From 6dca7799e6a06d6c73b98617619397cb21683e46 Mon Sep 17 00:00:00 2001 From: Anders Goncalves da Silva Date: Fri, 12 Feb 2021 16:02:10 -0800 Subject: [PATCH 01/11] Add ivar trim --- .github/filters.yml | 4 ++ software/ivar/trim/functions.nf | 59 ++++++++++++++++++++++++++++ software/ivar/trim/main.nf | 43 ++++++++++++++++++++ tests/data/bed/test-sc2-artic-v3.bed | 4 ++ tests/software/ivar/trim/main.nf | 19 +++++++++ tests/software/ivar/trim/test.yml | 8 ++++ 6 files changed, 137 insertions(+) create mode 100644 software/ivar/trim/functions.nf create mode 100644 software/ivar/trim/main.nf create mode 100644 tests/data/bed/test-sc2-artic-v3.bed create mode 100644 tests/software/ivar/trim/main.nf create mode 100644 tests/software/ivar/trim/test.yml diff --git a/.github/filters.yml b/.github/filters.yml index f074dc9d..5a1ed42e 100644 --- a/.github/filters.yml +++ b/.github/filters.yml @@ -132,6 +132,10 @@ ivar_consensus: - software/ivar/consensus/** - tests/software/ivar/consensus/** +ivar_trim: + - software/ivar/trim/** + - tests/software/ivar/trim/** + minimap2_align: - software/minimap2/align/** - tests/software/minimap2/align/** diff --git a/software/ivar/trim/functions.nf b/software/ivar/trim/functions.nf new file mode 100644 index 00000000..d25eea86 --- /dev/null +++ b/software/ivar/trim/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)}/$args.filename" + } + } +} diff --git a/software/ivar/trim/main.nf b/software/ivar/trim/main.nf new file mode 100644 index 00000000..e6ac8888 --- /dev/null +++ b/software/ivar/trim/main.nf @@ -0,0 +1,43 @@ +// Import generic module functions +include { initOptions; saveFiles; getSoftwareName } from './functions' + +params.options = [:] +def options = initOptions(params.options) + +process IVAR_TRIM { + tag "$meta.id" + label 'process_low' + publishDir "${params.outdir}", + mode: params.publish_dir_mode, + saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) } + + conda (params.enable_conda ? "bioconda::ivar=1.3.1" : null) + + + if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) { + container "https://depot.galaxyproject.org/singularity/ivar:1.3.1--h089eab3_0" + } else { + container "quay.io/biocontainers/ivar:1.3.1--h089eab3_0" + } + + input: + tuple val(meta), path(bam) + path bed + + output: + tuple val(meta), path("*.bam"), emit: bam + path "*.version.txt" , emit: version + + script: + def software = getSoftwareName(task.process) + def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}" + """ + ivar trim \\ + $options.args \\ + -i $bam \\ + -b $bed \\ + -p $prefix + + ivar version | head -n1 2>&1 | sed 's/^.*iVar version //g' > ${software}.version.txt + """ +} diff --git a/tests/data/bed/test-sc2-artic-v3.bed b/tests/data/bed/test-sc2-artic-v3.bed new file mode 100644 index 00000000..fbd2c968 --- /dev/null +++ b/tests/data/bed/test-sc2-artic-v3.bed @@ -0,0 +1,4 @@ +MN908947.3 1242 1264 nCoV-2019_5_LEFT 1 + +MN908947.3 1623 1651 nCoV-2019_5_RIGHT 1 - +MN908947.3 1573 1595 nCoV-2019_6_LEFT 2 + +MN908947.3 1942 1964 nCoV-2019_6_RIGHT 2 - \ No newline at end of file diff --git a/tests/software/ivar/trim/main.nf b/tests/software/ivar/trim/main.nf new file mode 100644 index 00000000..885da9ad --- /dev/null +++ b/tests/software/ivar/trim/main.nf @@ -0,0 +1,19 @@ +#!/usr/bin/env nextflow + +nextflow.enable.dsl = 2 +params.publish_dir_mode = 'link' +params.enable_conda = false +params.run_id = "test-run" + +include { IVAR_TRIM } from '../../../../software/ivar/trim/main.nf' addParams([:]) + +workflow test_ivar_trim { + bed_file = file("${launchDir}/tests/data/bed/test-sc2-artic-v3.bed", checkIfExists: true) + + def input = [] + input = [ [ id:'test'], + file("${launchDir}/tests/data/bam/test-sc2-artic-v3.bam", checkIfExists: true) ] + + main: + IVAR_TRIM ( input, bed_file ) +} diff --git a/tests/software/ivar/trim/test.yml b/tests/software/ivar/trim/test.yml new file mode 100644 index 00000000..75f1138c --- /dev/null +++ b/tests/software/ivar/trim/test.yml @@ -0,0 +1,8 @@ +- name: Run ivar trim test workflow + command: nextflow run ./tests/software/ivar/trim -profile docker -entry test_ivar_trim -c tests/config/nextflow.config + tags: + - ivar + - ivar_consensus + files: + - path: output/ivar/test.bam + md5sum: 