io/biocontainers/mulled-v2-03bfeb32fe80910c231f630d4262b83677c8c0f4:5bb5ed4307a8187a7f34730b00431de93688fa59-0' } - + input: tuple val(meta), path(bedgraph), path(ctrlbedgraph) - + output: tuple val(meta), path("*.bed"), emit: bed path "*.version.txt" , emit: version @@ -39,4 +39,4 @@ process SEACR_CALLPEAK { echo $VERSION > ${software}.version.txt """ -} +} \ No newline at end of file From c110088b5e72760345725b464f333f9a220cc172 Mon Sep 17 00:00:00 2001 From: Chris Cheshire Date: Tue, 5 Jan 2021 09:56:15 +0000 Subject: [PATCH 13/42] Updated line endings --- software/seacr/callpeak/functions.nf | 118 +++++++++++++-------------- 1 file changed, 59 insertions(+), 59 deletions(-) diff --git a/software/seacr/callpeak/functions.nf b/software/seacr/callpeak/functions.nf index b3ac3801..d25eea86 100644 --- a/software/seacr/callpeak/functions.nf +++ b/software/seacr/callpeak/functions.nf @@ -1,59 +1,59 @@ -/* - * ----------------------------------------------------- - * Utility functions used in nf-core DSL2 module files - * ----------------------------------------------------- - */ - -/* - * Extract name of software tool from process name using $task.process - */ -def getSoftwareName(task_process) { - return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase() -} - -/* - * Function to initialise default values and to generate a Groovy Map of available options for nf-core modules - */ -def initOptions(Map args) { - def Map options = [:] - options.args = args.args ?: '' - options.args2 = args.args2 ?: '' - options.publish_by_id = args.publish_by_id ?: false - options.publish_dir = args.publish_dir ?: '' - options.publish_files = args.publish_files - options.suffix = args.suffix ?: '' - return options -} - -/* - * Tidy up and join elements of a list to return a path string - */ -def getPathFromList(path_list) { - def paths = path_list.findAll { item -> !item?.trim().isEmpty() } // Remove empty entries - paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes - return paths.join('/') -} - -/* - * Function to save/publish module results - */ -def saveFiles(Map args) { - if (!args.filename.endsWith('.version.txt')) { - def ioptions = initOptions(args.options) - def path_list = [ ioptions.publish_dir ?: args.publish_dir ] - if (ioptions.publish_by_id) { - path_list.add(args.publish_id) - } - if (ioptions.publish_files instanceof Map) { - for (ext in ioptions.publish_files) { - if (args.filename.endsWith(ext.key)) { - def ext_list = path_list.collect() - ext_list.add(ext.value) - return "${getPathFromList(ext_list)}/$args.filename" - } - } - } else if (ioptions.publish_files == null) { - return "${getPathFromList(path_list)}/$args.filename" - } - } -} +/* + * ----------------------------------------------------- + * Utility functions used in nf-core DSL2 module files + * ----------------------------------------------------- + */ + +/* + * Extract name of software tool from process name using $task.process + */ +def getSoftwareName(task_process) { + return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase() +} + +/* + * Function to initialise default values and to generate a Groovy Map of available options for nf-core modules + */ +def initOptions(Map args) { + def Map options = [:] + options.args = args.args ?: '' + options.args2 = args.args2 ?: '' + options.publish_by_id = args.publish_by_id ?: false + options.publish_dir = args.publish_dir ?: '' + options.publish_files = args.publish_files + options.suffix = args.suffix ?: '' + return options +} + +/* + * Tidy up and join elements of a list to return a path string + */ +def getPathFromList(path_list) { + def paths = path_list.findAll { item -> !item?.trim().isEmpty() } // Remove empty entries + paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes + return paths.join('/') +} + +/* + * Function to save/publish module results + */ +def saveFiles(Map args) { + if (!args.filename.endsWith('.version.txt')) { + def ioptions = initOptions(args.options) + def path_list = [ ioptions.publish_dir ?: args.publish_dir ] + if (ioptions.publish_by_id) { + path_list.add(args.publish_id) + } + if (ioptions.publish_files instanceof Map) { + for (ext in ioptions.publish_files) { + if (args.filename.endsWith(ext.key)) { + def ext_list = path_list.collect() + ext_list.add(ext.value) + return "${getPathFromList(ext_list)}/$args.filename" + } + } + } else if (ioptions.publish_files == null) { + return "${getPathFromList(path_list)}/$args.filename" + } + } +} From e25edbf7b8180043791ce6295ab669efbd0f0e64 Mon Sep 17 00:00:00 2001 From: Chris Cheshire Date: Tue, 5 Jan 2021 10:18:00 +0000 Subject: [PATCH 14/42] seacr | Added meta file --- software/seacr/callpeak/meta.yml | 69 ++++++++++++++++++++++++++++++++ 1 file changed, 69 insertions(+) diff --git a/software/seacr/callpeak/meta.yml b/software/seacr/callpeak/meta.yml index e69de29b..3f7cbabc 100644 --- a/software/seacr/callpeak/meta.yml +++ b/software/seacr/callpeak/meta.yml @@ -0,0 +1,69 @@ +name: seacr_callpeak +description: Call peaks using SEACR on sequenced reads in bedgraph format +keywords: + - peak-caller + - peaks + - bedgraph + - cut&tag + - cut&run + - chromatin + - seacr +tools: + - seacr: + description: | + SEACR is intended to call peaks and enriched regions from sparse CUT&RUN + or chromatin profiling data in which background is dominated by "zeroes" + (i.e. regions with no read coverage). + homepage: https://github.com/FredHutch/SEACR + documentation: https://github.com/FredHutch/SEACR +params: + - outdir: + type: string + description: | + The pipeline's output directory. By default, the module will + output files into `$params.outdir/` + - publish_dir_mode: + type: string + description: | + Value for the Nextflow `publishDir` mode parameter. + Available: symlink, rellink, link, copy, copyNoFollow, move. + - enable_conda: + type: boolean + description: | + Run the module with Conda using the software specified + via the `conda` directive + - singularity_pull_docker_container: + type: boolean + description: | + Instead of directly downloading Singularity images for use with Singularity, + force the workflow to pull and convert Docker containers instead. +input: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bedgraph: + type: file + description: | + The target bedgraph file from which the peaks will be calculated. + - ctrlbedgraph: + type: file + description: | + Control (IgG) data bedgraph file to generate an empirical threshold for peak calling. +output: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bed: + type: file + description: Bed file containing the calculated peaks. + pattern: "*.bed" + - version: + type: file + description: File containing software version + pattern: "*.{version.txt}" +authors: + - "@chris-cheshire" \ No newline at end of file From 6d34e6964fe4eed6a9a5eedb652c97de28f5839b Mon Sep 17 00:00:00 2001 From: Chris Cheshire Date: Tue, 5 Jan 2021 10:20:13 +0000 Subject: [PATCH 15/42] seacr | added new line at end --- software/seacr/callpeak/main.nf | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/software/seacr/callpeak/main.nf b/software/seacr/callpeak/main.nf index 7931e31a..3d67a058 100644 --- a/software/seacr/callpeak/main.nf +++ b/software/seacr/callpeak/main.nf @@ -39,4 +39,4 @@ process SEACR_CALLPEAK { echo $VERSION > ${software}.version.txt """ -} \ No newline at end of file +} From d9818cf3ab6149b6eb277ebea178ee73311bb8b9 Mon Sep 17 00:00:00 2001 From: Chris Cheshire Date: Tue, 5 Jan 2021 10:21:32 +0000 Subject: [PATCH 16/42] seacr | updated whitespace --- software/seacr/callpeak/meta.yml | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/software/seacr/callpeak/meta.yml b/software/seacr/callpeak/meta.yml index 3f7cbabc..4efedd4f 100644 --- a/software/seacr/callpeak/meta.yml +++ b/software/seacr/callpeak/meta.yml @@ -11,9 +11,9 @@ keywords: tools: - seacr: description: | - SEACR is intended to call peaks and enriched regions from sparse CUT&RUN - or chromatin profiling data in which background is dominated by "zeroes" - (i.e. regions with no read coverage). + SEACR is intended to call peaks and enriched regions from sparse CUT&RUN + or chromatin profiling data in which background is dominated by "zeroes" + (i.e. regions with no read coverage). homepage: https://github.com/FredHutch/SEACR documentation: https://github.com/FredHutch/SEACR params: @@ -66,4 +66,4 @@ output: description: File containing software version pattern: "*.{version.txt}" authors: - - "@chris-cheshire" \ No newline at end of file + - "@chris-cheshire" From f6432d3c9c64460f66d6e9ddd16e19e4e902ec91 Mon Sep 17 00:00:00 2001 From: Chris Cheshire Date: Tue, 5 Jan 2021 10:22:37 +0000 Subject: [PATCH 17/42] seacr | updated whitespace --- software/seacr/callpeak/meta.yml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/software/seacr/callpeak/meta.yml b/software/seacr/callpeak/meta.yml index 4efedd4f..f95725c9 100644 --- a/software/seacr/callpeak/meta.yml +++ b/software/seacr/callpeak/meta.yml @@ -12,8 +12,8 @@ tools: - seacr: description: | SEACR is intended to call peaks and enriched regions from sparse CUT&RUN - or chromatin profiling data in which background is dominated by "zeroes" - (i.e. regions with no read coverage). + or chromatin profiling data in which background is dominated by "zeroes" + (i.e. regions with no read coverage). homepage: https://github.com/FredHutch/SEACR documentation: https://github.com/FredHutch/SEACR params: From 10bb80743a738a9dd18326f4eae36fef686f6f48 Mon Sep 17 00:00:00 2001 From: kevinmenden Date: Fri, 29 Jan 2021 16:06:14 +0100 Subject: [PATCH 18/42] started adding quast modules --- software/quast/quast_noref/functions.nf | 59 ++++++++++++++++++++++++ software/quast/quast_noref/main.nf | 41 +++++++++++++++++ software/quast/quast_noref/meta.yml | 54 ++++++++++++++++++++++ software/quast/quast_ref/functions.nf | 59 ++++++++++++++++++++++++ software/quast/quast_ref/main.nf | 46 +++++++++++++++++++ software/quast/quast_ref/meta.yml | 61 +++++++++++++++++++++++++ tests/software/quast/main.nf | 20 ++++++++ tests/software/quast/test.yml | 0 8 files changed, 340 insertions(+) create mode 100644 software/quast/quast_noref/functions.nf create mode 100644 software/quast/quast_noref/main.nf create mode 100644 software/quast/quast_noref/meta.yml create mode 100644 software/quast/quast_ref/functions.nf create mode 100644 software/quast/quast_ref/main.nf create mode 100644 software/quast/quast_ref/meta.yml create mode 100644 tests/software/quast/main.nf create mode 100644 tests/software/quast/test.yml diff --git a/software/quast/quast_noref/functions.nf b/software/quast/quast_noref/functions.nf new file mode 100644 index 00000000..d25eea86 --- /dev/null +++ b/software/quast/quast_noref/functions.nf @@ -0,0 +1,59 @@ +/* + * ----------------------------------------------------- + * Utility functions used in nf-core DSL2 module files + * ----------------------------------------------------- + */ + +/* + * Extract name of software tool from process name using $task.process + */ +def getSoftwareName(task_process) { + return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase() +} + +/* + * Function to initialise default values and to generate a Groovy Map of available options for nf-core modules + */ +def initOptions(Map args) { + def Map options = [:] + options.args = args.args ?: '' + options.args2 = args.args2 ?: '' + options.publish_by_id = args.publish_by_id ?: false + options.publish_dir = args.publish_dir ?: '' + options.publish_files = args.publish_files + options.suffix = args.suffix ?: '' + return options +} + +/* + * Tidy up and join elements of a list to return a path string + */ +def getPathFromList(path_list) { + def paths = path_list.findAll { item -> !item?.trim().isEmpty() } // Remove empty entries + paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes + return paths.join('/') +} + +/* + * Function to save/publish module results + */ +def saveFiles(Map args) { + if (!args.filename.endsWith('.version.txt')) { + def ioptions = initOptions(args.options) + def path_list = [ ioptions.publish_dir ?: args.publish_dir ] + if (ioptions.publish_by_id) { + path_list.add(args.publish_id) + } + if (ioptions.publish_files instanceof Map) { + for (ext in ioptions.publish_files) { + if (args.filename.endsWith(ext.key)) { + def ext_list = path_list.collect() + ext_list.add(ext.value) + return "${getPathFromList(ext_list)}/$args.filename" + } + } + } else if (ioptions.publish_files == null) { + return "${getPathFromList(path_list)}/$args.filename" + } + } +} diff --git a/software/quast/quast_noref/main.nf b/software/quast/quast_noref/main.nf new file mode 100644 index 00000000..2ad9ac79 --- /dev/null +++ b/software/quast/quast_noref/main.nf @@ -0,0 +1,41 @@ +// Import generic module functions +include { initOptions; saveFiles; getSoftwareName } from './functions' + +params.options = [:] +def options = initOptions(params.options) + +process QUAST { + tag "$fasta" + label 'process_medium' + publishDir "${params.outdir}", + mode: params.publish_dir_mode, + saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:'') } + + conda (params.enable_conda ? 