From f65d896f57a5564a40278f4df7f627e8f8a17d6b Mon Sep 17 00:00:00 2001 From: Mahesh Binzer-Panchal Date: Mon, 9 May 2022 15:09:15 +0000 Subject: [PATCH 1/6] create genomescope2 module --- modules/genomescope2/main.nf | 42 +++++++++++++++++++++ modules/genomescope2/meta.yml | 43 ++++++++++++++++++++++ tests/config/pytest_modules.yml | 12 ++++-- tests/modules/genomescope2/main.nf | 19 ++++++++++ tests/modules/genomescope2/nextflow.config | 13 +++++++ tests/modules/genomescope2/test.yml | 12 ++++++ 6 files changed, 137 insertions(+), 4 deletions(-) create mode 100644 modules/genomescope2/main.nf create mode 100644 modules/genomescope2/meta.yml create mode 100644 tests/modules/genomescope2/main.nf create mode 100644 tests/modules/genomescope2/nextflow.config create mode 100644 tests/modules/genomescope2/test.yml diff --git a/modules/genomescope2/main.nf b/modules/genomescope2/main.nf new file mode 100644 index 00000000..d81ed27a --- /dev/null +++ b/modules/genomescope2/main.nf @@ -0,0 +1,42 @@ +process GENOMESCOPE2 { + tag "$meta.id" + label 'process_low' + + conda (params.enable_conda ? "bioconda::genomescope2=2.0" : null) + container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + 'https://depot.galaxyproject.org/singularity/genomescope2:2.0--py310r41hdfd78af_5': + 'quay.io/biocontainers/genomescope2:2.0--py310r41hdfd78af_5' }" + + input: + tuple val(meta), path(histogram) + + output: + tuple val(meta), path("$prefix-linear_plot.png") , emit: linear_plot_png + tuple val(meta), path("$prefix-transformed_linear_plot.png"), emit: transformed_linear_plot_png + tuple val(meta), path("$prefix-log_plot.png") , emit: log_plot_png + tuple val(meta), path("$prefix-transformed_log_plot.png") , emit: transformed_log_plot_png + tuple val(meta), path("$prefix-model.txt") , emit: model + tuple val(meta), path("$prefix-summary.txt") , emit: summary + path "versions.yml" , emit: versions + + when: + task.ext.when == null || task.ext.when + + script: + def args = task.ext.args ?: '' + prefix = task.ext.prefix ?: "${meta.id}" + """ + genomescope2 \\ + --input $histogram \\ + $args \\ + --output . \\ + --name_prefix $prefix + + ls -l + + cat <<-END_VERSIONS > versions.yml + '${task.process}': + genomescope2: \$( genomescope2 -v | sed 's/GenomeScope //' ) + END_VERSIONS + """ +} diff --git a/modules/genomescope2/meta.yml b/modules/genomescope2/meta.yml new file mode 100644 index 00000000..b680bb8f --- /dev/null +++ b/modules/genomescope2/meta.yml @@ -0,0 +1,43 @@ +name: "genomescope2" +description: Estimate genome heterozygosity, repeat content, and size from sequencing reads using a kmer-based statistical approach +keywords: + - "genome size" + - "genome heterozygosity" + - "repeat content" +tools: + - "genomescope2": + description: "Reference-free profiling of polyploid genomes" + homepage: "http://qb.cshl.edu/genomescope/genomescope2.0/" + documentation: "https://github.com/tbenavi1/genomescope2.0/blob/master/README.md" + tool_dev_url: "https://github.com/tbenavi1/genomescope2.0" + doi: "https://doi.org/10.1038/s41467-020-14998-3" + licence: "['Apache License, Version 2.0 (Apache-2.0)']" + +input: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - histogram: + type: file + description: A K-mer histogram file + pattern: "*.hist" + +output: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - versions: + type: file + description: File containing software versions + pattern: "versions.yml" + - linear_plot_png: + type: file + description: A genomescope2 linear plot in PNG format + pattern: "*.png" + +authors: + - "@mahesh-panchal" diff --git a/tests/config/pytest_modules.yml b/tests/config/pytest_modules.yml index ba292bce..286bd8b8 100644 --- a/tests/config/pytest_modules.yml +++ b/tests/config/pytest_modules.yml @@ -835,6 +835,10 @@ genmap/mappability: - modules/genmap/mappability/** - tests/modules/genmap/mappability/** +genomescope2: + - modules/genomescope2/** + - tests/modules/genomescope2/** + genrich: - modules/genrich/** - tests/modules/genrich/** @@ -1639,14 +1643,14 @@ samtools/bam2fq: - modules/samtools/bam2fq/** - tests/modules/samtools/bam2fq/** -samtools/convert: - - modules/samtools/convert/** - - tests/modules/samtools/convert/** - samtools/collatefastq: - modules/samtools/collatefastq/** - tests/modules/samtools/collatefastq/** +samtools/convert: + - modules/samtools/convert/** + - tests/modules/samtools/convert/** + samtools/depth: - modules/samtools/depth/** - tests/modules/samtools/depth/** diff --git a/tests/modules/genomescope2/main.nf b/tests/modules/genomescope2/main.nf new file mode 100644 index 00000000..9f15be88 --- /dev/null +++ b/tests/modules/genomescope2/main.nf @@ -0,0 +1,19 @@ +#!/usr/bin/env nextflow + +nextflow.enable.dsl = 2 + +include { MERYL_COUNT } from '../../../modules/meryl/count/main.nf' +include { MERYL_HISTOGRAM } from '../../../modules/meryl/histogram/main.nf' +include { GENOMESCOPE2 } from '../../../modules/genomescope2/main.nf' + +workflow test_genomescope2 { + + input = [ + [ id:'test', single_end:false ], // meta map + file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true) + ] + + MERYL_COUNT ( input ) + MERYL_HISTOGRAM ( MERYL_COUNT.out.meryl_db ) + GENOMESCOPE2 ( MERYL_HISTOGRAM.out.hist ) +} diff --git a/tests/modules/genomescope2/nextflow.config b/tests/modules/genomescope2/nextflow.config new file mode 100644 index 00000000..29a0be3a --- /dev/null +++ b/tests/modules/genomescope2/nextflow.config @@ -0,0 +1,13 @@ +process { + + publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" } + + withName: 'MERYL.*' { + ext.args = 'k=21' + } + + withName: 'GENOMESCOPE2' { + ext.args = '-k 21 -p 1' + } + +} diff --git a/tests/modules/genomescope2/test.yml b/tests/modules/genomescope2/test.yml new file mode 100644 index 00000000..d2a664d9 --- /dev/null +++ b/tests/modules/genomescope2/test.yml @@ -0,0 +1,12 @@ +## TODO nf-core: Please run the following command to build this file: +# nf-core modules create-test-yml genomescope2 +- name: "genomescope2" + command: nextflow run ./tests/modules/genomescope2 -entry test_genomescope2 -c ./tests/config/nextflow.config -c ./tests/modules/genomescope2/nextflow.config + tags: + - "genomescope2" + # + files: + - path: "output/genomescope2/test.bam" + md5sum: e667c7caad0bc4b7ac383fd023c654fc + - path: output/genomescope2/versions.yml + md5sum: a01fe51bc4c6a3a6226fbf77b2c7cf3b From d54cf467f47461e8304e6fc4a4a1192869bfd792 Mon Sep 17 00:00:00 2001 From: Mahesh Binzer-Panchal Date: Wed, 11 May 2022 10:42:17 +0000 Subject: [PATCH 2/6] Update outputs and test data set --- modules/genomescope2/main.nf | 16 +++++++--------- modules/genomescope2/meta.yml | 26 +++++++++++++++++++++++++- tests/modules/genomescope2/main.nf | 2 +- tests/modules/genomescope2/test.yml | 29 ++++++++++++++++++++--------- 4 files changed, 53 insertions(+), 20 deletions(-) diff --git a/modules/genomescope2/main.nf b/modules/genomescope2/main.nf index d81ed27a..2ddf9e43 100644 --- a/modules/genomescope2/main.nf +++ b/modules/genomescope2/main.nf @@ -11,13 +11,13 @@ process GENOMESCOPE2 { tuple val(meta), path(histogram) output: - tuple val(meta), path("$prefix-linear_plot.png") , emit: linear_plot_png - tuple val(meta), path("$prefix-transformed_linear_plot.png"), emit: transformed_linear_plot_png - tuple val(meta), path("$prefix-log_plot.png") , emit: log_plot_png - tuple val(meta), path("$prefix-transformed_log_plot.png") , emit: transformed_log_plot_png - tuple val(meta), path("$prefix-model.txt") , emit: model - tuple val(meta), path("$prefix-summary.txt") , emit: summary - path "versions.yml" , emit: versions + tuple val(meta), path("*_linear_plot.png") , emit: linear_plot_png + tuple val(meta), path("*_transformed_linear_plot.png"), emit: transformed_linear_plot_png + tuple val(meta), path("*_log_plot.png") , emit: log_plot_png + tuple val(meta), path("*_transformed_log_plot.png") , emit: transformed_log_plot_png + tuple val(meta), path("*_model.txt") , emit: model + tuple val(meta), path("*_summary.txt") , emit: summary + path "versions.yml" , emit: versions when: task.ext.when == null || task.ext.when @@ -32,8 +32,6 @@ process GENOMESCOPE2 { --output . \\ --name_prefix $prefix - ls -l - cat <<-END_VERSIONS > versions.yml '${task.process}': genomescope2: \$( genomescope2 -v | sed 's/GenomeScope //' ) diff --git a/modules/genomescope2/meta.yml b/modules/genomescope2/meta.yml index b680bb8f..505daafe 100644 --- a/modules/genomescope2/meta.yml +++ b/modules/genomescope2/meta.yml @@ -37,7 +37,31 @@ output: - linear_plot_png: type: file description: A genomescope2 linear plot in PNG format - pattern: "*.png" + pattern: "*_linear_plot.png" + - linear_plot_png: + type: file + description: A genomescope2 linear plot in PNG format + pattern: "*_linear_plot.png" + - transformed_linear_plot_png: + type: file + description: A genomescope2 transformed linear plot in PNG format + pattern: "*_transformed_linear_plot.png" + - log_plot_png: + type: file + description: A genomescope2 log plot in PNG format + pattern: "*_log_plot.png" + - transformed_log_plot_png: + type: file + description: A genomescope2 transformed log plot in PNG format + pattern: "*_transformed_log_plot.png" + - model: + type: file + description: Genomescope2 model fit summary + pattern: "*_model.txt" + - summary: + type: file + description: Genomescope2 histogram summary + pattern: "*_summary.txt" authors: - "@mahesh-panchal" diff --git a/tests/modules/genomescope2/main.nf b/tests/modules/genomescope2/main.nf index 9f15be88..5ceebfd6 100644 --- a/tests/modules/genomescope2/main.nf +++ b/tests/modules/genomescope2/main.nf @@ -10,7 +10,7 @@ workflow test_genomescope2 { input = [ [ id:'test', single_end:false ], // meta map - file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true) + file(params.test_data['bacteroides_fragilis']['illumina']['test1_1_fastq_gz'], checkIfExists: true) ] MERYL_COUNT ( input ) diff --git a/tests/modules/genomescope2/test.yml b/tests/modules/genomescope2/test.yml index d2a664d9..accd2a14 100644 --- a/tests/modules/genomescope2/test.yml +++ b/tests/modules/genomescope2/test.yml @@ -1,12 +1,23 @@ -## TODO nf-core: Please run the following command to build this file: -# nf-core modules create-test-yml genomescope2 -- name: "genomescope2" - command: nextflow run ./tests/modules/genomescope2 -entry test_genomescope2 -c ./tests/config/nextflow.config -c ./tests/modules/genomescope2/nextflow.config +- name: genomescope2 test_genomescope2 + command: nextflow run tests/modules/genomescope2 -entry test_genomescope2 -c tests/config/nextflow.config tags: - - "genomescope2" - # + - genomescope2 files: - - path: "output/genomescope2/test.bam" - md5sum: e667c7caad0bc4b7ac383fd023c654fc + - path: output/genomescope2/test_linear_plot.png + md5sum: 94c165c5028156299a1d4d05766cac51 + - path: output/genomescope2/test_log_plot.png + md5sum: 9d25ca463d92a0c73a893da7fd3979ba + - path: output/genomescope2/test_model.txt + md5sum: 3caf62f715f64a2f2b8fdff5d079cb84 + - path: output/genomescope2/test_summary.txt + md5sum: 7452860e2cea99b85f3ff60daeac77f5 + - path: output/genomescope2/test_transformed_linear_plot.png + md5sum: 99a64c1c18d8670f64cb863d4334abbb + - path: output/genomescope2/test_transformed_log_plot.png + md5sum: b4e029c9fb9987ca33b17392a691c1b4 - path: output/genomescope2/versions.yml - md5sum: a01fe51bc4c6a3a6226fbf77b2c7cf3b + md5sum: 18afeb26f62a47f680b2bb3e27da9cbc + - path: output/meryl/test.hist + md5sum: f75362ab9cd70d96621b3690e952085f + - path: output/meryl/versions.yml + md5sum: 944b7ea81a82bd20174c5042857003fc From 90c67794bfe33cd82954ca482979d5e8d5d3fc12 Mon Sep 17 00:00:00 2001 From: Chris Cheshire Date: Thu, 12 May 2022 10:01:33 +0100 Subject: [PATCH 3/6] Added extra tests but error with collection --- modules/bowtie2/align/main.nf | 1 - tests/modules/bowtie2/align/main.nf | 29 +++++++++++ tests/modules/bowtie2/align/nextflow.config | 1 + tests/modules/bowtie2/align/test.yml | 56 +++++++++++++++------ 4 files changed, 71 insertions(+), 16 deletions(-) diff --git a/modules/bowtie2/align/main.nf b/modules/bowtie2/align/main.nf index 38242fcb..e4bb4327 100644 --- a/modules/bowtie2/align/main.nf +++ b/modules/bowtie2/align/main.nf @@ -69,4 +69,3 @@ process BOWTIE2_ALIGN { END_VERSIONS """ } - diff --git a/tests/modules/bowtie2/align/main.nf b/tests/modules/bowtie2/align/main.nf index f91394ff..42e2306a 100644 --- a/tests/modules/bowtie2/align/main.nf +++ b/tests/modules/bowtie2/align/main.nf @@ -30,6 +30,35 @@ workflow test_bowtie2_align_paired_end { fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) save_unaligned = false + BOWTIE2_BUILD ( fasta ) + BOWTIE2_ALIGN ( input, BOWTIE2_BUILD.out.index, save_unaligned ) +} + +workflow test_bowtie2_align_single_end_large_index { + input = [ + [ id:'test', single_end:true ], // meta map + [ + file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true) + ] + ] + fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) + save_unaligned = false + + BOWTIE2_BUILD ( fasta ) + BOWTIE2_ALIGN ( input, BOWTIE2_BUILD.out.index, save_unaligned ) +} + +workflow test_bowtie2_align_paired_end_large_index { + input = [ + [ id:'test', single_end:false ], // meta map + [ + file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true), + file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true) + ] + ] + fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) + save_unaligned = false + BOWTIE2_BUILD ( fasta ) BOWTIE2_ALIGN ( input, BOWTIE2_BUILD.out.index, save_unaligned ) } \ No newline at end of file diff --git a/tests/modules/bowtie2/align/nextflow.config b/tests/modules/bowtie2/align/nextflow.config index b4640de7..08f7bed0 100644 --- a/tests/modules/bowtie2/align/nextflow.config +++ b/tests/modules/bowtie2/align/nextflow.config @@ -5,6 +5,7 @@ params { process { publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" } + } if (params.force_large_index) { diff --git a/tests/modules/bowtie2/align/test.yml b/tests/modules/bowtie2/align/test.yml index ef05d70d..8a33c928 100644 --- a/tests/modules/bowtie2/align/test.yml +++ b/tests/modules/bowtie2/align/test.yml @@ -1,21 +1,47 @@ - name: bowtie2 align test_bowtie2_align_single_end command: nextflow run ./tests/modules/bowtie2/align -entry test_bowtie2_align_single_end -c ./tests/config/nextflow.config -c ./tests/modules/bowtie2/align/nextflow.config tags: - - bowtie2/align - bowtie2 + - bowtie2/align files: - - path: output/bowtie2/test.bam - - path: output/bowtie2/test.bowtie2.log - md5sum: 7b8a9e61b7646da1089b041333c41a87 - - path: output/bowtie2/versions.yml + - path: ./output/bowtie2/test.bam + # - path: output/bowtie2/test.bowtie2.log + # md5sum: 7b8a9e61b7646da1089b041333c41a87 + # - path: output/bowtie2/versions.yml + # md5sum: 24621c58884fe90c2255ccd1fe4352ae -- name: bowtie2 align test_bowtie2_align_paired_end - command: nextflow run ./tests/modules/bowtie2/align -entry test_bowtie2_align_paired_end -c ./tests/config/nextflow.config -c ./tests/modules/bowtie2/align/nextflow.config - tags: - - bowtie2/align - - bowtie2 - files: - - path: output/bowtie2/test.bam - - path: output/bowtie2/test.bowtie2.log - md5sum: bd89ce1b28c93bf822bae391ffcedd19 - - path: output/bowtie2/versions.yml +# - name: bowtie2 align test_bowtie2_align_paired_end +# command: nextflow run tests/modules/bowtie2/align -entry test_bowtie2_align_paired_end -c tests/config/nextflow.config -c tests/modules/bowtie2/align/nextflow.config +# tags: +# - bowtie2 +# - bowtie2/align +# files: +# - path: output/bowtie2/test.bam +# - path: output/bowtie2/test.bowtie2.log +# md5sum: bd89ce1b28c93bf822bae391ffcedd19 +# - path: output/bowtie2/versions.yml +# md5sum: f9712ca6d75393ad5c1781a2dcf82d32 + +# - name: bowtie2 align test_bowtie2_align_single_end_large_index +# command: nextflow run tests/modules/bowtie2/align -entry test_bowtie2_align_single_end_large_index -c tests/config/nextflow.config -c tests/modules/bowtie2/align/nextflow.config --force_large_index +# tags: +# - bowtie2 +# - bowtie2/align +# files: +# - path: output/bowtie2/test.bam +# - path: output/bowtie2/test.bowtie2.log +# md5sum: 7b8a9e61b7646da1089b041333c41a87 +# - path: output/bowtie2/versions.yml +# md5sum: bf0537964a85ce9461ae1b0e2f260211 + +# - name: bowtie2 align test_bowtie2_align_paired_end_large_index +# command: nextflow run tests/modules/bowtie2/align -entry test_bowtie2_align_paired_end_large_index -c tests/config/nextflow.config -c tests/modules/bowtie2/align/nextflow.config --force_large_index +# tags: +# - bowtie2 +# - bowtie2/align +# files: +# - path: output/bowtie2/test.bam +# - path: output/bowtie2/test.bowtie2.log +# md5sum: bd89ce1b28c93bf822bae391ffcedd19 +# - path: output/bowtie2/versions.yml +# md5sum: c0a88953500eaf46de7ff378a7de4a37 From 5df0bcf1bed5e5fd4e2d1850694e386e0b85b240 Mon Sep 17 00:00:00 2001 From: Mahesh Binzer-Panchal Date: Fri, 13 May 2022 11:27:42 +0200 Subject: [PATCH 4/6] Update tests/modules/genomescope2/test.yml Co-authored-by: FriederikeHanssen --- tests/modules/genomescope2/test.yml | 1 - 1 file changed, 1 deletion(-) diff --git a/tests/modules/genomescope2/test.yml b/tests/modules/genomescope2/test.yml index accd2a14..5b03f545 100644 --- a/tests/modules/genomescope2/test.yml +++ b/tests/modules/genomescope2/test.yml @@ -20,4 +20,3 @@ - path: output/meryl/test.hist md5sum: f75362ab9cd70d96621b3690e952085f - path: output/meryl/versions.yml - md5sum: 944b7ea81a82bd20174c5042857003fc From d816f2bc5d5338526919d7e1eea42ca6143513fb Mon Sep 17 00:00:00 2001 From: Chris Cheshire Date: Fri, 13 May 2022 12:01:16 +0100 Subject: [PATCH 5/6] Reactivated all tests --- tests/modules/bowtie2/align/test.yml | 70 +++++++++++++--------------- 1 file changed, 33 insertions(+), 37 deletions(-) diff --git a/tests/modules/bowtie2/align/test.yml b/tests/modules/bowtie2/align/test.yml index 8a33c928..56a8bf53 100644 --- a/tests/modules/bowtie2/align/test.yml +++ b/tests/modules/bowtie2/align/test.yml @@ -5,43 +5,39 @@ - bowtie2/align files: - path: ./output/bowtie2/test.bam - # - path: output/bowtie2/test.bowtie2.log - # md5sum: 7b8a9e61b7646da1089b041333c41a87 - # - path: output/bowtie2/versions.yml - # md5sum: 24621c58884fe90c2255ccd1fe4352ae + - path: ./output/bowtie2/test.bowtie2.log + - path: ./output/bowtie2/versions.yml + md5sum: 24621c58884fe90c2255ccd1fe4352ae -# - name: bowtie2 align test_bowtie2_align_paired_end -# command: nextflow run tests/modules/bowtie2/align -entry test_bowtie2_align_paired_end -c tests/config/nextflow.config -c tests/modules/bowtie2/align/nextflow.config -# tags: -# - bowtie2 -# - bowtie2/align -# files: -# - path: output/bowtie2/test.bam -# - path: output/bowtie2/test.bowtie2.log -# md5sum: bd89ce1b28c93bf822bae391ffcedd19 -# - path: output/bowtie2/versions.yml -# md5sum: f9712ca6d75393ad5c1781a2dcf82d32 +- name: bowtie2 align test_bowtie2_align_paired_end + command: nextflow run tests/modules/bowtie2/align -entry test_bowtie2_align_paired_end -c tests/config/nextflow.config -c tests/modules/bowtie2/align/nextflow.config + tags: + - bowtie2 + - bowtie2/align + files: + - path: ./output/bowtie2/test.bam + - path: ./output/bowtie2/test.bowtie2.log + - path: ./output/bowtie2/versions.yml + md5sum: f9712ca6d75393ad5c1781a2dcf82d32 -# - name: bowtie2 align test_bowtie2_align_single_end_large_index -# command: nextflow run tests/modules/bowtie2/align -entry test_bowtie2_align_single_end_large_index -c tests/config/nextflow.config -c tests/modules/bowtie2/align/nextflow.config --force_large_index -# tags: -# - bowtie2 -# - bowtie2/align -# files: -# - path: output/bowtie2/test.bam -# - path: output/bowtie2/test.bowtie2.log -# md5sum: 7b8a9e61b7646da1089b041333c41a87 -# - path: output/bowtie2/versions.yml -# md5sum: bf0537964a85ce9461ae1b0e2f260211 +- name: bowtie2 align test_bowtie2_align_single_end_large_index + command: nextflow