09fc287d484f3a56d6868e5a3deace78 \ No newline at end of file From 7c9766962d26d1e1d47f2ab5e003e8cd969dfc59 Mon Sep 17 00:00:00 2001 From: Anders Goncalves da Silva Date: Fri, 12 Feb 2021 16:02:48 -0800 Subject: [PATCH 02/11] Add ivar trim meta.yml --- software/ivar/trim/meta.yml | 72 +++++++++++++++++++++++++++++++++++++ 1 file changed, 72 insertions(+) create mode 100644 software/ivar/trim/meta.yml diff --git a/software/ivar/trim/meta.yml b/software/ivar/trim/meta.yml new file mode 100644 index 00000000..e574beed --- /dev/null +++ b/software/ivar/trim/meta.yml @@ -0,0 +1,72 @@ +name: ivar_trim +description: Trim primer sequences rom a BAM file with iVar +keywords: + - amplicon sequencing + - trimming + - fasta +tools: + - ivar: + description: | + iVar - a computational package that contains functions broadly useful for viral amplicon-based sequencing. + homepage: https://github.com/andersen-lab/ivar + documentation: https://andersen-lab.github.io/ivar/html/manualpage.html +params: + - outdir: + type: string + description: | + The pipeline's output directory. By default, the module will + output files into `$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 ] + - bam: + type: file + description: A sorted (with samtools sort) bam file + pattern: "*.bam" + - bed: + type: file + description: BED file with primer labels and positions + pattern: "*.bed" +output: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - fasta: + type: file + description: iVar generated consensus sequence + pattern: "*.fa" + - qual: + type: file + description: iVar generated quality file + pattern: "*.qual.txt" + - mpileup: + type: file + description: mpileup output from samtools mpileup [OPTIONAL] + pattern: "*.mpileup" + - version: + type: file + description: File containing software version + pattern: "*.{version.txt}" +authors: + - "@andersgs" + - "@drpatelh" From ed74d366bf56b0f2b0a698c0cf61fabc450a703a Mon Sep 17 00:00:00 2001 From: Anders Goncalves da Silva Date: Fri, 12 Feb 2021 16:03:07 -0800 Subject: [PATCH 03/11] Clean up ivar trim main.nf --- tests/software/ivar/trim/main.nf | 3 --- 1 file changed, 3 deletions(-) diff --git a/tests/software/ivar/trim/main.nf b/tests/software/ivar/trim/main.nf index 885da9ad..b77d104f 100644 --- a/tests/software/ivar/trim/main.nf +++ b/tests/software/ivar/trim/main.nf @@ -1,9 +1,6 @@ #!/usr/bin/env nextflow nextflow.enable.dsl = 2 -params.publish_dir_mode = 'link' -params.enable_conda = false -params.run_id = "test-run" include { IVAR_TRIM } from '../../../../software/ivar/trim/main.nf' addParams([:]) From 47670a12ad139dd7996982fb831ba9fde9f59310 Mon Sep 17 00:00:00 2001 From: Anders Goncalves da Silva Date: Fri, 12 Feb 2021 16:03:18 -0800 Subject: [PATCH 04/11] Fix ivar trim test.yml --- tests/software/ivar/trim/test.yml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/tests/software/ivar/trim/test.yml b/tests/software/ivar/trim/test.yml index 75f1138c..ae1207e5 100644 --- a/tests/software/ivar/trim/test.yml +++ b/tests/software/ivar/trim/test.yml @@ -1,8 +1,8 @@ -- name: Run ivar trim test workflow - command: nextflow run ./tests/software/ivar/trim -profile docker -entry test_ivar_trim -c tests/config/nextflow.config +- name: ivar trim + command: nextflow run ./tests/software/ivar/trim -entry test_ivar_trim -c tests/config/nextflow.config tags: - ivar - - ivar_consensus + - ivar_trim files: - path: output/ivar/test.bam md5sum: 09fc287d484f3a56d6868e5a3deace78 \ No newline at end of file From bbdca4fa76e8888642c5d5ed5b6845d50c85cae1 Mon Sep 17 00:00:00 2001 From: Anders Goncalves da Silva Date: Fri, 12 Feb 2021 16:14:46 -0800 Subject: [PATCH 05/11] Fix output files --- software/ivar/trim/meta.yml | 12 ++---------- 1 file changed, 2 insertions(+), 10 deletions(-) diff --git a/software/ivar/trim/meta.yml b/software/ivar/trim/meta.yml index e574beed..f35627e9 100644 --- a/software/ivar/trim/meta.yml +++ b/software/ivar/trim/meta.yml @@ -51,18 +51,10 @@ output: description: | Groovy Map containing sample information e.g. [ id:'test', single_end:false ] - - fasta: + - bam: type: file - description: iVar generated consensus sequence + description: iVar generated trimmed bam file (unsorted) pattern: "*.fa" - - qual: - type: file - description: iVar generated quality file - pattern: "*.qual.txt" - - mpileup: - type: file - description: mpileup output from samtools mpileup [OPTIONAL] - pattern: "*.mpileup" - version: type: file description: File containing software version From cdd9be0a2d5b941ae02458d6fdf44adb433fc5a6 Mon Sep 17 00:00:00 2001 From: Harshil Patel Date: Sat, 13 Feb 2021 08:16:44 +0000 Subject: [PATCH 06/11] Update tests/software/ivar/trim/main.nf --- tests/software/ivar/trim/main.nf | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/tests/software/ivar/trim/main.nf b/tests/software/ivar/trim/main.nf index b77d104f..b18358cd 100644 --- a/tests/software/ivar/trim/main.nf +++ b/tests/software/ivar/trim/main.nf @@ -12,5 +12,5 @@ workflow test_ivar_trim { file("${launchDir}/tests/data/bam/test-sc2-artic-v3.bam", checkIfExists: true) ] main: - IVAR_TRIM ( input, bed_file ) + IVAR_TRIM ( input, bed_file ) } From 25f3d46f683169878affbcec86e96dac1471138e Mon Sep 17 00:00:00 2001 From: Harshil Patel Date: Sat, 13 Feb 2021 08:17:03 +0000 Subject: [PATCH 07/11] Update software/ivar/trim/meta.yml --- software/ivar/trim/meta.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/software/ivar/trim/meta.yml b/software/ivar/trim/meta.yml index f35627e9..4b72d968 100644 --- a/software/ivar/trim/meta.yml +++ b/software/ivar/trim/meta.yml @@ -54,7 +54,7 @@ output: - bam: type: file description: iVar generated trimmed bam file (unsorted) - pattern: "*.fa" + pattern: "*.bam" - version: type: file description: File containing software version From 9d6f29fc61631bcffdc1794bedc67d3573415f71 Mon Sep 17 00:00:00 2001 From: Harshil Patel Date: Sat, 13 Feb 2021 08:17:15 +0000 Subject: [PATCH 08/11] Update tests/software/ivar/trim/main.nf --- tests/software/ivar/trim/main.nf | 1 - 1 file changed, 1 deletion(-) diff --git a/tests/software/ivar/trim/main.nf b/tests/software/ivar/trim/main.nf index b18358cd..91f1fcdb 100644 --- a/tests/software/ivar/trim/main.nf +++ b/tests/software/ivar/trim/main.nf @@ -11,6 +11,5 @@ workflow test_ivar_trim { input = [ [ id:'test'], file("${launchDir}/tests/data/bam/test-sc2-artic-v3.bam", checkIfExists: true) ] - main: IVAR_TRIM ( input, bed_file ) } From f51f8c640015660ba00e19a820ea7d613bd2c083 Mon Sep 17 00:00:00 2001 From: Harshil Patel Date: Sat, 13 Feb 2021 08:18:32 +0000 Subject: [PATCH 09/11] Update tests/software/ivar/trim/main.nf --- tests/software/ivar/trim/main.nf | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/tests/software/ivar/trim/main.nf b/tests/software/ivar/trim/main.nf index 91f1fcdb..94fc1e10 100644 --- a/tests/software/ivar/trim/main.nf +++ b/tests/software/ivar/trim/main.nf @@ -11,5 +11,5 @@ workflow test_ivar_trim { input = [ [ id:'test'], file("${launchDir}/tests/data/bam/test-sc2-artic-v3.bam", checkIfExists: true) ] - IVAR_TRIM ( input, bed_file ) + IVAR_TRIM ( input, bed_file ) } From a5686ed14e21f98f96dfdb9488523f8e427a7cd3 Mon Sep 17 00:00:00 2001 From: Harshil Patel Date: Sat, 13 Feb 2021 08:19:55 +0000 Subject: [PATCH 10/11] Update software/ivar/trim/main.nf --- software/ivar/trim/main.nf | 1 - 1 file changed, 1 deletion(-) diff --git a/software/ivar/trim/main.nf b/software/ivar/trim/main.nf index e6ac8888..756a064a 100644 --- a/software/ivar/trim/main.nf +++ b/software/ivar/trim/main.nf @@ -13,7 +13,6 @@ process IVAR_TRIM { conda (params.enable_conda ? "bioconda::ivar=1.3.1" : null) - if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) { container "https://depot.galaxyproject.org/singularity/ivar:1.3.1--h089eab3_0" } else { From 4af9417b6d7c9db2160fc6a23f63970a046292ba Mon Sep 17 00:00:00 2001 From: Harshil Patel Date: Sat, 13 Feb 2021 08:20:06 +0000 Subject: [PATCH 11/11] Update software/ivar/trim/main.nf --- software/ivar/trim/main.nf | 1 - 1 file changed, 1 deletion(-) diff --git a/software/ivar/trim/main.nf b/software/ivar/trim/main.nf index 756a064a..f46070e8 100644 --- a/software/ivar/trim/main.nf +++ b/software/ivar/trim/main.nf @@ -12,7 +12,6 @@ process IVAR_TRIM { saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) } conda (params.enable_conda ? "bioconda::ivar=1.3.1" : null) - if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) { container "https://depot.galaxyproject.org/singularity/ivar:1.3.1--h089eab3_0" } else {