'bioconda::quast=5.0.2' : null) + if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) { + container 'https://depot.galaxyproject.org/singularity/quast:5.0.2--py37pl526hb5aa323_2' + } else { + container 'quay.io/biocontainers/quast:5.0.2--py37pl526hb5aa323_2' + } + + input: + path consensus + + output: + path "${prefix}" , emit: results + path '*.tsv' , emit: tsv + path '*.version.txt', emit: version + + script: + def software = getSoftwareName(task.process) + prefix = options.suffix ?: software + """ + quast.py \\ + --output-dir $prefix \\ + --threads $task.cpus \\ + $options.args \\ + $consensus + ln -s ${prefix}/report.tsv + echo \$(quast.py --version 2>&1) | sed 's/^.*QUAST v//; s/ .*\$//' > ${software}.version.txt + """ +} diff --git a/software/quast/quast_noref/meta.yml b/software/quast/quast_noref/meta.yml new file mode 100644 index 00000000..9b46bf42 --- /dev/null +++ b/software/quast/quast_noref/meta.yml @@ -0,0 +1,54 @@ +name: quast +description: Quality Assessment Tool for Genome Assemblies +keywords: + - quast + - assembly + - quality +tools: + - star: + description: | + QUAST calculate quality metrics for genome assemblies + homepage: http://bioinf.spbau.ru/quast + doi: +params: + - outdir: + type: string + description: | + The pipeline's output directory. By default, the module will + output files into `$params.outdir/` + - publish_dir_mode: + type: string + description: | + Value for the Nextflow `publishDir` mode parameter. + Available: symlink, rellink, link, copy, copyNoFollow, move. + - enable_conda: + type: boolean + description: | + Run the module with Conda using the software specified + via the `conda` directive + - singularity_pull_docker_container: + type: boolean + description: | + Instead of directly downloading Singularity images for use with Singularity, + force the workflow to pull and convert Docker containers instead. + +input: + - consensus: + type: map + description: | + Groovy Map containing sample information + +output: + - report: + type: file + description: The lineage report + pattern: "{prefix}.lineage_report.csv" + + - version: + type: file + description: File containing software version + pattern: "*.{version.txt}" + +authors: + - "@drpatelh" + - "@kevinmenden" diff --git a/software/quast/quast_ref/functions.nf b/software/quast/quast_ref/functions.nf new file mode 100644 index 00000000..d25eea86 --- /dev/null +++ b/software/quast/quast_ref/functions.nf @@ -0,0 +1,59 @@ +/* + * ----------------------------------------------------- + * Utility functions used in nf-core DSL2 module files + * ----------------------------------------------------- + */ + +/* + * Extract name of software tool from process name using $task.process + */ +def getSoftwareName(task_process) { + return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase() +} + +/* + * Function to initialise default values and to generate a Groovy Map of available options for nf-core modules + */ +def initOptions(Map args) { + def Map options = [:] + options.args = args.args ?: '' + options.args2 = args.args2 ?: '' + options.publish_by_id = args.publish_by_id ?: false + options.publish_dir = args.publish_dir ?: '' + options.publish_files = args.publish_files + options.suffix = args.suffix ?: '' + return options +} + +/* + * Tidy up and join elements of a list to return a path string + */ +def getPathFromList(path_list) { + def paths = path_list.findAll { item -> !item?.trim().isEmpty() } // Remove empty entries + paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes + return paths.join('/') +} + +/* + * Function to save/publish module results + */ +def saveFiles(Map args) { + if (!args.filename.endsWith('.version.txt')) { + def ioptions = initOptions(args.options) + def path_list = [ ioptions.publish_dir ?: args.publish_dir ] + if (ioptions.publish_by_id) { + path_list.add(args.publish_id) + } + if (ioptions.publish_files instanceof Map) { + for (ext in ioptions.publish_files) { + if (args.filename.endsWith(ext.key)) { + def ext_list = path_list.collect() + ext_list.add(ext.value) + return "${getPathFromList(ext_list)}/$args.filename" + } + } + } else if (ioptions.publish_files == null) { + return "${getPathFromList(path_list)}/$args.filename" + } + } +} diff --git a/software/quast/quast_ref/main.nf b/software/quast/quast_ref/main.nf new file mode 100644 index 00000000..0a811445 --- /dev/null +++ b/software/quast/quast_ref/main.nf @@ -0,0 +1,46 @@ +// Import generic module functions +include { initOptions; saveFiles; getSoftwareName } from './functions' + +params.options = [:] +def options = initOptions(params.options) + +process QUAST { + tag "$fasta" + label 'process_medium' + publishDir "${params.outdir}", + mode: params.publish_dir_mode, + saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:'') } + + conda (params.enable_conda ? 'bioconda::quast=5.0.2' : null) + if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) { + container 'https://depot.galaxyproject.org/singularity/quast:5.0.2--py37pl526hb5aa323_2' + } else { + container 'quay.io/biocontainers/quast:5.0.2--py37pl526hb5aa323_2' + } + + input: + path consensus + path fasta + path gff + + output: + path "${prefix}" , emit: results + path '*.tsv' , emit: tsv + path '*.version.txt', emit: version + + script: + def software = getSoftwareName(task.process) + prefix = options.suffix ?: software + def features = params.gff ? "--features $gff" : '' + """ + quast.py \\ + --output-dir $prefix \\ + -r $fasta \\ + $features \\ + --threads $task.cpus \\ + $options.args \\ + ${consensus.join(' ')} + ln -s ${prefix}/report.tsv + echo \$(quast.py --version 2>&1) | sed 's/^.*QUAST v//; s/ .*\$//' > ${software}.version.txt + """ +} diff --git a/software/quast/quast_ref/meta.yml b/software/quast/quast_ref/meta.yml new file mode 100644 index 00000000..a1ca27b3 --- /dev/null +++ b/software/quast/quast_ref/meta.yml @@ -0,0 +1,61 @@ +name: quast +description: Quality Assessment Tool for Genome Assemblies +keywords: + - quast + - assembly + - quality +tools: + - star: + description: | + QUAST calculate quality metrics for genome assemblies + homepage: http://bioinf.spbau.ru/quast + doi: +params: + - outdir: + type: string + description: | + The pipeline's output directory. By default, the module will + output files into `$params.outdir/` + - publish_dir_mode: + type: string + description: | + Value for the Nextflow `publishDir` mode parameter. + Available: symlink, rellink, link, copy, copyNoFollow, move. + - enable_conda: + type: boolean + description: | + Run the module with Conda using the software specified + via the `conda` directive + - singularity_pull_docker_container: + type: boolean + description: | + Instead of directly downloading Singularity images for use with Singularity, + force the workflow to pull and convert Docker containers instead. + +input: + - consensus: + type: map + description: | + Groovy Map containing sample information + - fasta: + type: file + description: | + The genome assembly to be evaluated + - gff: + type: file + description: The genome GFF file + +output: + - report: + type: file + description: The lineage report + pattern: "{prefix}.lineage_report.csv" + + - version: + type: file + description: File containing software version + pattern: "*.{version.txt}" + +authors: + - "@drpatelh" + - "@kevinmenden" diff --git a/tests/software/quast/main.nf b/tests/software/quast/main.nf new file mode 100644 index 00000000..366b0c90 --- /dev/null +++ b/tests/software/quast/main.nf @@ -0,0 +1,20 @@ +#!/usr/bin/env nextflow + +nextflow.enable.dsl = 2 + +include { QUAST as QUAST_NOREF } from '../../../software/quast/quast_noref/main.nf' addParams(options: [:]) +include { QUAST as QUAST_REF } from '../../../software/quast/quast_ref/main.nf' addParams(options: [:]) + +workflow test_quast_noref { + consensus = file("${launchDir}/tests/data/fasta/sarscov2/GCA_011545545.1_ASM1154554v1_genomic.fna", checkIfExists: true) + + QUAST_NOREF( consensus ) +} + +workflow test_quast_ref { + consensus = file("${launchDir}/tests/data/fasta/sarscov2/GCA_011545545.1_ASM1154554v1_cds_from_genomic.fna", checkIfExists: true) + gff = file("${launchDir}/tests/data/gff/sarscov2/GCA_011545545.1_ASM1154554v1_genomic.gtf", checkIfExists: true) + fasta = file("${launchDir}/tests/data/fasta/sarscov2/GCA_011545545.1_ASM1154554v1_genomic.fna", checkIfExists: true) + + QUAST_REF( consensus, fasta, gff ) +} diff --git a/tests/software/quast/test.yml b/tests/software/quast/test.yml new file mode 100644 index 00000000..e69de29b From e8bd730164f01b9409a87968ed54c55ad40b7fd0 Mon Sep 17 00:00:00 2001 From: kevinmenden Date: Fri, 29 Jan 2021 16:14:33 +0100 Subject: [PATCH 19/42] added quast tests --- tests/software/quast/test.yml | 114 ++++++++++++++++++++++++++++++++++ 1 file changed, 114 insertions(+) diff --git a/tests/software/quast/test.yml b/tests/software/quast/test.yml index e69de29b..6d895298 100644 --- a/tests/software/quast/test.yml +++ b/tests/software/quast/test.yml @@ -0,0 +1,114 @@ +- name: quast_ref + command: nextflow run ./tests/software/quast -profile docker -entry test_quast_ref -c ./tests/config/nextflow.config + tags: + - quast + - quast_reference + files: + - path: ./output/quast/quast/contigs_reports/transposed_report_misassemblies.tsv + md5sum: 4d24cc0da823a100a076aef36f9fd75e + - path: ./output/quast/quast/contigs_reports/GCA_011545545_1_ASM1154554v1_cds_from_genomic.mis_contigs.fa + - path: ./output/quast/quast/contigs_reports/contigs_report_GCA_011545545-1_ASM1154554v1_cds_from_genomic.stdout + - path: ./output/quast/quast/aligned_stats/NGAx_plot.pdf + - path: ./output/quast/quast/report.pdf + - path: ./output/quast/quast/contigs_reports/misassemblies_report.tex + md5sum: ffe19cf4d5332952f0627e9cd82e3375 + - path: ./output/quast/quast/aligned_stats/NAx_plot.pdf + - path: ./output/quast/quast/icarus.html + - path: ./output/quast/quast/report.tsv + md5sum: 503ebb57ffed0422fd7aff4025e21143 + - path: ./output/quast/quast/contigs_reports/transposed_report_misassemblies.tex + md5sum: 85614257e0bb62ac750f7872886b2fbf + - path: ./output/quast/quast/basic_stats/gc.icarus.txt + md5sum: b3a770802ff9b2dd4ee8e47bddb2df3e + - path: ./output/quast/quast/aligned_stats/cumulative_plot.pdf + - path: ./output/quast/quast/contigs_reports/minimap_output/GCA_011545545-1_ASM1154554v1_cds_from_genomic.coords.filtered + md5sum: ec9191d0acb5d5bce56b4842551a8598 + - path: ./output/quast/quast/basic_stats/Nx_plot.pdf + - path: ./output/quast/quast/contigs_reports/minimap_output/GCA_011545545-1_ASM1154554v1_cds_from_genomic.coords + md5sum: dda3fc0addc41ecc0d5183dee6f95886 + - path: ./output/quast/quast/contigs_reports/minimap_output/GCA_011545545-1_ASM1154554v1_cds_from_genomic.coords_tmp + md5sum: ce66eaeb99fdc11e4d50efadc1816e04 + - path: ./output/quast/quast/contigs_reports/unaligned_report.tsv + md5sum: 769f2d9d7deb5e7a63e238d8ba0cfe13 + - path: ./output/quast/quast/basic_stats/GC_content_plot.pdf + - path: ./output/quast/quast/contigs_reports/contigs_report_GCA_011545545-1_ASM1154554v1_cds_from_genomic.mis_contigs.info + md5sum: d41d8cd98f00b204e9800998ecf8427e + - path: ./output/quast/quast/contigs_reports/contigs_report_GCA_011545545-1_ASM1154554v1_cds_from_genomic.unaligned.info + md5sum: a8505cf206bf53ca369f7e3073fee587 + - path: ./output/quast/quast/contigs_reports/minimap_output/GCA_011545545-1_ASM1154554v1_cds_from_genomic.sf + - path: ./output/quast/quast/transposed_report.txt + md5sum: 389e9fa2b29b967cb658c0770c941ce6 + - path: ./output/quast/quast/genome_stats/GCA_011545545-1_ASM1154554v1_cds_from_genomic_gaps.txt + md5sum: c52381f09ea40b6141be5232494727b6 + - path: ./output/quast/quast/quast.log + - path: ./output/quast/report.tsv + md5sum: 503ebb57ffed0422fd7aff4025e21143 + - path: ./output/quast/quast/contigs_reports/transposed_report_misassemblies.txt + md5sum: 53c481fe8b3ef18280ea86cbded78b31 + - path: ./output/quast/quast/contigs_reports/unaligned_report.txt + md5sum: c1c26797084ea743ec5a224ab97adb1f + - path: ./output/quast/quast/report.txt + md5sum: 41bf3c24e68afce5ef0ba91004e57f7d + - path: ./output/quast/quast/transposed_report.tex + md5sum: 2a69aada90cc1e788a4bc877c44d79c8 + - path: ./output/quast/quast/basic_stats/GCA_011545545.1_ASM1154554v1_cds_from_genomic_GC_content_plot.pdf + - path: ./output/quast/quast/contigs_reports/misassemblies_report.tsv + md5sum: 33144f8d064782864e8400e3a08b2a3a + - path: ./output/quast/quast/contigs_reports/unaligned_report.tex + md5sum: 48562e30903fcf33946e13b602b0e324 + - path: ./output/quast/quast/contigs_reports/misassemblies_plot.pdf + - path: ./output/quast/quast/transposed_report.tsv + md5sum: baab35c91e87432432113db1e4085f7b + - path: ./output/quast/quast/report.tex + md5sum: 8e72428ff7e7175bf47d58c10d8332e8 + - path: ./output/quast/quast/contigs_reports/misassemblies_frcurve_plot.pdf + - path: ./output/quast/quast/contigs_reports/minimap_output/GCA_011545545-1_ASM1154554v1_cds_from_genomic.used_snps.gz + md5sum: 7b1db1b433cd95243a949bcb72e7e3a6 + - path: ./output/quast/quast/contigs_reports/misassemblies_report.txt + md5sum: 0784e0d31e9f2a165730cc0029023427 + - path: ./output/quast/quast/icarus_viewers/alignment_viewer.html + md5sum: bd63165a204a2ab424f8e81c647038d1 + - path: ./output/quast/quast/contigs_reports/all_alignments_GCA_011545545-1_ASM1154554v1_cds_from_genomic.tsv + md5sum: c247152eb82b361106492642fd796e2c + - path: ./output/quast/quast/genome_stats/genome_info.txt + md5sum: 7c622ab66040d413a229419bf6b5181f + - path: ./output/quast/quast/basic_stats/NGx_plot.pdf + - path: ./output/quast/quast/contigs_reports/minimap_output/GCA_011545545-1_ASM1154554v1_cds_from_genomic.unaligned + md5sum: d41d8cd98f00b204e9800998ecf8427e + - path: ./output/quast/quast/contigs_reports/contigs_report_GCA_011545545-1_ASM1154554v1_cds_from_genomic.stderr + - path: ./output/quast/quast/icarus_viewers/contig_size_viewer.html + md5sum: c42838b1553759fb0460a9854e39da36 + - path: ./output/quast/quast/report.html + - path: ./output/quast/quast/basic_stats/cumulative_plot.pdf + +- name: quast_noref + command: nextflow run ./tests/software/quast -profile docker -entry test_quast_noref -c ./tests/config/nextflow.config + tags: + - quast + - quast_no_reference + files: + - path: ./output/quast/quast/report.pdf + - path: ./output/quast/quast/basic_stats/GC_content_plot.pdf + - path: ./output/quast/quast/transposed_report.tsv + md5sum: 1a82adfc057b6dc788034a6ce023cb56 + - path: ./output/quast/quast/basic_stats/Nx_plot.pdf + - path: ./output/quast/quast/quast.log + - path: ./output/quast/quast/basic_stats/cumulative_plot.pdf + - path: ./output/quast/quast/transposed_report.tex + md5sum: a86aa094f9ab4bc1df35c5a7add2d0b0 + - path: ./output/quast/quast/basic_stats/GCA_011545545.1_ASM1154554v1_genomic_GC_content_plot.pdf + - path: ./output/quast/quast/report.txt + md5sum: 7a2e442c18dd2730cfd38723f1c9c8f9 + - path: ./output/quast/quast/icarus_viewers/contig_size_viewer.html + md5sum: dcf600c49ee86783475cb25215072630 + - path: ./output/quast/quast/report.tsv + md5sum: 75882c0a5d811246395f5ea56146ce76 + - path: ./output/quast/quast/report.tex + md5sum: 132edd2e916fc2a76a7b13973a0ffa4b + - path: ./output/quast/quast/icarus.html + md5sum: 9d7429362288c5078e6d6e7efcfc1ff7 + - path: ./output/quast/quast/transposed_report.txt + md5sum: 154d88ec197c7b1bda5938232a79a00a + - path: ./output/quast/report.tsv + md5sum: 75882c0a5d811246395f5ea56146ce76 + - path: ./output/quast/quast/report.html From 34cfc32c29c7435f4463120714e708b60788ba81 Mon Sep 17 00:00:00 2001 From: kevinmenden Date: Fri, 29 Jan 2021 16:15:45 +0100 Subject: [PATCH 20/42] added quast workflow --- .github/workflows/quast.yml | 40 +++++++++++++++++++++++++++++++++++++ 1 file changed, 40 insertions(+) create mode 100644 .github/workflows/quast.yml diff --git a/.github/workflows/quast.yml b/.github/workflows/quast.yml new file mode 100644 index 00000000..7030d638 --- /dev/null +++ b/.github/workflows/quast.yml @@ -0,0 +1,40 @@ +name: quast +on: + push: + paths: + - software/quast/** + - .github/workflows/quast.yml + - tests + pull_request: + paths: + - software/pquast/** + - .github/workflows/quest.yml + - tests + +jobs: + ci_test: + runs-on: ubuntu-latest + strategy: + matrix: + nxf_version: [20.11.0-edge] + env: + NXF_ANSI_LOG: false + steps: + - uses: actions/checkout@v2 + + - name: Install Nextflow + env: + NXF_VER: ${{ matrix.nxf_version }} + run: | + wget -qO- get.nextflow.io | bash + sudo mv nextflow /usr/local/bin/ + + - name: Set up Python + uses: actions/setup-python@v2 + with: + python-version: "3.x" + - name: Install dependencies + run: python -m pip install --upgrade pip pytest-workflow + + # Test the module + - run: pytest --tag quest --symlink --wt 2 From 2f9934c563293fc1517451a92f0777af23abceb3 Mon Sep 17 00:00:00 2001 From: JoseEspinosa Date: Fri, 29 Jan 2021 18:57:27 +0100 Subject: [PATCH 21/42] Adding bowtie2_build module --- software/bowtie2/build/functions.nf | 60 +++++++++++++++++++++++++++++ software/bowtie2/build/main.nf | 35 +++++++++++++++++ software/bowtie2/build/meta.yml | 51 ++++++++++++++++++++++++ 3 files changed, 146 insertions(+) create mode 100644 software/bowtie2/build/functions.nf create mode 100644 software/bowtie2/build/main.nf create mode 100644 software/bowtie2/build/meta.yml diff --git a/software/bowtie2/build/functions.nf b/software/bowtie2/build/functions.nf new file mode 100644 index 00000000..6f3b4b29 --- /dev/null +++ b/software/bowtie2/build/functions.nf @@ -0,0 +1,60 @@ + +/* + * ----------------------------------------------------- + * Utility functions used in nf-core DSL2 module files + * ----------------------------------------------------- + */ + +/* + * Extract name of software tool from process name using $task.process + */ +def getSoftwareName(task_process) { + return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase() +} + +/* + * Function to initialise default values and to generate a Groovy Map of available options for nf-core modules + */ +def initOptions(Map args) { + def Map options = [:] + options.args = args.args ?: '' + options.args2 = args.args2 ?: '' + options.publish_by_id = args.publish_by_id ?: false + options.publish_dir = args.publish_dir ?: '' + options.publish_files = args.publish_files + options.suffix = args.suffix ?: '' + return options +} + +/* + * Tidy up and join elements of a list to return a path string + */ +def getPathFromList(path_list) { + def paths = path_list.findAll { item -> !item?.trim().isEmpty() } // Remove empty entries + paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", '') } // Trim whitespace and trailing slashes + return paths.join('/') +} + +/* + * Function to save/publish module results + */ +def saveFiles(Map args) { + if (!args.filename.endsWith('.version.txt')) { + def ioptions = initOptions(args.options) + def path_list = [ ioptions.publish_dir ?: args.publish_dir ] + if (ioptions.publish_by_id) { + path_list.add(args.publish_id) + } + if (ioptions.publish_files instanceof Map) { + for (ext in ioptions.publish_files) { + if (args.filename.endsWith(ext.key)) { + def ext_list = path_list.collect() + ext_list.add(ext.value) + return "${getPathFromList(ext_list)}/$args.filename" + } + } + } else if (ioptions.publish_files == null) { + return "${getPathFromList(path_list)}/$args.filename" + } + } +} diff --git a/software/bowtie2/build/main.nf b/software/bowtie2/build/main.nf new file mode 100644 index 00000000..b2ff6fb8 --- /dev/null +++ b/software/bowtie2/build/main.nf @@ -0,0 +1,35 @@ +// Import generic module functions +include { initOptions; saveFiles; getSoftwareName } from './functions' + +params.options = [:] +def options = initOptions(params.options) + +process BOWTIE2_BUILD { + tag "$fasta" + label 'process_high' + publishDir "${params.outdir}", + mode: params.publish_dir_mode, + saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:'') } + + conda (params.enable_conda ? 'bioconda::bowtie2=2.4.2' : null) + if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) { + container 'https://depot.galaxyproject.org/singularity/bowtie2:2.4.2--py38h1c8e9b9_1' + } else { + container 'quay.io/biocontainers/bowtie2:2.4.2--py38h1c8e9b9_1' + } + + input: + path fasta + + output: + path 'bowtie2' , emit: index + path '*.version.txt', emit: version + + script: + def software = getSoftwareName(task.process) + """ + mkdir bowtie2 + bowtie2-build $options.args --threads $task.cpus $fasta bowtie2/${fasta.baseName} + echo \$(bowtie2 --version 2>&1) | sed 's/^.*bowtie2-align-s version //; s/ .*\$//' > ${software}.version.txt + """ +} diff --git a/software/bowtie2/build/meta.yml b/software/bowtie2/build/meta.yml new file mode 100644 index 00000000..f9d43138 --- /dev/null +++ b/software/bowtie2/build/meta.yml @@ -0,0 +1,51 @@ +name: bowtie2_build +description: Builds bowtie index for reference genome +keywords: + - build + - index + - fasta + - genome + - reference +tools: + - bowtie: + description: | + Bowtie 2 is an ultrafast and memory-efficient tool for aligning sequencing reads to long reference sequences. + homepage: http://bowtie-bio.sourceforge.net/bowtie2/index.shtml + documentation: http://bowtie-bio.sourceforge.net/bowtie2/manual.shtml + doi: 10.1038/nmeth.1923 +params: + - outdir: + type: string + description: | + The pipeline's output directory. By default, the module will + output files into `$params.outdir/` + - publish_dir_mode: + type: string + description: | + Value for the Nextflow `publishDir` mode parameter. + Available: symlink, rellink, link, copy, copyNoFollow, move. + - enable_conda: + type: boolean + description: | + Run the module with Conda using the software specified + via the `conda` directive + - singularity_pull_docker_container: + type: boolean + description: | + Instead of directly downloading Singularity images for use with Singularity, + force the workflow to pull and convert Docker containers instead. +input: + - fasta: + type: file + description: Input genome fasta file +output: + - index: + type: file + description: Bowtie2 genome index files + pattern: "*.bt2" + - version: + type: file + description: File containing software version + pattern: "*.{version.txt}" +authors: + - "@kevinmenden" From 43f9815621d7517ff88d15ac32c7f735575494a8 Mon Sep 17 00:00:00 2001 From: JoseEspinosa Date: Fri, 29 Jan 2021 19:29:32 +0100 Subject: [PATCH 22/42] Adding module bowtie2 align --- software/bowtie2/align/functions.nf | 60 ++++++++++++++++++++++++ software/bowtie2/align/main.nf | 72 +++++++++++++++++++++++++++++ software/bowtie2/build/meta.yml | 7 ++- 3 files changed, 137 insertions(+), 2 deletions(-) create mode 100644 software/bowtie2/align/functions.nf create mode 100644 software/bowtie2/align/main.nf diff --git a/software/bowtie2/align/functions.nf b/software/bowtie2/align/functions.nf new file mode 100644 index 00000000..6f3b4b29 --- /dev/null +++ b/software/bowtie2/align/functions.nf @@ -0,0 +1,60 @@ + +/* + * ----------------------------------------------------- + * Utility functions used in nf-core DSL2 module files + * ----------------------------------------------------- + */ + +/* + * Extract name of software tool from process name using $task.process + */ +def getSoftwareName(task_process) { + return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase() +} + +/* + * Function to initialise default values and to generate a Groovy Map of available options for nf-core modules + */ +def initOptions(Map args) { + def Map options = [:] + options.args = args.args ?: '' + options.args2 = args.args2 ?: '' + options.publish_by_id = args.publish_by_id ?: false + options.publish_dir = args.publish_dir ?: '' + options.publish_files = args.publish_files + options.suffix = args.suffix ?: '' + return options +} + +/* + * Tidy up and join elements of a list to return a path string + */ +def getPathFromList(path_list) { + def paths = path_list.findAll { item -> !item?.trim().isEmpty() } // Remove empty entries + paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", '') } // Trim whitespace and trailing slashes + return paths.join('/') +} + +/* + * Function to save/publish module results + */ +def saveFiles(Map args) { + if (!args.filename.endsWith('.version.txt')) { + def ioptions = initOptions(args.options) + def path_list = [ ioptions.publish_dir ?: args.publish_dir ] + if (ioptions.publish_by_id) { + path_list.add(args.publish_id) + } + if (ioptions.publish_files instanceof Map) { + for (ext in ioptions.publish_files) { + if (args.filename.endsWith(ext.key)) { + def ext_list = path_list.collect() + ext_list.add(ext.value) + return "${getPathFromList(ext_list)}/$args.filename" + } + } + } else if (ioptions.publish_files == null) { + return "${getPathFromList(path_list)}/$args.filename" + } + } +} diff --git a/software/bowtie2/align/main.nf b/software/bowtie2/align/main.nf new file mode 100644 index 00000000..4c018aa9 --- /dev/null +++ b/software/bowtie2/align/main.nf @@ -0,0 +1,72 @@ +// Import generic module functions +include { initOptions; saveFiles; getSoftwareName } from './functions' + +params.options = [:] +def options = initOptions(params.options) + +process BOWTIE2_ALIGN { + tag "$meta.id" + label 'process_high' + publishDir "${params.outdir}", + mode: params.publish_dir_mode, + saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) } + + conda (params.enable_conda ? 'bioconda::bowtie2=2.4.2 bioconda::samtools=1.11 conda-forge::pigz=2.3.4' : null) + if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) { + container "https://depot.galaxyproject.org/singularity/mulled-v2-ac74a7f02cebcfcc07d8e8d1d750af9c83b4d45a:577a697be67b5ae9b16f637fd723b8263a3898b3-0" + } else { + container "quay.io/biocontainers/mulled-v2-ac74a7f02cebcfcc07d8e8d1d750af9c83b4d45a:577a697be67b5ae9b16f637fd723b8263a3898b3-0" + } + + input: + tuple val(meta), path(reads) + path index + + output: + tuple val(meta), path('*.bam'), emit: bam + tuple val(meta), path('*.log'), emit: log + path '*.version.txt' , emit: version + tuple val(meta), path('*fastq.gz'), optional:true, emit: fastq + + script: + def software = getSoftwareName(task.process) + def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}" + if (meta.single_end) { + def unaligned = params.save_unaligned ? "--un-gz ${prefix}.unmapped.fastq.gz" : '' + """ + INDEX=`find -L ./ -name "*.rev.1.bt2" | sed 's/.rev.1.bt2//'` + bowtie2 \\ + -x \$INDEX \\ + -U $reads \\ + --threads $task.cpus \\ + $unaligned \\ + $options.args \\ + 2> ${prefix}.bowtie2.log \\ + | samtools view -@ $task.cpus $options.args2 -bhS -o ${prefix}.bam - + + echo \$(bowtie2 --version 2>&1) | sed 's/^.