run tests/modules/bowtie2/align -entry test_bowtie2_align_single_end_large_index -c tests/config/nextflow.config -c tests/modules/bowtie2/align/nextflow.config --force_large_index + tags: + - bowtie2 + - bowtie2/align + files: + - path: ./output/bowtie2/test.bam + - path: ./output/bowtie2/test.bowtie2.log + - path: ./output/bowtie2/versions.yml + md5sum: bf0537964a85ce9461ae1b0e2f260211 -# - name: bowtie2 align test_bowtie2_align_paired_end_large_index -# command: nextflow run tests/modules/bowtie2/align -entry test_bowtie2_align_paired_end_large_index -c tests/config/nextflow.config -c tests/modules/bowtie2/align/nextflow.config --force_large_index -# tags: -# - bowtie2 -# - bowtie2/align -# files: -# - path: output/bowtie2/test.bam -# - path: output/bowtie2/test.bowtie2.log -# md5sum: bd89ce1b28c93bf822bae391ffcedd19 -# - path: output/bowtie2/versions.yml -# md5sum: c0a88953500eaf46de7ff378a7de4a37 +- name: bowtie2 align test_bowtie2_align_paired_end_large_index + command: nextflow run tests/modules/bowtie2/align -entry test_bowtie2_align_paired_end_large_index -c tests/config/nextflow.config -c tests/modules/bowtie2/align/nextflow.config --force_large_index + tags: + - bowtie2 + - bowtie2/align + files: + - path: ./output/bowtie2/test.bam + - path: ./output/bowtie2/test.bowtie2.log + - path: ./output/bowtie2/versions.yml + md5sum: c0a88953500eaf46de7ff378a7de4a37 From ea55129ba3e3cef1a38df236c95d3d4daca63265 Mon Sep 17 00:00:00 2001 From: Chris Cheshire Date: Fri, 13 May 2022 12:20:41 +0100 Subject: [PATCH 6/6] Removed version file checksums --- tests/modules/bowtie2/align/test.yml | 4 ---- 1 file changed, 4 deletions(-) diff --git a/tests/modules/bowtie2/align/test.yml b/tests/modules/bowtie2/align/test.yml index 56a8bf53..103d65e9 100644 --- a/tests/modules/bowtie2/align/test.yml +++ b/tests/modules/bowtie2/align/test.yml @@ -7,7 +7,6 @@ - path: ./output/bowtie2/test.bam - path: ./output/bowtie2/test.bowtie2.log - path: ./output/bowtie2/versions.yml - md5sum: 24621c58884fe90c2255ccd1fe4352ae - name: bowtie2 align test_bowtie2_align_paired_end command: nextflow run tests/modules/bowtie2/align -entry test_bowtie2_align_paired_end -c tests/config/nextflow.config -c tests/modules/bowtie2/align/nextflow.config @@ -18,7 +17,6 @@ - path: ./output/bowtie2/test.bam - path: ./output/bowtie2/test.bowtie2.log - path: ./output/bowtie2/versions.yml - md5sum: f9712ca6d75393ad5c1781a2dcf82d32 - name: bowtie2 align test_bowtie2_align_single_end_large_index command: nextflow run tests/modules/bowtie2/align -entry test_bowtie2_align_single_end_large_index -c tests/config/nextflow.config -c tests/modules/bowtie2/align/nextflow.config --force_large_index @@ -29,7 +27,6 @@ - path: ./output/bowtie2/test.bam - path: ./output/bowtie2/test.bowtie2.log - path: ./output/bowtie2/versions.yml - md5sum: bf0537964a85ce9461ae1b0e2f260211 - name: bowtie2 align test_bowtie2_align_paired_end_large_index command: nextflow run tests/modules/bowtie2/align -entry test_bowtie2_align_paired_end_large_index -c tests/config/nextflow.config -c tests/modules/bowtie2/align/nextflow.config --force_large_index @@ -40,4 +37,3 @@ - path: ./output/bowtie2/test.bam - path: ./output/bowtie2/test.bowtie2.log - path: ./output/bowtie2/versions.yml - md5sum: c0a88953500eaf46de7ff378a7de4a37