diff --git a/modules/nf-core/gatk4/addorreplacereadgroups/environment.yml b/modules/nf-core/gatk4/addorreplacereadgroups/environment.yml new file mode 100644 index 00000000000..82f9173806e --- /dev/null +++ b/modules/nf-core/gatk4/addorreplacereadgroups/environment.yml @@ -0,0 +1,7 @@ +name: gatk4_addorreplacereadgroups +channels: + - conda-forge + - bioconda + - defaults +dependencies: + - bioconda::gatk4=4.5.0.0 diff --git a/modules/nf-core/gatk4/addorreplacereadgroups/main.nf b/modules/nf-core/gatk4/addorreplacereadgroups/main.nf new file mode 100644 index 00000000000..861f7045a14 --- /dev/null +++ b/modules/nf-core/gatk4/addorreplacereadgroups/main.nf @@ -0,0 +1,71 @@ +process GATK4_ADDORREPLACEREADGROUPS { + tag "$meta.id" + label 'process_low' + + conda "${moduleDir}/environment.yml" + container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + 'https://depot.galaxyproject.org/singularity/gatk4:4.5.0.0--py36hdfd78af_0': + 'biocontainers/gatk4:4.5.0.0--py36hdfd78af_0' }" + + input: + tuple val(meta), path(bam) + tuple val(meta2), path(fasta) + tuple val(meta3), path(fasta_index) + + output: + tuple val(meta), path("*.bam") , emit: bam, optional: true + tuple val(meta), path("*.bai") , emit: bai, optional: true + tuple val(meta), path("*.cram"), emit: cram, optional: true + path "versions.yml" , emit: versions + + when: + task.ext.when == null || task.ext.when + + script: + def args = task.ext.args ?: '' + def prefix = task.ext.prefix ?: "${meta.id}" + def suffix = task.ext.suffix ?: "${bam.getExtension()}" + def reference = fasta ? "--REFERENCE_SEQUENCE ${fasta}" : "" + def create_index = ( suffix == "bam" )? "--CREATE_INDEX" : "" + def avail_mem = 3072 + if (!task.memory) { + log.info '[GATK AddOrReplaceReadGroups] Available memory not known - defaulting to 3GB. Specify process memory requirements to change this.' + } else { + avail_mem = (task.memory.mega*0.8).intValue() + } + + if ("$bam" == "${prefix}.${suffix}") error "Input and output names are the same, use \"task.ext.prefix\" to disambiguate!" + + """ + gatk --java-options "-Xmx${avail_mem}M -XX:-UsePerfData" \\ + AddOrReplaceReadGroups \\ + $args \\ + $reference \\ + $create_index \\ + --INPUT ${bam} \\ + --OUTPUT ${prefix}.${suffix} + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + gatk4: \$(echo \$(gatk AddOrReplaceReadGroups --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//') + END_VERSIONS + """ + + stub: + def prefix = task.ext.prefix ?: "${meta.id}" + def suffix = task.ext.suffix ?: "${bam.getExtension()}" + if ("$bam" == "${prefix}.${suffix}") error "Input and output names are the same, use \"task.ext.prefix\" to disambiguate!" + def create_index = "" + if (suffix == "bam") { + create_index = "touch ${prefix}.${suffix}.bai" + } + """ + touch ${prefix}.${suffix} + ${create_index} + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + gatk4: \$(echo \$(gatk AddOrReplaceReadGroups --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//') + END_VERSIONS + """ +} diff --git a/modules/nf-core/gatk4/addorreplacereadgroups/meta.yml b/modules/nf-core/gatk4/addorreplacereadgroups/meta.yml new file mode 100644 index 00000000000..d78081d5db9 --- /dev/null +++ b/modules/nf-core/gatk4/addorreplacereadgroups/meta.yml @@ -0,0 +1,80 @@ +name: gatk4_addorreplacereadgroups +description: Assigns all the reads in a file to a single new read-group +keywords: + - add + - replace + - read-group + - picard + - gatk +tools: + - gatk4: + description: | + Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools + with a primary focus on variant discovery and genotyping. Its powerful processing engine + and high-performance computing features make it capable of taking on projects of any size. + homepage: https://gatk.broadinstitute.org/hc/en-us + documentation: https://gatk.broadinstitute.org/hc/en-us/categories/360002369672s + doi: 10.1158/1538-7445.AM2017-3590 + licence: ["Apache-2.0"] +input: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - meta2: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - meta3: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bam: + type: file + description: Input BAM file + pattern: "*.