*bowtie2-align-s version //; s/ .*\$//' > ${software}.version.txt + """ + } else { + def unaligned = params.save_unaligned ? "--un-conc-gz ${prefix}.unmapped.fastq.gz" : '' + """ + INDEX=`find -L ./ -name "*.rev.1.bt2" | sed 's/.rev.1.bt2//'` + bowtie2 \\ + -x \$INDEX \\ + -1 ${reads[0]} \\ + -2 ${reads[1]} \\ + --threads $task.cpus \\ + $unaligned \\ + $options.args \\ + 2> ${prefix}.bowtie2.log \\ + | samtools view -@ $task.cpus $options.args2 -bhS -o ${prefix}.bam - + + if [ -f ${prefix}.unmapped.fastq.1.gz ]; then + mv ${prefix}.unmapped.fastq.1.gz ${prefix}.unmapped_1.fastq.gz + fi + if [ -f ${prefix}.unmapped.fastq.2.gz ]; then + mv ${prefix}.unmapped.fastq.2.gz ${prefix}.unmapped_2.fastq.gz + fi + echo \$(bowtie2 --version 2>&1) | sed 's/^.*bowtie2-align-s version //; s/ .*\$//' > ${software}.version.txt + """ + } +} diff --git a/software/bowtie2/build/meta.yml b/software/bowtie2/build/meta.yml index f9d43138..e4330967 100644 --- a/software/bowtie2/build/meta.yml +++ b/software/bowtie2/build/meta.yml @@ -7,9 +7,10 @@ keywords: - genome - reference tools: - - bowtie: + - bowtie2: description: | - Bowtie 2 is an ultrafast and memory-efficient tool for aligning sequencing reads to long reference sequences. + Bowtie 2 is an ultrafast and memory-efficient tool for aligning + sequencing reads to long reference sequences. homepage: http://bowtie-bio.sourceforge.net/bowtie2/index.shtml documentation: http://bowtie-bio.sourceforge.net/bowtie2/manual.shtml doi: 10.1038/nmeth.1923 @@ -49,3 +50,5 @@ output: pattern: "*.{version.txt}" authors: - "@kevinmenden" + - "@joseespinosa" + - "drpatelh" From ddbe8055c2c59d36a94e332bf4224ab032d5cd13 Mon Sep 17 00:00:00 2001 From: JoseEspinosa Date: Fri, 29 Jan 2021 19:31:33 +0100 Subject: [PATCH 23/42] Adding tests --- software/bowtie2/align/meta.yml | 75 +++++++++++++++++++++++++++++++++ tests/software/bowtie2/main.nf | 33 +++++++++++++++ tests/software/bowtie2/test.yml | 64 ++++++++++++++++++++++++++++ 3 files changed, 172 insertions(+) create mode 100644 software/bowtie2/align/meta.yml create mode 100644 tests/software/bowtie2/main.nf create mode 100644 tests/software/bowtie2/test.yml diff --git a/software/bowtie2/align/meta.yml b/software/bowtie2/align/meta.yml new file mode 100644 index 00000000..9a2ecf40 --- /dev/null +++ b/software/bowtie2/align/meta.yml @@ -0,0 +1,75 @@ +name: bowtie2_align +description: Align reads to a reference genome using bowtie2 +keywords: + - align + - fasta + - genome + - reference +tools: + - bowtie2: + description: | + Bowtie 2 is an ultrafast and memory-efficient tool for aligning + sequencing reads to long reference sequences. + homepage: http://bowtie-bio.sourceforge.net/bowtie2/index.shtml + documentation: http://bowtie-bio.sourceforge.net/bowtie2/manual.shtml + doi: 10.1038/nmeth.1923 +params: + - outdir: + type: string + description: | + The pipeline's output directory. By default, the module will + output files into `$params.outdir/` + - publish_dir_mode: + type: string + description: | + Value for the Nextflow `publishDir` mode parameter. + Available: symlink, rellink, link, copy, copyNoFollow, move. + - enable_conda: + type: boolean + description: | + Run the module with Conda using the software specified + via the `conda` directive + - singularity_pull_docker_container: + type: boolean + description: | + Instead of directly downloading Singularity images for use with Singularity, + force the workflow to pull and convert Docker containers instead. + - save_unaligned: + type: boolean + description: Save unaligned reads +input: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - reads: + type: file + description: | + List of input FastQ files of size 1 and 2 for single-end and paired-end data, + respectively. + - index: + type: file + description: Bowtie2 genome index files + pattern: "*.ebwt" +output: + - bam: + type: file + description: Output BAM file containing read alignments + pattern: "*.{bam}" + - version: + type: file + description: File containing software version + pattern: "*.{version.txt}" + - fastq: + type: file + description: Unaligned FastQ files + pattern: "*.fastq.gz" + - log: + type: file + description: Aligment log + pattern: "*.log" +authors: + - "@kevinmenden" + - "@joseespinosa" + - "@drpatelh" diff --git a/tests/software/bowtie2/main.nf b/tests/software/bowtie2/main.nf new file mode 100644 index 00000000..a5a56cae --- /dev/null +++ b/tests/software/bowtie2/main.nf @@ -0,0 +1,33 @@ +#!/usr/bin/env nextflow + +nextflow.enable.dsl = 2 + +include { BOWTIE2_BUILD } from '../../../software/bowtie2/build/main.nf' addParams( options: [:] ) +include { BOWTIE2_ALIGN } from '../../../software/bowtie2/align/main.nf' addParams( options: [:] ) + +workflow test_bowtie2_build { + fasta = file("${launchDir}/tests/data/fasta/E_coli/NC_010473.fa", checkIfExists: true) + BOWTIE2_BUILD ( fasta ) +} + +workflow test_bowtie2_alignment_single_end { + + fasta = file("${launchDir}/tests/data/fasta/E_coli/NC_010473.fa", checkIfExists: true) + BOWTIE2_BUILD ( fasta ) + + def input = [] + input = [ [ id:'test', single_end:true ], // meta map + [ file("${launchDir}/tests/data/fastq/rna/test_R1.fastq.gz", checkIfExists: true) ] ] + BOWTIE2_ALIGN ( input, BOWTIE2_BUILD.out.index ) +} + +workflow test_bowtie2_alignment_paired_end { + fasta = file("${launchDir}/tests/data/fasta/E_coli/NC_010473.fa", checkIfExists: true) + BOWTIE2_BUILD ( fasta ) + + def input = [] + input = [ [ id:'test', single_end:false ], // meta map + [ file("${launchDir}/tests/data/fastq/rna/test_R1.fastq.gz", checkIfExists: true), + file("${launchDir}/tests/data/fastq/rna/test_R2.fastq.gz", checkIfExists: true) ] ] + BOWTIE2_ALIGN ( input, BOWTIE2_BUILD.out.index ) +} diff --git a/tests/software/bowtie2/test.yml b/tests/software/bowtie2/test.yml new file mode 100644 index 00000000..85bb01c8 --- /dev/null +++ b/tests/software/bowtie2/test.yml @@ -0,0 +1,64 @@ +- name: Run bowtie2 build + command: nextflow run ./tests/software/bowtie2 -profile docker -entry test_bowtie2_build -c tests/config/nextflow.config + tags: + - bowtie2 + - bowtie2_build + files: + - path: output/bowtie2/bowtie2/NC_010473.1.bt2 + md5sum: 4db22d92e72111a5fbf609b3d9a43015 + - path: output/bowtie2/bowtie2/NC_010473.2.bt2 + md5sum: f4429ec74ee0064732c4bb26718a3eb1 + - path: output/bowtie2/bowtie2/NC_010473.3.bt2 + md5sum: cd201e81724f3099131aec16ef2cc53b + - path: output/bowtie2/bowtie2/NC_010473.4.bt2 + md5sum: bbb9d6d21ad765d135f95290204e8433 + - path: output/bowtie2/bowtie2/NC_010473.rev.1.bt2 + md5sum: 4ccfee8857c3b1c69857e5ecdef597aa + - path: output/bowtie2/bowtie2/NC_010473.rev.2.bt2 + md5sum: 5e8fb4af677eb3a57a40e76dc3f6db72 + +- name: Run bowtie2 index and align single-end + command: nextflow run ./tests/software/bowtie2 -profile docker -entry test_bowtie2_alignment_single_end -c tests/config/nextflow.config + tags: + - bowtie2 + - bowtie2_align + files: + - path: output/bowtie2/bowtie2/NC_010473.1.bt2 + md5sum: 4db22d92e72111a5fbf609b3d9a43015 + - path: output/bowtie2/bowtie2/NC_010473.2.bt2 + md5sum: f4429ec74ee0064732c4bb26718a3eb1 + - path: output/bowtie2/bowtie2/NC_010473.3.bt2 + md5sum: cd201e81724f3099131aec16ef2cc53b + - path: output/bowtie2/bowtie2/NC_010473.4.bt2 + md5sum: bbb9d6d21ad765d135f95290204e8433 + - path: output/bowtie2/bowtie2/NC_010473.rev.1.bt2 + md5sum: 4ccfee8857c3b1c69857e5ecdef597aa + - path: output/bowtie2/bowtie2/NC_010473.rev.2.bt2 + md5sum: 5e8fb4af677eb3a57a40e76dc3f6db72 + - path: output/bowtie2/test.bowtie2.log + md5sum: 90041c264231be535042adb93a279356 + - path: output/bowtie2/test.bam + md5sum: 906102f401d8234b6473790988fb09cf + +- name: Run bowtie2 index and align paired-end + command: nextflow run ./tests/software/bowtie2 -profile docker -entry test_bowtie2_alignment_paired_end -c tests/config/nextflow.config + tags: + - bowtie2 + - bowtie2_align + files: + - path: output/bowtie2/bowtie2/NC_010473.1.bt2 + md5sum: 90f0b7aa5bbaeaaa999839ac13ad203c + - path: output/bowtie2/bowtie2/NC_010473.2.bt2 + md5sum: bfd10c5319c6a0dbc540fd789254a5dd + - path: output/bowtie2/bowtie2/NC_010473.3.bt2 + md5sum: cd201e81724f3099131aec16ef2cc53b + - path: output/bowtie2/bowtie2/NC_010473.4.bt2 + md5sum: bbb9d6d21ad765d135f95290204e8433 + - path: output/bowtie2/bowtie2/NC_010473.rev.1.bt2 + md5sum: 44f719c2fe42e1f35d54e798775846d1 + - path: output/bowtie2/bowtie2/NC_010473.rev.2.bt2 + md5sum: f3c398bba5158f4039334a932d79c051 + - path: output/bowtie2/test.bowtie2.log + md5sum: 9f9eb40b5f57e0f2d5c874f2c1b5cfd5 + - path: output/bowtie2/test.bam + md5sum: 732a33cd9816b38ea9b919c25eeb78f8 From 29989035a5e1ddaeddec3dfa737f56edfbe16649 Mon Sep 17 00:00:00 2001 From: JoseEspinosa Date: Sat, 30 Jan 2021 09:29:53 +0100 Subject: [PATCH 24/42] Remove author entry from yml (copy-pasted :P) --- software/bcftools/bgzip/meta.yml | 75 ++++++++++++++++++++++++++++++++ software/bowtie2/build/meta.yml | 1 - 2 files changed, 75 insertions(+), 1 deletion(-) create mode 100644 software/bcftools/bgzip/meta.yml diff --git a/software/bcftools/bgzip/meta.yml b/software/bcftools/bgzip/meta.yml new file mode 100644 index 00000000..21424516 --- /dev/null +++ b/software/bcftools/bgzip/meta.yml @@ -0,0 +1,75 @@ +name: bcftoos_ +description: foo +keywords: + - align + - fasta + - genome + - reference +tools: + - bowtie2: + description: | + BCFtools is a set of utilities that manipulate variant calls in the + Variant Call Format (VCF) and its binary counterpart BCF. + homepage: http://samtools.github.io/bcftools/bcftools.html + documentation: http://www.htslib.org/doc/bcftools.html + doi: 10.1038/nmeth.1923 +params: + - outdir: + type: string + description: | + The pipeline's output directory. By default, the module will + output files into `$params.outdir/` + - publish_dir_mode: + type: string + description: | + Value for the Nextflow `publishDir` mode parameter. + Available: symlink, rellink, link, copy, copyNoFollow, move. + - enable_conda: + type: boolean + description: | + Run the module with Conda using the software specified + via the `conda` directive + - singularity_pull_docker_container: + type: boolean + description: | + Instead of directly downloading Singularity images for use with Singularity, + force the workflow to pull and convert Docker containers instead. + - save_unaligned: + type: boolean + description: Save unaligned reads +input: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - reads: + type: file + description: | + List of input FastQ files of size 1 and 2 for single-end and paired-end data, + respectively. + - index: + type: file + description: Bowtie2 genome index files + pattern: "*.ebwt" +output: + - bam: + type: file + description: Output BAM file containing read alignments + pattern: "*.{bam}" + - version: + type: file + description: File containing software version + pattern: "*.{version.txt}" + - fastq: + type: file + description: Unaligned FastQ files + pattern: "*.fastq.gz" + - log: + type: file + description: Aligment log + pattern: "*.log" +authors: + - "@kevinmenden" + - "@joseespinosa" + - "@drpatelh" diff --git a/software/bowtie2/build/meta.yml b/software/bowtie2/build/meta.yml index e4330967..c25b862a 100644 --- a/software/bowtie2/build/meta.yml +++ b/software/bowtie2/build/meta.yml @@ -49,6 +49,5 @@ output: description: File containing software version pattern: "*.{version.txt}" authors: - - "@kevinmenden" - "@joseespinosa" - "drpatelh" From 986b72cee9efab4c4b1071a32c337d209ba22d0f Mon Sep 17 00:00:00 2001 From: JoseEspinosa Date: Sat, 30 Jan 2021 09:35:25 +0100 Subject: [PATCH 25/42] Fix error on previous commit --- software/bcftools/bgzip/meta.yml | 75 -------------------------------- software/bowtie2/align/meta.yml | 1 - 2 files changed, 76 deletions(-) delete mode 100644 software/bcftools/bgzip/meta.yml diff --git a/software/bcftools/bgzip/meta.yml b/software/bcftools/bgzip/meta.yml deleted file mode 100644 index 21424516..00000000 --- a/software/bcftools/bgzip/meta.yml +++ /dev/null @@ -1,75 +0,0 @@ -name: bcftoos_ -description: foo -keywords: - - align - - fasta - - genome - - reference -tools: - - bowtie2: - description: | - BCFtools is a set of utilities that manipulate variant calls in the - Variant Call Format (VCF) and its binary counterpart BCF. - homepage: http://samtools.github.io/bcftools/bcftools.html - documentation: http://www.htslib.org/doc/bcftools.html - doi: 10.1038/nmeth.1923 -params: - - outdir: - type: string - description: | - The pipeline's output directory. By default, the module will - output files into `$params.outdir/` - - publish_dir_mode: - type: string - description: | - Value for the Nextflow `publishDir` mode parameter. - Available: symlink, rellink, link, copy, copyNoFollow, move. - - enable_conda: - type: boolean - description: | - Run the module with Conda using the software specified - via the `conda` directive - - singularity_pull_docker_container: - type: boolean - description: | - Instead of directly downloading Singularity images for use with Singularity, - force the workflow to pull and convert Docker containers instead. - - save_unaligned: - type: boolean - description: Save unaligned reads -input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - reads: - type: file - description: | - List of input FastQ files of size 1 and 2 for single-end and paired-end data, - respectively. - - index: - type: file - description: Bowtie2 genome index files - pattern: "*.ebwt" -output: - - bam: - type: file - description: Output BAM file containing read alignments - pattern: "*.