{bam}" + - fasta: + type: file + description: Reference genome file + pattern: "*.{fasta,fa,fasta.gz,fa.gz}" + - fasta_index: + type: file + description: Reference genome index file + pattern: "*.{fai,fasta.fai,fa.fai,fasta.gz.fai,fa.gz.fai}" +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" + - bam: + type: file + description: Output BAM file + pattern: "*.{bam}" + - bai: + type: file + description: An optional BAM index file + pattern: "*.{bai}" + - cram: + type: file + description: Output CRAM file + pattern: "*.{cram}" +authors: + - "@sateeshperi" + - "@mjcipriano" + - "@hseabolt" + - "@cmatKhan" + - "@muffato" +maintainers: + - "@sateeshperi" + - "@mjcipriano" + - "@hseabolt" + - "@cmatKhan" + - "@muffato" diff --git a/modules/nf-core/gatk4/addorreplacereadgroups/tests/bam.config b/modules/nf-core/gatk4/addorreplacereadgroups/tests/bam.config new file mode 100644 index 00000000000..21573297604 --- /dev/null +++ b/modules/nf-core/gatk4/addorreplacereadgroups/tests/bam.config @@ -0,0 +1,12 @@ +process { + withName: 'GATK4_ADDORREPLACEREADGROUPS'{ + ext.prefix = { "${meta.id}.replaced"} + ext.args = {[ + "-LB ${meta.id}", + "-PL ILLUMINA", + "-PU bc1", + "-SM ${meta.id}" + ].join(' ').trim()} + } + +} diff --git a/modules/nf-core/gatk4/addorreplacereadgroups/tests/cram.config b/modules/nf-core/gatk4/addorreplacereadgroups/tests/cram.config new file mode 100644 index 00000000000..3885afca292 --- /dev/null +++ b/modules/nf-core/gatk4/addorreplacereadgroups/tests/cram.config @@ -0,0 +1,13 @@ +process { + withName: 'GATK4_ADDORREPLACEREADGROUPS'{ + ext.prefix = { "${meta.id}.replaced"} + ext.args = {[ + "-LB ${meta.id}", + "-PL ILLUMINA", + "-PU bc1", + "-SM ${meta.id}" + ].join(' ').trim()} + ext.suffix = { "cram" } + } + +} diff --git a/modules/nf-core/gatk4/addorreplacereadgroups/tests/main.nf.test b/modules/nf-core/gatk4/addorreplacereadgroups/tests/main.nf.test new file mode 100644 index 00000000000..cd140e82776 --- /dev/null +++ b/modules/nf-core/gatk4/addorreplacereadgroups/tests/main.nf.test @@ -0,0 +1,85 @@ +nextflow_process { + + name "Test Process GATK4_ADDORREPLACEREADGROUPS" + script "../main.nf" + process "GATK4_ADDORREPLACEREADGROUPS" + + tag "modules" + tag "modules_nfcore" + tag "gatk4" + tag "gatk4/addorreplacereadgroups" + + test("sarscov2 - bam") { + config "./bam.config" + + when { + process { + """ + input[0] = [ [:], file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true) ] + input[1] = [ [:], [] ] + input[2] = [ [:], [] ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(file(process.out.bam[0][1]).name).match("bam_name") }, + { assert snapshot(file(process.out.bai[0][1]).name).match("bai_name") }, + ) + } + + } + + test("homo_sapiens - cram") { + config "./cram.config" + + when { + process { + """ + input[0] = [ + [ id:'test' ], // meta map + [ + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram', checkIfExists: true), ] + ] + input[1] = [ [:], file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) ] + input[2] = [ [:], file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists: true) ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(file(process.out.cram[0][1]).name).match("cram_name") }, + { assert snapshot(process.out.versions).match("versions") }, + ) + } + + } + + test("sarscov2 - bam - stub") { + config "./bam.config" + options "-stub" + + when { + process { + """ + input[0] = [ [:], file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true) ] + input[1] = [ [:], [] ] + input[2] = [ [:], [] ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + + } + +} diff --git a/modules/nf-core/gatk4/addorreplacereadgroups/tests/main.nf.test.snap b/modules/nf-core/gatk4/addorreplacereadgroups/tests/main.nf.test.snap new file mode 100644 index 00000000000..93a87cc39eb --- /dev/null +++ b/modules/nf-core/gatk4/addorreplacereadgroups/tests/main.nf.test.snap @@ -0,0 +1,99 @@ +{ + "bam_name": { + "content": [ + "null.replaced.bam" + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-03-20T12:05:21.587215" + }, + "sarscov2 - bam - stub": { + "content": [ + { + "0": [ + [ + { + + }, + "null.replaced.bam:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "1": [ + [ + { + + }, + "null.replaced.bam.bai:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "2": [ + + ], + "3": [ + "versions.yml:md5,da55295b55986cfcf65d41745c7bda4c" + ], + "bai": [ + [ + { + + }, + "null.replaced.bam.bai:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "bam": [ + [ + { + + }, + "null.replaced.bam:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "cram": [ + + ], + "versions": [ + "versions.yml:md5,da55295b55986cfcf65d41745c7bda4c" + ] + } + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-03-20T13:19:33.815262" + }, + "versions": { + "content": [ + [ + "versions.yml:md5,da55295b55986cfcf65d41745c7bda4c" + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-03-20T13:19:18.103325" + }, + "cram_name": { + "content": [ + "test.replaced.cram" + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-03-20T12:06:05.10743" + }, + "bai_name": { + "content": [ + "null.replaced.bai" + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-03-20T12:05:21.604866" + } +} \ No newline at end of file diff --git a/modules/nf-core/gatk4/addorreplacereadgroups/tests/tags.yml b/modules/nf-core/gatk4/addorreplacereadgroups/tests/tags.yml new file mode 100644 index 00000000000..246ed5573bc --- /dev/null +++ b/modules/nf-core/gatk4/addorreplacereadgroups/tests/tags.yml @@ -0,0 +1,2 @@ +gatk4/addorreplacereadgroups: + - "modules/nf-core/gatk4/addorreplacereadgroups/**" diff --git a/modules/nf-core/picard/addorreplacereadgroups/main.nf b/modules/nf-core/picard/addorreplacereadgroups/main.nf index dc1a387d3e6..4ea018d56bd 100644 --- a/modules/nf-core/picard/addorreplacereadgroups/main.nf +++ b/modules/nf-core/picard/addorreplacereadgroups/main.nf @@ -9,11 +9,14 @@ process PICARD_ADDORREPLACEREADGROUPS { input: tuple val(meta), path(bam) + tuple val(meta2), path(fasta) + tuple val(meta3), path(fasta_index) output: - tuple val(meta), path("*.bam"), emit: bam - tuple val(meta), path("*.bai"), emit: bai, optional: true - path "versions.yml" , emit: versions + tuple val(meta), path("*.bam") , emit: bam, optional: true + tuple val(meta), path("*.bai") , emit: bai, optional: true + tuple val(meta), path("*.cram"), emit: cram, optional: true + path "versions.yml" , emit: versions when: task.ext.when == null || task.ext.when @@ -21,6 +24,9 @@ process PICARD_ADDORREPLACEREADGROUPS { script: def args = task.ext.args ?: '' def prefix = task.ext.prefix ?: "${meta.id}" + def suffix = task.ext.suffix ?: "${bam.getExtension()}" + def reference = fasta ? "--REFERENCE_SEQUENCE ${fasta}" : "" + def create_index = ( suffix == "bam" )? "--CREATE_INDEX" : "" def avail_mem = 3072 if (!task.memory) { log.info '[Picard AddOrReplaceReadGroups] Available memory not known - defaulting to 3GB. Specify process memory requirements to change this.' @@ -28,15 +34,17 @@ process PICARD_ADDORREPLACEREADGROUPS { avail_mem = (task.memory.mega*0.8).intValue() } - if ("$bam" == "${prefix}.bam") error "Input and output names are the same, use \"task.ext.prefix\" to disambiguate!" + if ("$bam" == "${prefix}.