{bam}" - - version: - type: file - description: File containing software version - pattern: "*.{version.txt}" - - fastq: - type: file - description: Unaligned FastQ files - pattern: "*.fastq.gz" - - log: - type: file - description: Aligment log - pattern: "*.log" -authors: - - "@kevinmenden" - - "@joseespinosa" - - "@drpatelh" diff --git a/software/bowtie2/align/meta.yml b/software/bowtie2/align/meta.yml index 9a2ecf40..eb78e9f9 100644 --- a/software/bowtie2/align/meta.yml +++ b/software/bowtie2/align/meta.yml @@ -70,6 +70,5 @@ output: description: Aligment log pattern: "*.log" authors: - - "@kevinmenden" - "@joseespinosa" - "@drpatelh" From eab633776efee520148a59be72126b5b37afc2be Mon Sep 17 00:00:00 2001 From: Harshil Patel Date: Sat, 30 Jan 2021 13:21:56 +0000 Subject: [PATCH 26/42] Update software/bowtie2/build/meta.yml --- software/bowtie2/build/meta.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/software/bowtie2/build/meta.yml b/software/bowtie2/build/meta.yml index c25b862a..959a9b09 100644 --- a/software/bowtie2/build/meta.yml +++ b/software/bowtie2/build/meta.yml @@ -50,4 +50,4 @@ output: pattern: "*.{version.txt}" authors: - "@joseespinosa" - - "drpatelh" + - "@drpatelh" From 177693de49c5a0400e3419f6dddc1900762031cf Mon Sep 17 00:00:00 2001 From: JoseEspinosa Date: Sat, 30 Jan 2021 22:53:27 +0100 Subject: [PATCH 27/42] Adding worflow yml for bowtie2_align and bowtie2_build --- .github/workflows/bowtie2_align.yml | 42 +++++++++++++++++++++++++++++ .github/workflows/bowtie2_build.yml | 40 +++++++++++++++++++++++++++ 2 files changed, 82 insertions(+) create mode 100644 .github/workflows/bowtie2_align.yml create mode 100644 .github/workflows/bowtie2_build.yml diff --git a/.github/workflows/bowtie2_align.yml b/.github/workflows/bowtie2_align.yml new file mode 100644 index 00000000..3642b5c9 --- /dev/null +++ b/.github/workflows/bowtie2_align.yml @@ -0,0 +1,42 @@ +name: bowtie2_align +on: + push: + paths: + - software/bowtie2/align/** + - software/bowtie2/build/** + - .github/workflows/bowtie2_align.yml + - tests/software/bowtie2/** + pull_request: + paths: + - software/bowtie2/align/** + - software/bowtie2/build/** + - .github/workflows/bowtie2_align.yml + - tests/software/bowtie2/** + +jobs: + ci_test: + runs-on: ubuntu-latest + strategy: + matrix: + nxf_version: [20.11.0-edge] + env: + NXF_ANSI_LOG: false + steps: + - uses: actions/checkout@v2 + + - name: Install Nextflow + env: + NXF_VER: ${{ matrix.nxf_version }} + run: | + wget -qO- get.nextflow.io | bash + sudo mv nextflow /usr/local/bin/ + + - name: Set up Python + uses: actions/setup-python@v2 + with: + python-version: "3.x" + - name: Install dependencies + run: python -m pip install --upgrade pip pytest-workflow + + # Test the module + - run: pytest --tag bowtie2_align --symlink --wt 2 diff --git a/.github/workflows/bowtie2_build.yml b/.github/workflows/bowtie2_build.yml new file mode 100644 index 00000000..21ddde78 --- /dev/null +++ b/.github/workflows/bowtie2_build.yml @@ -0,0 +1,40 @@ +name: bowtie2_build +on: + push: + paths: + - software/bowtie2/build/** + - .github/workflows/bowtie2_build.yml + - tests/software/bowtie2/** + pull_request: + paths: + - software/bowtie2/build/** + - .github/workflows/bowtie2_build.yml + - tests/software/bowtie2/** + +jobs: + ci_test: + runs-on: ubuntu-latest + strategy: + matrix: + nxf_version: [20.11.0-edge] + env: + NXF_ANSI_LOG: false + steps: + - uses: actions/checkout@v2 + + - name: Install Nextflow + env: + NXF_VER: ${{ matrix.nxf_version }} + run: | + wget -qO- get.nextflow.io | bash + sudo mv nextflow /usr/local/bin/ + + - name: Set up Python + uses: actions/setup-python@v2 + with: + python-version: "3.x" + - name: Install dependencies + run: python -m pip install --upgrade pip pytest-workflow + + # Test the module + - run: pytest --tag bowtie2_build --symlink --wt 2 From 8fb6b80abd3de476dc7bf67e12fb7f9b100e3a0d Mon Sep 17 00:00:00 2001 From: JoseEspinosa Date: Sat, 30 Jan 2021 23:08:17 +0100 Subject: [PATCH 28/42] Fixing some md5 hashes --- tests/software/bowtie2/test.yml | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/tests/software/bowtie2/test.yml b/tests/software/bowtie2/test.yml index 85bb01c8..a3c6f31d 100644 --- a/tests/software/bowtie2/test.yml +++ b/tests/software/bowtie2/test.yml @@ -47,17 +47,17 @@ - bowtie2_align files: - path: output/bowtie2/bowtie2/NC_010473.1.bt2 - md5sum: 90f0b7aa5bbaeaaa999839ac13ad203c + md5sum: 4db22d92e72111a5fbf609b3d9a43015 - path: output/bowtie2/bowtie2/NC_010473.2.bt2 - md5sum: bfd10c5319c6a0dbc540fd789254a5dd + md5sum: f4429ec74ee0064732c4bb26718a3eb1 - path: output/bowtie2/bowtie2/NC_010473.3.bt2 md5sum: cd201e81724f3099131aec16ef2cc53b - path: output/bowtie2/bowtie2/NC_010473.4.bt2 md5sum: bbb9d6d21ad765d135f95290204e8433 - path: output/bowtie2/bowtie2/NC_010473.rev.1.bt2 - md5sum: 44f719c2fe42e1f35d54e798775846d1 + md5sum: 4ccfee8857c3b1c69857e5ecdef597aa - path: output/bowtie2/bowtie2/NC_010473.rev.2.bt2 - md5sum: f3c398bba5158f4039334a932d79c051 + md5sum: 5e8fb4af677eb3a57a40e76dc3f6db72 - path: output/bowtie2/test.bowtie2.log md5sum: 9f9eb40b5f57e0f2d5c874f2c1b5cfd5 - path: output/bowtie2/test.bam From 956bf22a58c00da45c6dbbd82a970c724a655ebf Mon Sep 17 00:00:00 2001 From: kevinmenden Date: Mon, 1 Feb 2021 07:44:26 +0100 Subject: [PATCH 29/42] fixed bug; updated meta.yml --- .github/workflows/quast.yml | 2 +- software/quast/quast_noref/meta.yml | 11 ++++++----- software/quast/quast_ref/meta.yml | 17 +++++++++-------- 3 files changed, 16 insertions(+), 14 deletions(-) diff --git a/.github/workflows/quast.yml b/.github/workflows/quast.yml index 7030d638..669d916b 100644 --- a/.github/workflows/quast.yml +++ b/.github/workflows/quast.yml @@ -37,4 +37,4 @@ jobs: run: python -m pip install --upgrade pip pytest-workflow # Test the module - - run: pytest --tag quest --symlink --wt 2 + - run: pytest --tag quast --symlink --wt 2 diff --git a/software/quast/quast_noref/meta.yml b/software/quast/quast_noref/meta.yml index 9b46bf42..8f758b10 100644 --- a/software/quast/quast_noref/meta.yml +++ b/software/quast/quast_noref/meta.yml @@ -5,9 +5,9 @@ keywords: - assembly - quality tools: - - star: + - quast: description: | - QUAST calculate quality metrics for genome assemblies + QUAST calculates quality metrics for genome assemblies homepage: http://bioinf.spbau.ru/quast doi: params: @@ -34,15 +34,16 @@ params: input: - consensus: - type: map + type: file description: | - Groovy Map containing sample information + Fasta file containing the assembly of interest output: - - report: + - results: type: file description: The lineage report pattern: "{prefix}.lineage_report.csv" + - tsv: - version: type: file diff --git a/software/quast/quast_ref/meta.yml b/software/quast/quast_ref/meta.yml index a1ca27b3..03526be7 100644 --- a/software/quast/quast_ref/meta.yml +++ b/software/quast/quast_ref/meta.yml @@ -1,13 +1,13 @@ -name: quast +name: quast_reference description: Quality Assessment Tool for Genome Assemblies keywords: - quast - assembly - quality tools: - - star: + - quast: description: | - QUAST calculate quality metrics for genome assemblies + QUAST calculates quality metrics for genome assemblies homepage: http://bioinf.spbau.ru/quast doi: params: @@ -34,9 +34,9 @@ params: input: - consensus: - type: map + type: file description: | - Groovy Map containing sample information + Fasta file containing the assembly of interest - fasta: type: file description: | @@ -46,10 +46,11 @@ input: description: The genome GFF file output: - - report: - type: file - description: The lineage report + - quast: + type: directory + description: Directory containing complete quast report pattern: "{prefix}.lineage_report.csv" + - report: - version: type: file From 41233763ae55f160e431fabac8ca4873d345a3de Mon Sep 17 00:00:00 2001 From: Chris Cheshire Date: Mon, 1 Feb 2021 09:46:24 +0000 Subject: [PATCH 30/42] Removed test-datasets submodule --- .gitmodules | 3 --- test-datasets | 1 - 2 files changed, 4 deletions(-) delete mode 100644 .gitmodules delete mode 160000 test-datasets diff --git a/.gitmodules b/.gitmodules deleted file mode 100644 index 44e06649..00000000 --- a/.gitmodules +++ /dev/null @@ -1,3 +0,0 @@ -[submodule "test-datasets"] - path = test-datasets - url = https://github.com/nf-core/test-datasets.git diff --git a/test-datasets b/test-datasets deleted file mode 160000 index aae85a5c..00000000 --- a/test-datasets +++ /dev/null @@ -1 +0,0 @@ -Subproject commit aae85a5c9c72238959108212481ce83bae569709 From b5298f94d80a40b609632f82761dfee41a9ae2c3 Mon Sep 17 00:00:00 2001 From: kevinmenden Date: Mon, 1 Feb 2021 13:13:21 +0100 Subject: [PATCH 31/42] refactored quast module --- software/quast/{quast_noref => }/functions.nf | 0 software/quast/{quast_ref => }/main.nf | 13 ++-- software/quast/{quast_ref => }/meta.yml | 12 +++- software/quast/quast_noref/main.nf | 41 ------------- software/quast/quast_noref/meta.yml | 55 ----------------- software/quast/quast_ref/functions.nf | 59 ------------------- tests/software/quast/main.nf | 23 +++++--- 7 files changed, 31 insertions(+), 172 deletions(-) rename software/quast/{quast_noref => }/functions.nf (100%) rename software/quast/{quast_ref => }/main.nf (82%) rename software/quast/{quast_ref => }/meta.yml (80%) delete mode 100644 software/quast/quast_noref/main.nf delete mode 100644 software/quast/quast_noref/meta.yml delete mode 100644 software/quast/quast_ref/functions.nf diff --git a/software/quast/quast_noref/functions.nf b/software/quast/functions.nf similarity index 100% rename from software/quast/quast_noref/functions.nf rename to software/quast/functions.nf diff --git a/software/quast/quast_ref/main.nf b/software/quast/main.nf similarity index 82% rename from software/quast/quast_ref/main.nf rename to software/quast/main.nf index 0a811445..3690c08b 100644 --- a/software/quast/quast_ref/main.nf +++ b/software/quast/main.nf @@ -21,7 +21,9 @@ process QUAST { input: path consensus path fasta + val use_fasta path gff + val use_gff output: path "${prefix}" , emit: results @@ -29,14 +31,15 @@ process QUAST { path '*.version.txt', emit: version script: - def software = getSoftwareName(task.process) - prefix = options.suffix ?: software - def features = params.gff ? "--features $gff" : '' + def software = getSoftwareName(task.process) + prefix = options.suffix ?: software + def features = use_gff ? "--features $gff" : '' + def reference = use_fasta ? "-r $fasta" : '' """ quast.py \\ --output-dir $prefix \\ - -r $fasta \\ - $features \\ + ${reference} \\ + ${features} \\ --threads $task.cpus \\ $options.args \\ ${consensus.join(' ')} diff --git a/software/quast/quast_ref/meta.yml b/software/quast/meta.yml similarity index 80% rename from software/quast/quast_ref/meta.yml rename to software/quast/meta.yml index 03526be7..ae63de65 100644 --- a/software/quast/quast_ref/meta.yml +++ b/software/quast/meta.yml @@ -1,4 +1,4 @@ -name: quast_reference +name: quast description: Quality Assessment Tool for Genome Assemblies keywords: - quast @@ -40,10 +40,16 @@ input: - fasta: type: file description: | - The genome assembly to be evaluated + The genome assembly to be evaluated. Has to contain at least a non-empty string dummy value. + - use_fasta: + type: boolean + description: Whether to use a fasta reference - gff: type: file - description: The genome GFF file + description: The genome GFF file. Has to contain at least a non-empty string dummy value. + - use_gff: + type: boolean + description: Whether to use a gff reference output: - quast: diff --git a/software/quast/quast_noref/main.nf b/software/quast/quast_noref/main.nf deleted file mode 100644 index 2ad9ac79..00000000 --- a/software/quast/quast_noref/main.nf +++ /dev/null @@ -1,41 +0,0 @@ -// Import generic module functions -include { initOptions; saveFiles; getSoftwareName } from './functions' - -params.options = [:] -def options = initOptions(params.options) - -process QUAST { - tag "$fasta" - label 'process_medium' - publishDir "${params.outdir}", - mode: params.publish_dir_mode, - saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:'') } - - conda (params.enable_conda ? 'bioconda::quast=5.0.2' : null) - if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) { - container 'https://depot.galaxyproject.org/singularity/quast:5.0.2--py37pl526hb5aa323_2' - } else { - container 'quay.io/biocontainers/quast:5.0.2--py37pl526hb5aa323_2' - } - - input: - path consensus - - output: - path "${prefix}" , emit: results - path '*.tsv' , emit: tsv - path '*.version.txt', emit: version - - script: - def software = getSoftwareName(task.process) - prefix = options.suffix ?: software - """ - quast.py \\ - --output-dir $prefix \\ - --threads $task.cpus \\ - $options.args \\ - $consensus - ln -s ${prefix}/report.tsv - echo \$(quast.py --version 2>&1) | sed 's/^.*QUAST v//; s/ .*\$//' > ${software}.version.txt - """ -} diff --git a/software/quast/quast_noref/meta.yml b/software/quast/quast_noref/meta.yml deleted file mode 100644 index 8f758b10..00000000 --- a/software/quast/quast_noref/meta.yml +++ /dev/null @@ -1,55 +0,0 @@ -name: quast -description: Quality Assessment Tool for Genome Assemblies -keywords: - - quast - - assembly - - quality -tools: - - quast: - description: | - QUAST calculates quality metrics for genome assemblies - homepage: http://bioinf.spbau.ru/quast - doi: -params: - - outdir: - type: string - description: | - The pipeline's output directory. By default, the module will - output files into `$params.outdir/` - - publish_dir_mode: - type: string - description: | - Value for the Nextflow `publishDir` mode parameter. - Available: symlink, rellink, link, copy, copyNoFollow, move. - - enable_conda: - type: boolean - description: | - Run the module with Conda using the software specified - via the `conda` directive - - singularity_pull_docker_container: - type: boolean - description: | - Instead of directly downloading Singularity images for use with Singularity, - force the workflow to pull and convert Docker containers instead. - -input: - - consensus: - type: file - description: | - Fasta file containing the assembly of interest - -output: - - results: - type: file - description: The lineage report - pattern: "{prefix}.lineage_report.csv" - - tsv: - - - version: - type: file - description: File containing software version - pattern: "*.{version.txt}" - -authors: - - "@drpatelh" - - "@kevinmenden" diff --git a/software/quast/quast_ref/functions.nf b/software/quast/quast_ref/functions.nf deleted file mode 100644 index d25eea86..00000000 --- a/software/quast/quast_ref/functions.nf +++ /dev/null @@ -1,59 +0,0 @@ -/* - * ----------------------------------------------------- - * Utility functions used in nf-core DSL2 module files - * ----------------------------------------------------- - */ - -/* - * Extract name of software tool from process name using $task.process - */ -def getSoftwareName(task_process) { - return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase() -} - -/* - * Function to initialise default values and to generate a Groovy Map of available options for nf-core modules - */ -def initOptions(Map args) { - def Map options = [:] - options.args = args.args ?: '' - options.args2 = args.args2 ?: '' - options.publish_by_id = args.publish_by_id ?: false - options.publish_dir = args.publish_dir ?: '' - options.publish_files = args.publish_files - options.suffix = args.suffix ?: '' - return options -} - -/* - * Tidy up and join elements of a list to return a path string - */ -def getPathFromList(path_list) { - def paths = path_list.findAll { item -> !item?.trim().isEmpty() } // Remove empty entries - paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes - return paths.join('/') -} - -/* - * Function to save/publish module results - */ -def saveFiles(Map args) { - if (!args.filename.endsWith('.version.txt')) { - def ioptions = initOptions(args.options) - def path_list = [ ioptions.publish_dir ?: args.publish_dir ] - if (ioptions.publish_by_id) { - path_list.add(args.publish_id) - } - if (ioptions.publish_files instanceof Map) { - for (ext in ioptions.publish_files) { - if (args.filename.endsWith(ext.key)) { - def ext_list = path_list.collect() - ext_list.add(ext.value) - return "${getPathFromList(ext_list)}/$args.filename" - } - } - } else if (ioptions.publish_files == null) { - return "${getPathFromList(path_list)}/$args.filename" - } - } -} diff --git a/tests/software/quast/main.nf b/tests/software/quast/main.nf index 366b0c90..7ef3d9ac 100644 --- a/tests/software/quast/main.nf +++ b/tests/software/quast/main.nf @@ -2,19 +2,24 @@ nextflow.enable.dsl = 2 -include { QUAST as QUAST_NOREF } from '../../../software/quast/quast_noref/main.nf' addParams(options: [:]) -include { QUAST as QUAST_REF } from '../../../software/quast/quast_ref/main.nf' addParams(options: [:]) - -workflow test_quast_noref { - consensus = file("${launchDir}/tests/data/fasta/sarscov2/GCA_011545545.1_ASM1154554v1_genomic.fna", checkIfExists: true) - - QUAST_NOREF( consensus ) -} +include { QUAST } from '../../../software/quast/main.nf' addParams(options: [:]) workflow test_quast_ref { consensus = file("${launchDir}/tests/data/fasta/sarscov2/GCA_011545545.1_ASM1154554v1_cds_from_genomic.fna", checkIfExists: true) gff = file("${launchDir}/tests/data/gff/sarscov2/GCA_011545545.1_ASM1154554v1_genomic.gtf", checkIfExists: true) fasta = file("${launchDir}/tests/data/fasta/sarscov2/GCA_011545545.1_ASM1154554v1_genomic.fna", checkIfExists: true) + def use_fasta = true + def use_gtf = true - QUAST_REF( consensus, fasta, gff ) + QUAST( consensus, fasta, use_fasta, gff, use_gtf) +} + +workflow test_quast_noref { + consensus = file("${launchDir}/tests/data/fasta/sarscov2/GCA_011545545.1_ASM1154554v1_cds_from_genomic.fna", checkIfExists: true) + gff = file('gff_dummy') + fasta = file('fasta_dummy') + def use_fasta = false + def use_gtf = false + + QUAST( consensus, fasta, use_fasta, gff, use_gtf) } From a342296d7013301f3ad1769cfb492ddc3f14e8df Mon Sep 17 00:00:00 2001 From: kevinmenden Date: Mon, 1 Feb 2021 13:36:25 +0100 Subject: [PATCH 32/42] fixed test md5s --- tests/software/quast/test.yml | 188 ++++++++++++++++++---------------- 1 file changed, 97 insertions(+), 91 deletions(-) diff --git a/tests/software/quast/test.yml b/tests/software/quast/test.yml index 6d895298..2ceccc54 100644 --- a/tests/software/quast/test.yml +++ b/tests/software/quast/test.yml @@ -4,82 +4,88 @@ - quast - quast_reference files: - - path: ./output/quast/quast/contigs_reports/transposed_report_misassemblies.tsv - md5sum: 4d24cc0da823a100a076aef36f9fd75e - - path: ./output/quast/quast/contigs_reports/GCA_011545545_1_ASM1154554v1_cds_from_genomic.mis_contigs.fa - - path: ./output/quast/quast/contigs_reports/contigs_report_GCA_011545545-1_ASM1154554v1_cds_from_genomic.stdout - - path: ./output/quast/quast/aligned_stats/NGAx_plot.pdf - - path: ./output/quast/quast/report.pdf - - path: ./output/quast/quast/contigs_reports/misassemblies_report.tex - md5sum: ffe19cf4d5332952f0627e9cd82e3375 - - path: ./output/quast/quast/aligned_stats/NAx_plot.pdf - - path: ./output/quast/quast/icarus.html - - path: ./output/quast/quast/report.tsv - md5sum: 503ebb57ffed0422fd7aff4025e21143 - - path: ./output/quast/quast/contigs_reports/transposed_report_misassemblies.tex - md5sum: 85614257e0bb62ac750f7872886b2fbf - - path: ./output/quast/quast/basic_stats/gc.icarus.txt - md5sum: b3a770802ff9b2dd4ee8e47bddb2df3e - - path: ./output/quast/quast/aligned_stats/cumulative_plot.pdf + - path: ./output/quast/quast/basic_stats/NGx_plot.pdf - path: ./output/quast/quast/contigs_reports/minimap_output/GCA_011545545-1_ASM1154554v1_cds_from_genomic.coords.filtered md5sum: ec9191d0acb5d5bce56b4842551a8598 - - path: ./output/quast/quast/basic_stats/Nx_plot.pdf - - path: ./output/quast/quast/contigs_reports/minimap_output/GCA_011545545-1_ASM1154554v1_cds_from_genomic.coords - md5sum: dda3fc0addc41ecc0d5183dee6f95886 - - path: ./output/quast/quast/contigs_reports/minimap_output/GCA_011545545-1_ASM1154554v1_cds_from_genomic.coords_tmp - md5sum: ce66eaeb99fdc11e4d50efadc1816e04 - - path: ./output/quast/quast/contigs_reports/unaligned_report.tsv - md5sum: 769f2d9d7deb5e7a63e238d8ba0cfe13 - - path: ./output/quast/quast/basic_stats/GC_content_plot.pdf - - path: ./output/quast/quast/contigs_reports/contigs_report_GCA_011545545-1_ASM1154554v1_cds_from_genomic.mis_contigs.info - md5sum: d41d8cd98f00b204e9800998ecf8427e - - path: ./output/quast/quast/contigs_reports/contigs_report_GCA_011545545-1_ASM1154554v1_cds_from_genomic.unaligned.info - md5sum: a8505cf206bf53ca369f7e3073fee587 - - path: ./output/quast/quast/contigs_reports/minimap_output/GCA_011545545-1_ASM1154554v1_cds_from_genomic.sf - - path: ./output/quast/quast/transposed_report.txt - md5sum: 389e9fa2b29b967cb658c0770c941ce6 - - path: ./output/quast/quast/genome_stats/GCA_011545545-1_ASM1154554v1_cds_from_genomic_gaps.txt - md5sum: c52381f09ea40b6141be5232494727b6 - - path: ./output/quast/quast/quast.log - - path: ./output/quast/report.tsv - md5sum: 503ebb57ffed0422fd7aff4025e21143 - - path: ./output/quast/quast/contigs_reports/transposed_report_misassemblies.txt - md5sum: 53c481fe8b3ef18280ea86cbded78b31 - - path: ./output/quast/quast/contigs_reports/unaligned_report.txt - md5sum: c1c26797084ea743ec5a224ab97adb1f - - path: ./output/quast/quast/report.txt - md5sum: 41bf3c24e68afce5ef0ba91004e57f7d - - path: ./output/quast/quast/transposed_report.tex - md5sum: 2a69aada90cc1e788a4bc877c44d79c8 - - path: ./output/quast/quast/basic_stats/GCA_011545545.1_ASM1154554v1_cds_from_genomic_GC_content_plot.pdf - - path: ./output/quast/quast/contigs_reports/misassemblies_report.tsv - md5sum: 33144f8d064782864e8400e3a08b2a3a - - path: ./output/quast/quast/contigs_reports/unaligned_report.tex - md5sum: 48562e30903fcf33946e13b602b0e324 - - path: ./output/quast/quast/contigs_reports/misassemblies_plot.pdf - - path: ./output/quast/quast/transposed_report.tsv - md5sum: baab35c91e87432432113db1e4085f7b - - path: ./output/quast/quast/report.tex - md5sum: 8e72428ff7e7175bf47d58c10d8332e8 - - path: ./output/quast/quast/contigs_reports/misassemblies_frcurve_plot.pdf - - path: ./output/quast/quast/contigs_reports/minimap_output/GCA_011545545-1_ASM1154554v1_cds_from_genomic.used_snps.gz - md5sum: 7b1db1b433cd95243a949bcb72e7e3a6 - - path: ./output/quast/quast/contigs_reports/misassemblies_report.txt - md5sum: 0784e0d31e9f2a165730cc0029023427 - - path: ./output/quast/quast/icarus_viewers/alignment_viewer.html - md5sum: bd63165a204a2ab424f8e81c647038d1 - - path: ./output/quast/quast/contigs_reports/all_alignments_GCA_011545545-1_ASM1154554v1_cds_from_genomic.tsv - md5sum: c247152eb82b361106492642fd796e2c - - path: ./output/quast/quast/genome_stats/genome_info.txt - md5sum: 7c622ab66040d413a229419bf6b5181f - - path: ./output/quast/quast/basic_stats/NGx_plot.pdf - - path: ./output/quast/quast/contigs_reports/minimap_output/GCA_011545545-1_ASM1154554v1_cds_from_genomic.unaligned - md5sum: d41d8cd98f00b204e9800998ecf8427e - - path: ./output/quast/quast/contigs_reports/contigs_report_GCA_011545545-1_ASM1154554v1_cds_from_genomic.stderr + - path: ./output/quast/quast/aligned_stats/NGAx_plot.pdf - path: ./output/quast/quast/icarus_viewers/contig_size_viewer.html md5sum: c42838b1553759fb0460a9854e39da36 + - path: ./output/quast/report.tsv + md5sum: b203a9d2c995bd66552eeb5cb0a98762 + - path: ./output/quast/quast/report.tex + md5sum: 8168f197dfb2f781accdefaa0d90fc87 + - path: ./output/quast/quast/contigs_reports/misassemblies_frcurve_plot.pdf + - path: ./output/quast/quast/transposed_report.tex + md5sum: 0b8fd00649a5758024c8093d5919f71c + - path: ./output/quast/quast/contigs_reports/minimap_output/GCA_011545545-1_ASM1154554v1_cds_from_genomic.coords + md5sum: dda3fc0addc41ecc0d5183dee6f95886 + - path: ./output/quast/quast/transposed_report.txt + md5sum: 73216314e65ef91c24422d5bdd0795e4 - path: ./output/quast/quast/report.html + - path: ./output/quast/quast/report.pdf + - path: ./output/quast/quast/contigs_reports/all_alignments_GCA_011545545-1_ASM1154554v1_cds_from_genomic.tsv + md5sum: c247152eb82b361106492642fd796e2c + - path: ./output/quast/quast/contigs_reports/minimap_output/GCA_011545545-1_ASM1154554v1_cds_from_genomic.used_snps.gz + md5sum: 7b1db1b433cd95243a949bcb72e7e3a6 + - path: ./output/quast/quast/contigs_reports/unaligned_report.tex + md5sum: 48562e30903fcf33946e13b602b0e324 + - path: ./output/quast/quast/contigs_reports/minimap_output/GCA_011545545-1_ASM1154554v1_cds_from_genomic.sf + - path: ./output/quast/quast/contigs_reports/transposed_report_misassemblies.txt + md5sum: 53c481fe8b3ef18280ea86cbded78b31 + - path: ./output/quast/quast/contigs_reports/contigs_report_GCA_011545545-1_ASM1154554v1_cds_from_genomic.mis_contigs.info + md5sum: d41d8cd98f00b204e9800998ecf8427e + - path: ./output/quast/quast/contigs_reports/unaligned_report.tsv + md5sum: 769f2d9d7deb5e7a63e238d8ba0cfe13 + - path: ./output/quast/quast/basic_stats/GCA_011545545.1_ASM1154554v1_cds_from_genomic_GC_content_plot.pdf + - path: ./output/quast/quast/genome_stats/features_cumulative_plot.pdf + - path: ./output/quast/quast/basic_stats/GC_content_plot.pdf + - path: ./output/quast/quast/contigs_reports/transposed_report_misassemblies.tex + md5sum: 85614257e0bb62ac750f7872886b2fbf + - path: ./output/quast/quast/quast.log + - path: ./output/quast/quast/contigs_reports/misassemblies_report.tsv + md5sum: 33144f8d064782864e8400e3a08b2a3a + - path: ./output/quast/quast/contigs_reports/contigs_report_GCA_011545545-1_ASM1154554v1_cds_from_genomic.unaligned.info + md5sum: a8505cf206bf53ca369f7e3073fee587 + - path: ./output/quast/quast/genome_stats/GCA_011545545-1_ASM1154554v1_cds_from_genomic_genomic_features_any.txt + md5sum: 307b3bb1f42fc2f11a60a2e9846021d7 + - path: ./output/quast/quast/icarus.html + md5sum: 6e57f5f7d07528496fc2f35b449951fe + - path: ./output/quast/quast/contigs_reports/transposed_report_misassemblies.tsv + md5sum: 4d24cc0da823a100a076aef36f9fd75e + - path: ./output/quast/quast/contigs_reports/contigs_report_GCA_011545545-1_ASM1154554v1_cds_from_genomic.stderr + - path: ./output/quast/quast/aligned_stats/cumulative_plot.pdf + - path: ./output/quast/quast/genome_stats/genome_info.txt + md5sum: bc3df27ad7356c045c9a108f9d4bcfbe + - path: ./output/quast/quast/genome_stats/features_frcurve_plot.pdf + - path: ./output/quast/quast/contigs_reports/misassemblies_report.txt + md5sum: 0784e0d31e9f2a165730cc0029023427 + - path: ./output/quast/quast/contigs_reports/minimap_output/GCA_011545545-1_ASM1154554v1_cds_from_genomic.unaligned + md5sum: d41d8cd98f00b204e9800998ecf8427e + - path: ./output/quast/quast/contigs_reports/contigs_report_GCA_011545545-1_ASM1154554v1_cds_from_genomic.stdout + - path: ./output/quast/quast/contigs_reports/unaligned_report.txt + md5sum: c1c26797084ea743ec5a224ab97adb1f + - path: ./output/quast/quast/genome_stats/GCA_011545545-1_ASM1154554v1_cds_from_genomic_gaps.txt + md5sum: c52381f09ea40b6141be5232494727b6 + - path: ./output/quast/quast/icarus_viewers/alignment_viewer.html + md5sum: ad5176f21d3c4809a9a8f9c27bb8d70a + - path: ./output/quast/quast/contigs_reports/misassemblies_report.tex + md5sum: ffe19cf4d5332952f0627e9cd82e3375 + - path: ./output/quast/quast/contigs_reports/minimap_output/GCA_011545545-1_ASM1154554v1_cds_from_genomic.coords_tmp + md5sum: ce66eaeb99fdc11e4d50efadc1816e04 + - path: ./output/quast/quast/basic_stats/gc.icarus.txt + md5sum: b3a770802ff9b2dd4ee8e47bddb2df3e + - path: ./output/quast/quast/basic_stats/Nx_plot.pdf + - path: ./output/quast/quast/transposed_report.tsv + md5sum: 1754bd6c6fa8a0172a342a48dd3ca505 - path: ./output/quast/quast/basic_stats/cumulative_plot.pdf + - path: ./output/quast/quast/report.txt + md5sum: e334b3390a5028cbf88fe4ccab2b6499 + - path: ./output/quast/quast/contigs_reports/misassemblies_plot.pdf + - path: ./output/quast/quast/report.tsv + md5sum: b203a9d2c995bd66552eeb5cb0a98762 + - path: ./output/quast/quast/contigs_reports/GCA_011545545_1_ASM1154554v1_cds_from_genomic.mis_contigs.fa + md5sum: d41d8cd98f00b204e9800998ecf8427e + - path: ./output/quast/quast/aligned_stats/NAx_plot.pdf - name: quast_noref command: nextflow run ./tests/software/quast -profile docker -entry test_quast_noref -c ./tests/config/nextflow.config @@ -87,28 +93,28 @@ - quast - quast_no_reference files: - - path: ./output/quast/quast/report.pdf - - path: ./output/quast/quast/basic_stats/GC_content_plot.pdf - - path: ./output/quast/quast/transposed_report.tsv - md5sum: 1a82adfc057b6dc788034a6ce023cb56 - - path: ./output/quast/quast/basic_stats/Nx_plot.pdf - - path: ./output/quast/quast/quast.log - - path: ./output/quast/quast/basic_stats/cumulative_plot.pdf - - path: ./output/quast/quast/transposed_report.tex - md5sum: a86aa094f9ab4bc1df35c5a7add2d0b0 - - path: ./output/quast/quast/basic_stats/GCA_011545545.1_ASM1154554v1_genomic_GC_content_plot.pdf - - path: ./output/quast/quast/report.txt - md5sum: 7a2e442c18dd2730cfd38723f1c9c8f9 - path: ./output/quast/quast/icarus_viewers/contig_size_viewer.html - md5sum: dcf600c49ee86783475cb25215072630 - - path: ./output/quast/quast/report.tsv - md5sum: 75882c0a5d811246395f5ea56146ce76 - - path: ./output/quast/quast/report.tex - md5sum: 132edd2e916fc2a76a7b13973a0ffa4b - - path: ./output/quast/quast/icarus.html - md5sum: 9d7429362288c5078e6d6e7efcfc1ff7 + md5sum: d2680b8083139e62baf7af0f852d52b8 - path: ./output/quast/quast/transposed_report.txt - md5sum: 154d88ec197c7b1bda5938232a79a00a + md5sum: b6b126e9dcfd8c8e7bd36dff9220caf0 - path: ./output/quast/report.tsv - md5sum: 75882c0a5d811246395f5ea56146ce76 + md5sum: 55d2938fcdb678e97d441cf32b9c740e + - path: ./output/quast/quast/icarus.html + md5sum: dcb11b4c7b6c21190c1344c46288d3f4 + - path: ./output/quast/quast/report.txt + md5sum: c8e87f40e888a0395be04f78532d9deb + - path: ./output/quast/quast/transposed_report.tsv + md5sum: 27b6c755be5d70e3eed22e1bf3f68ce5 + - path: ./output/quast/quast/quast.log + - path: ./output/quast/quast/report.tex + md5sum: 69c31172ae6257663b22bb192ba84682 + - path: ./output/quast/quast/report.pdf + - path: ./output/quast/quast/basic_stats/GCA_011545545.1_ASM1154554v1_cds_from_genomic_GC_content_plot.pdf + - path: ./output/quast/quast/basic_stats/cumulative_plot.pdf + - path: ./output/quast/quast/report.tsv + md5sum: 55d2938fcdb678e97d441cf32b9c740e + - path: ./output/quast/quast/transposed_report.tex + md5sum: 213fb615afe21904e52d670e602c1f62 + - path: ./output/quast/quast/basic_stats/GC_content_plot.pdf + - path: ./output/quast/quast/basic_stats/Nx_plot.pdf - path: ./output/quast/quast/report.html From 038381de99f027b5b3f61d05e0695d4fb148d163 Mon Sep 17 00:00:00 2001 From: kevinmenden Date: Mon, 1 Feb 2021 13:54:08 +0100 Subject: [PATCH 33/42] added fastp module --- software/fastp/functions.nf | 59 +++++++++++++++++++++++++++ software/fastp/main.nf | 72 +++++++++++++++++++++++++++++++++ software/fastp/meta.yml | 79 +++++++++++++++++++++++++++++++++++++ 3 files changed, 210 insertions(+) create mode 100644 software/fastp/functions.nf create mode 100644 software/fastp/main.nf create mode 100644 software/fastp/meta.yml diff --git a/software/fastp/functions.nf b/software/fastp/functions.nf new file mode 100644 index 00000000..d25eea86 --- /dev/null +++ b/software/fastp/functions.nf @@ -0,0 +1,59 @@ +/* + * ----------------------------------------------------- + * Utility functions used in nf-core DSL2 module files + * ----------------------------------------------------- + */ + +/* + * Extract name of software tool from process name using $task.process + */ +def getSoftwareName(task_process) { + return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase() +} + +/* + * Function to initialise default values and to generate a Groovy Map of available options for nf-core modules + */ +def initOptions(Map args) { + def Map options = [:] + options.args = args.args ?: '' + options.args2 = args.args2 ?: '' + options.publish_by_id = args.publish_by_id ?: false + options.publish_dir = args.publish_dir ?: '' + options.publish_files = args.publish_files + options.suffix = args.suffix ?: '' + return options +} + +/* + * Tidy up and join elements of a list to return a path string + */ +def getPathFromList(path_list) { + def paths = path_list.findAll { item -> !item?.trim().isEmpty() } // Remove empty entries + paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes + return paths.join('/') +} + +/* + * Function to save/publish module results + */ +def saveFiles(Map args) { + if (!args.filename.endsWith('.version.txt')) { + def ioptions = initOptions(args.options) + def path_list = [ ioptions.publish_dir ?: args.publish_dir ] + if (ioptions.publish_by_id) { + path_list.add(args.publish_id) + } + if (ioptions.publish_files instanceof Map) { + for (ext in ioptions.publish_files) { + if (args.filename.endsWith(ext.key)) { + def ext_list = path_list.collect() + ext_list.add(ext.value) + return "${getPathFromList(ext_list)}/$args.filename" + } + } + } else if (ioptions.publish_files == null) { + return "${getPathFromList(path_list)}/$args.filename" + } + } +} diff --git a/software/fastp/main.nf b/software/fastp/main.nf new file mode 100644 index 00000000..a9d048cf --- /dev/null +++ b/software/fastp/main.nf @@ -0,0 +1,72 @@ +// Import generic module functions +include { initOptions; saveFiles; getSoftwareName } from './functions' + +params.options = [:] +def options = initOptions(params.options) + +process FASTP { + tag "$meta.id" + label 'process_medium' + publishDir "${params.outdir}", + mode: params.publish_dir_mode, + saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) } + + conda (params.enable_conda ? 'bioconda::fastp=0.20.1' : null) + if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) { + container 'https://depot.galaxyproject.org/singularity/fastp:0.20.1--h8b12597_0' + } else { + container 'quay.io/biocontainers/fastp:0.20.1--h8b12597_0' + } + + input: + tuple val(meta), path(reads) + + output: + tuple val(meta), path('*.trim.fastq.gz'), emit: reads + tuple val(meta), path('*.json') , emit: json + tuple val(meta), path('*.html') , emit: html + tuple val(meta), path('*.log') , emit: log + path '*.version.txt' , emit: version + tuple val(meta), path('*.fail.fastq.gz'), optional:true, emit: reads_fail + + script: + // Added soft-links to original fastqs for consistent naming in MultiQC + def software = getSoftwareName(task.process) + def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}" + if (meta.single_end) { + def fail_fastq = params.save_trimmed_fail ? "--failed_out ${prefix}.fail.fastq.gz" : '' + """ + [ ! -f ${prefix}.fastq.gz ] && ln -s $reads ${prefix}.fastq.gz + fastp \\ + --in1 ${prefix}.fastq.gz \\ + --out1 ${prefix}.trim.fastq.gz \\ + --thread $task.cpus \\ + --json ${prefix}.fastp.json \\ + --html ${prefix}.fastp.html \\ + $fail_fastq \\ + $options.args \\ + 2> ${prefix}.fastp.log + echo \$(fastp --version 2>&1) | sed -e "s/fastp //g" > ${software}.version.txt + """ + } else { + def fail_fastq = params.save_trimmed_fail ? "--unpaired1 ${prefix}_1.fail.fastq.gz --unpaired2 ${prefix}_2.fail.fastq.gz" : '' + """ + [ ! -f ${prefix}_1.fastq.gz ] && ln -s ${reads[0]} ${prefix}_1.fastq.gz + [ ! -f ${prefix}_2.fastq.gz ] && ln -s ${reads[1]} ${prefix}_2.fastq.gz + fastp \\ + --in1 ${prefix}_1.fastq.gz \\ + --in2 ${prefix}_2.fastq.gz \\ + --out1 ${prefix}_1.trim.fastq.gz \\ + --out2 ${prefix}_2.trim.fastq.gz \\ + --json ${prefix}.fastp.json \\ + --html ${prefix}.fastp.html \\ + $fail_fastq \\ + --thread $task.cpus \\ + --detect_adapter_for_pe \\ + $options.args \\ + 2> ${prefix}.fastp.log + + echo \$(fastp --version 2>&1) | sed -e "s/fastp //g" > ${software}.version.txt + """ + } +} diff --git a/software/fastp/meta.yml b/software/fastp/meta.yml new file mode 100644 index 00000000..2846d834 --- /dev/null +++ b/software/fastp/meta.yml @@ -0,0 +1,79 @@ +name: fastp +description: Perform adapter/quality trimming on sequencing reads +keywords: + - trimming + - quality control + - fastq +tools: + - fastq: + description: | + A tool designed to provide fast all-in-one preprocessing for FastQ files. This tool is developed in C++ with multithreading supported to afford high performance. + documentation: https://github.com/OpenGene/fastp + doi: https://doi.org/10.1093/bioinformatics/bty560 +params: + - outdir: + type: string + description: | + The pipeline's output directory. By default, the module will + output files into `$params.outdir/` + - publish_dir_mode: + type: string + description: | + Value for the Nextflow `publishDir` mode parameter. + Available: symlink, rellink, link, copy, copyNoFollow, move. + - enable_conda: + type: boolean + description: | + Run the module with Conda using the software specified + via the `conda` directive + - singularity_pull_docker_container: + type: boolean + description: | + Instead of directly downloading Singularity images for use with Singularity, + force the workflow to pull and convert Docker containers instead. + +input: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - reads: + type: file + description: | + List of input FastQ files of size 1 and 2 for single-end and paired-end data, + respectively. + +output: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - reads: + type: file + description: The trimmed/modified fastq reads + pattern: "*trim.fastq.gz" + - json: + type: file + description: Results in JSON format + pattern: "*.json" + - html: + type: file + description: Results in HTML format + pattern: "*.thml" + - log: + type: file + description: fastq log file + pattern: "*.log" + - version: + type: file + description: File containing software version + pattern: "*.{version.txt}" + - reads_fail: + type: file + description: Reads the failed the preprocessing + pattern: "*fail.fastq.gz" +authors: + - "@drpatelh" + - "@kevinmenden" From e9e795633dbd91e356eaa6ba9e75ee350e2e186b Mon Sep 17 00:00:00 2001 From: kevinmenden Date: Mon, 1 Feb 2021 14:02:06 +0100 Subject: [PATCH 34/42] added fastp tests --- .github/workflows/fastp.yml | 40 +++++++++++++++++++++++++++++++++++ tests/software/fastp/main.nf | 30 ++++++++++++++++++++++++++ tests/software/fastp/test.yml | 27 +++++++++++++++++++++++ 3 files changed, 97 insertions(+) create mode 100644 .github/workflows/fastp.yml create mode 100644 tests/software/fastp/main.nf create mode 100644 tests/software/fastp/test.yml diff --git a/.github/workflows/fastp.yml b/.github/workflows/fastp.yml new file mode 100644 index 00000000..90ad15ef --- /dev/null +++ b/.github/workflows/fastp.yml @@ -0,0 +1,40 @@ +name: fastp +on: + push: + paths: + - software/fastp/** + - .github/workflows/fastp.yml + - tests + pull_request: + paths: + - software/fastp/** + - .github/workflows/fastp.yml + - tests + +jobs: + ci_test: + runs-on: ubuntu-latest + strategy: + matrix: + nxf_version: [20.11.0-edge] + env: + NXF_ANSI_LOG: false + steps: + - uses: actions/checkout@v2 + + - name: Install Nextflow + env: + NXF_VER: ${{ matrix.nxf_version }} + run: | + wget -qO- get.nextflow.io | bash + sudo mv nextflow /usr/local/bin/ + + - name: Set up Python + uses: actions/setup-python@v2 + with: + python-version: "3.x" + - name: Install dependencies + run: python -m pip install --upgrade pip pytest-workflow + + # Test the module + - run: pytest --tag fastp --symlink --wt 2 diff --git a/tests/software/fastp/main.nf b/tests/software/fastp/main.nf new file mode 100644 index 00000000..000fcdd8 --- /dev/null +++ b/tests/software/fastp/main.nf @@ -0,0 +1,30 @@ +#!/usr/bin/env nextflow + +nextflow.enable.dsl = 2 + +include { FASTP } from '../../../software/fastp/main.nf' addParams( options: [:] ) + +/* + * Test with single-end data + */ +workflow test_fastp_se { + def input = [] + input = [ [ id:'test', single_end:true ], // meta map + [ file("${launchDir}/tests/data/fastq/rna/test_single_end.fastq.gz", checkIfExists: true) ] ] + + FASTP( input ) +} + +/* + * Test with paired-end data + */ + +workflow test_fastp_pe { + def input = [] + input = [ [ id:'test', single_end:false ], // meta map + [ file("${launchDir}/tests/data/fastq/rna/test_R1.fastq.gz", checkIfExists: true), + file("${launchDir}/tests/data/fastq/rna/test_R2.fastq.gz", checkIfExists: true) ] ] + + FASTP( input ) +} + diff --git a/tests/software/fastp/test.yml b/tests/software/fastp/test.yml new file mode 100644 index 00000000..56cbcaa7 --- /dev/null +++ b/tests/software/fastp/test.yml @@ -0,0 +1,27 @@ +- name: fastp_se + command: nextflow run ./tests/software/fastp -profile docker -entry test_fastp_se -c ./tests/config/nextflow.config + tags: + - fastp + - fastp_se + files: + - path: ./output/fastp/test.fastp.json + md5sum: b81d53bfa5c1553bed89f6475edcf437 + - path: ./output/fastp/test.trim.fastq.gz + md5sum: 2f5516df477b123e3f78adb67effa3bc + - path: ./output/fastp/test.fastp.log + - path: ./output/fastp/test.fastp.html + +- name: fastp_pe + command: nextflow run ./tests/software/fastp -profile docker -entry test_fastp_pe -c ./tests/config/nextflow.config + tags: + - fastp + - fastp_pe + files: + - path: ./output/fastp/test.fastp.html + - path: ./output/fastp/test.fastp.json + md5sum: 40db7fcbed478b0a96a1c5c1bb5f737b + - path: ./output/fastp/test.fastp.log + - path: ./output/fastp/test_1.trim.fastq.gz + md5sum: c8844c05194b50ae368e6825e997aa7f + - path: ./output/fastp/test_2.trim.fastq.gz + md5sum: 9238b07bb1609e939be7c8889b72c209 From c43fe85a0c1e543ab9786348470492c7c22d9bc2 Mon Sep 17 00:00:00 2001 From: Kevin Menden Date: Mon, 1 Feb 2021 14:02:57 +0100 Subject: [PATCH 35/42] Update software/quast/main.nf Co-authored-by: Harshil Patel --- software/quast/main.nf | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/software/quast/main.nf b/software/quast/main.nf index 3690c08b..32a730fd 100644 --- a/software/quast/main.nf +++ b/software/quast/main.nf @@ -21,8 +21,8 @@ process QUAST { input: path consensus path fasta - val use_fasta path gff + val use_fasta val use_gff output: From d88bf3bddae8359506692b3b92c75039ad945aaf Mon Sep 17 00:00:00 2001 From: Kevin Menden Date: Mon, 1 Feb 2021 14:03:06 +0100 Subject: [PATCH 36/42] Update software/quast/main.nf Co-authored-by: Harshil Patel --- software/quast/main.nf | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/software/quast/main.nf b/software/quast/main.nf index 32a730fd..2acdc270 100644 --- a/software/quast/main.nf +++ b/software/quast/main.nf @@ -38,8 +38,8 @@ process QUAST { """ quast.py \\ --output-dir $prefix \\ - ${reference} \\ - ${features} \\ + $reference \\ + $features \\ --threads $task.cpus \\ $options.args \\ ${consensus.join(' ')} From c807c6c438a04967b05b4c54a2f463d12d7c24fb Mon Sep 17 00:00:00 2001 From: Kevin Menden Date: Mon, 1 Feb 2021 14:03:15 +0100 Subject: [PATCH 37/42] Update software/quast/main.nf Co-authored-by: Harshil Patel --- software/quast/main.nf | 1 - 1 file changed, 1 deletion(-) diff --git a/software/quast/main.nf b/software/quast/main.nf index 2acdc270..4d5ed531 100644 --- a/software/quast/main.nf +++ b/software/quast/main.nf @@ -5,7 +5,6 @@ params.options = [:] def options = initOptions(params.options) process QUAST { - tag "$fasta" label 'process_medium' publishDir "${params.outdir}", mode: params.publish_dir_mode, From 9885da628e6f170ca1375fbebdae27f9d8375d03 Mon Sep 17 00:00:00 2001 From: Kevin Menden Date: Mon, 1 Feb 2021 14:03:22 +0100 Subject: [PATCH 38/42] Update software/quast/meta.yml Co-authored-by: Harshil Patel --- software/quast/meta.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/software/quast/meta.yml b/software/quast/meta.yml index ae63de65..004b1554 100644 --- a/software/quast/meta.yml +++ b/software/quast/meta.yml @@ -49,7 +49,7 @@ input: description: The genome GFF file. Has to contain at least a non-empty string dummy value. - use_gff: type: boolean - description: Whether to use a gff reference + description: Whether to use the provided gff reference annotation file output: - quast: From f6c4e9d9c1d79e8846db04944734c7c93f1cad22 Mon Sep 17 00:00:00 2001 From: Kevin Menden Date: Mon, 1 Feb 2021 14:03:36 +0100 Subject: [PATCH 39/42] Update software/quast/meta.yml Co-authored-by: Harshil Patel --- software/quast/meta.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/software/quast/meta.yml b/software/quast/meta.yml index 004b1554..dde96c97 100644 --- a/software/quast/meta.yml +++ b/software/quast/meta.yml @@ -43,7 +43,7 @@ input: The genome assembly to be evaluated. Has to contain at least a non-empty string dummy value. - use_fasta: type: boolean - description: Whether to use a fasta reference + description: Whether to use the provided fasta reference genome file - gff: type: file description: The genome GFF file. Has to contain at least a non-empty string dummy value. From 05370b5e1609aa5bdaa7dca647e9cbcb2fdeaa54 Mon Sep 17 00:00:00 2001 From: Kevin Menden Date: Mon, 1 Feb 2021 14:03:49 +0100 Subject: [PATCH 40/42] Update tests/software/quast/main.nf Co-authored-by: Harshil Patel --- tests/software/quast/main.nf | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/tests/software/quast/main.nf b/tests/software/quast/main.nf index 7ef3d9ac..ab9862da 100644 --- a/tests/software/quast/main.nf +++ b/tests/software/quast/main.nf @@ -11,7 +11,7 @@ workflow test_quast_ref { def use_fasta = true def use_gtf = true - QUAST( consensus, fasta, use_fasta, gff, use_gtf) + QUAST( consensus, fasta, gff, use_fasta, use_gtf ) } workflow test_quast_noref { From 0bd8506ea10d5373c17f97ad43602bd0b203b8a8 Mon Sep 17 00:00:00 2001 From: Kevin Menden Date: Mon, 1 Feb 2021 14:04:08 +0100 Subject: [PATCH 41/42] Update tests/software/quast/main.nf Co-authored-by: Harshil Patel --- tests/software/quast/main.nf | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/tests/software/quast/main.nf b/tests/software/quast/main.nf index ab9862da..89a1637c 100644 --- a/tests/software/quast/main.nf +++ b/tests/software/quast/main.nf @@ -21,5 +21,5 @@ workflow test_quast_noref { def use_fasta = false def use_gtf = false - QUAST( consensus, fasta, use_fasta, gff, use_gtf) + QUAST( consensus, fasta, gff, use_fasta, use_gtf ) } From f84e5b59ca97ef04551c6134cae023164501137c Mon Sep 17 00:00:00 2001 From: drpatelh Date: Mon, 1 Feb 2021 17:53:31 +0000 Subject: [PATCH 42/42] Rename bowtie_index to bowtie_build --- .../{bowtie_index.yml => bowtie_build.yml} | 12 ++++++------ software/bowtie/{index => build}/functions.nf | 0 software/bowtie/{index => build}/main.nf | 6 +++--- software/bowtie/{index => build}/meta.yml | 3 ++- tests/software/bowtie/main.nf | 14 +++++++------- tests/software/bowtie/test.yml | 8 ++++---- 6 files changed, 22 insertions(+), 21 deletions(-) rename .github/workflows/{bowtie_index.yml => bowtie_build.yml} (76%) rename software/bowtie/{index => build}/functions.nf (100%) rename software/bowtie/{index => build}/main.nf (90%) rename software/bowtie/{index => build}/meta.yml (97%) diff --git a/.github/workflows/bowtie_index.yml b/.github/workflows/bowtie_build.yml similarity index 76% rename from .github/workflows/bowtie_index.yml rename to .github/workflows/bowtie_build.yml index 291d04f5..1a02341e 100644 --- a/.github/workflows/bowtie_index.yml +++ b/.github/workflows/bowtie_build.yml @@ -1,14 +1,14 @@ -name: bowtie_index +name: bowtie_build on: push: paths: - - software/bowtie/index/** - - .github/workflows/bowtie_index.yml + - software/bowtie/build/** + - .github/workflows/bowtie_build.yml - tests/software/bowtie/** pull_request: paths: - - software/bowtie/index/** - - .github/workflows/bowtie_index.yml + - software/bowtie/build/** + - .github/workflows/bowtie_build.yml - tests/software/bowtie/** jobs: @@ -37,4 +37,4 @@ jobs: run: python -m pip install --upgrade pip pytest-workflow # Test the module - - run: pytest --tag bowtie_index --symlink --wt 2 + - run: pytest --tag bowtie_build --symlink --wt 2 diff --git a/software/bowtie/index/functions.nf b/software/bowtie/build/functions.nf similarity index 100% rename from software/bowtie/index/functions.nf rename to software/bowtie/build/functions.nf diff --git a/software/bowtie/index/main.nf b/software/bowtie/build/main.nf similarity index 90% rename from software/bowtie/index/main.nf rename to software/bowtie/build/main.nf index 8b982bcf..4dd20b85 100644 --- a/software/bowtie/index/main.nf +++ b/software/bowtie/build/main.nf @@ -4,7 +4,7 @@ include { initOptions; saveFiles; getSoftwareName } from './functions' params.options = [:] def options = initOptions(params.options) -process BOWTIE_INDEX { +process BOWTIE_BUILD { tag "$fasta" label 'process_high' publishDir "${params.outdir}", @@ -22,11 +22,11 @@ process BOWTIE_INDEX { path fasta output: - path 'bowtie', emit: index + path 'bowtie' , emit: index path '*.version.txt', emit: version script: - def software = getSoftwareName(task.process) + def software = getSoftwareName(task.process) """ mkdir bowtie bowtie-build --threads $task.cpus $fasta bowtie/${fasta.baseName} diff --git a/software/bowtie/index/meta.yml b/software/bowtie/build/meta.yml similarity index 97% rename from software/bowtie/index/meta.yml rename to software/bowtie/build/meta.yml index e5296b05..f9a8f1c9 100644 --- a/software/bowtie/index/meta.yml +++ b/software/bowtie/build/meta.yml @@ -1,4 +1,4 @@ -name: bowtie_index +name: bowtie_build description: Create bowtie index for reference genome keywords: - index @@ -49,3 +49,4 @@ output: pattern: "*.{version.txt}" authors: - "@kevinmenden" + - "@drpatelh" diff --git a/tests/software/bowtie/main.nf b/tests/software/bowtie/main.nf index c496a619..1073195d 100644 --- a/tests/software/bowtie/main.nf +++ b/tests/software/bowtie/main.nf @@ -2,32 +2,32 @@ nextflow.enable.dsl = 2 -include { BOWTIE_INDEX } from '../../../software/bowtie/index/main.nf' addParams( options: [:] ) +include { BOWTIE_BUILD } from '../../../software/bowtie/build/main.nf' addParams( options: [:] ) include { BOWTIE_ALIGN } from '../../../software/bowtie/align/main.nf' addParams( options: [:] ) -workflow test_bowtie_index { +workflow test_bowtie_build { fasta = file("${launchDir}/tests/data/fasta/E_coli/NC_010473.fa", checkIfExists: true) - BOWTIE_INDEX ( fasta ) + BOWTIE_BUILD ( fasta ) } workflow test_bowtie_alignment_single_end { fasta = file("${launchDir}/tests/data/fasta/E_coli/NC_010473.fa", checkIfExists: true) - BOWTIE_INDEX ( fasta ) + BOWTIE_BUILD ( fasta ) def input = [] input = [ [ id:'test', single_end:true ], // meta map [ file("${launchDir}/tests/data/fastq/rna/test_R1.fastq.gz", checkIfExists: true) ] ] - BOWTIE_ALIGN ( input, BOWTIE_INDEX.out.index ) + BOWTIE_ALIGN ( input, BOWTIE_BUILD.out.index ) } workflow test_bowtie_alignment_paired_end { fasta = file("${launchDir}/tests/data/fasta/E_coli/NC_010473.fa", checkIfExists: true) - BOWTIE_INDEX ( fasta ) + BOWTIE_BUILD ( fasta ) def input = [] input = [ [ id:'test', single_end:false ], // meta map [ file("${launchDir}/tests/data/fastq/rna/test_R1.fastq.gz", checkIfExists: true), file("${launchDir}/tests/data/fastq/rna/test_R2.fastq.gz", checkIfExists: true) ] ] - BOWTIE_ALIGN ( input, BOWTIE_INDEX.out.index ) + BOWTIE_ALIGN ( input, BOWTIE_BUILD.out.index ) } diff --git a/tests/software/bowtie/test.yml b/tests/software/bowtie/test.yml index 229165ac..96037548 100644 --- a/tests/software/bowtie/test.yml +++ b/tests/software/bowtie/test.yml @@ -1,8 +1,8 @@ -- name: Run bowtie index - command: nextflow run ./tests/software/bowtie -profile docker -entry test_bowtie_index -c tests/config/nextflow.config +- name: Run bowtie build + command: nextflow run ./tests/software/bowtie -profile docker -entry test_bowtie_build -c tests/config/nextflow.config tags: - bowtie - - bowtie_index + - bowtie_build files: - path: output/bowtie/bowtie/NC_010473.1.ebwt md5sum: 90f0b7aa5bbaeaaa999839ac13ad203c @@ -17,7 +17,7 @@ - path: output/bowtie/bowtie/NC_010473.rev.2.ebwt md5sum: f3c398bba5158f4039334a932d79c051 -- name: Run bowtie index and align single-end +- name: Run bowtie build and align single-end command: nextflow run ./tests/software/bowtie -profile docker -entry test_bowtie_alignment_single_end -c tests/config/nextflow.config tags: - bowtie