${suffix}") error "Input and output names are the same, use \"task.ext.prefix\" to disambiguate!" """ picard \\ -Xmx${avail_mem}M \\ AddOrReplaceReadGroups \\ $args \\ + $reference \\ + $create_index \\ --INPUT ${bam} \\ - --OUTPUT ${prefix}.bam + --OUTPUT ${prefix}.${suffix} cat <<-END_VERSIONS > versions.yml "${task.process}": @@ -46,10 +54,15 @@ process PICARD_ADDORREPLACEREADGROUPS { stub: def prefix = task.ext.prefix ?: "${meta.id}" - - if ("$bam" == "${prefix}.bam") error "Input and output names are the same, use \"task.ext.prefix\" to disambiguate!" + def suffix = task.ext.suffix ?: "${bam.getExtension()}" + if ("$bam" == "${prefix}.${suffix}") error "Input and output names are the same, use \"task.ext.prefix\" to disambiguate!" + def create_index = "" + if (suffix == "bam") { + create_index = "touch ${prefix}.${suffix}.bai" + } """ - touch ${prefix}.bam + touch ${prefix}.${suffix} + ${create_index} cat <<-END_VERSIONS > versions.yml "${task.process}": diff --git a/modules/nf-core/picard/addorreplacereadgroups/meta.yml b/modules/nf-core/picard/addorreplacereadgroups/meta.yml index ab573ac850c..17110b7875f 100644 --- a/modules/nf-core/picard/addorreplacereadgroups/meta.yml +++ b/modules/nf-core/picard/addorreplacereadgroups/meta.yml @@ -20,10 +20,28 @@ input: description: | Groovy Map containing sample information e.g. [ id:'test', single_end:false ] + - meta2: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - meta3: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] - bam: type: file description: Input BAM file pattern: "*.{bam}" + - fasta: + type: file + description: Reference genome file + pattern: "*.{fasta,fa,fasta.gz,fa.gz}" + - fasta_index: + type: file + description: Reference genome index file + pattern: "*.{fai,fasta.fai,fa.fai,fasta.gz.fai,fa.gz.fai}" output: - meta: type: map @@ -40,8 +58,12 @@ output: pattern: "*.{bam}" - bai: type: file - description: BAM index file + description: An optional BAM index file pattern: "*.{bai}" + - cram: + type: file + description: Output CRAM file + pattern: "*.{cram}" authors: - "@sateeshperi" - "@mjcipriano" diff --git a/tests/modules/nf-core/picard/addorreplacereadgroups/nextflow.config b/modules/nf-core/picard/addorreplacereadgroups/tests/bam.config similarity index 71% rename from tests/modules/nf-core/picard/addorreplacereadgroups/nextflow.config rename to modules/nf-core/picard/addorreplacereadgroups/tests/bam.config index 4dc97d09e2f..8ce837e53f8 100644 --- a/tests/modules/nf-core/picard/addorreplacereadgroups/nextflow.config +++ b/modules/nf-core/picard/addorreplacereadgroups/tests/bam.config @@ -1,7 +1,4 @@ process { - - publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" } - withName: 'PICARD_ADDORREPLACEREADGROUPS'{ ext.prefix = { "${meta.id}.replaced"} ext.args = {[ @@ -11,4 +8,5 @@ process { "-SM ${meta.id}" ].join(' ').trim()} } + } diff --git a/modules/nf-core/picard/addorreplacereadgroups/tests/cram.config b/modules/nf-core/picard/addorreplacereadgroups/tests/cram.config new file mode 100644 index 00000000000..966c14d7955 --- /dev/null +++ b/modules/nf-core/picard/addorreplacereadgroups/tests/cram.config @@ -0,0 +1,13 @@ +process { + withName: 'PICARD_ADDORREPLACEREADGROUPS'{ + ext.prefix = { "${meta.id}.replaced"} + ext.args = {[ + "-LB ${meta.id}", + "-PL ILLUMINA", + "-PU bc1", + "-SM ${meta.id}" + ].join(' ').trim()} + ext.suffix = { "cram" } + } + +} diff --git a/modules/nf-core/picard/addorreplacereadgroups/tests/main.nf.test b/modules/nf-core/picard/addorreplacereadgroups/tests/main.nf.test new file mode 100644 index 00000000000..6d50cfe2689 --- /dev/null +++ b/modules/nf-core/picard/addorreplacereadgroups/tests/main.nf.test @@ -0,0 +1,86 @@ + +nextflow_process { + + name "Test Process PICARD_ADDORREPLACEREADGROUPS" + script "../main.nf" + process "PICARD_ADDORREPLACEREADGROUPS" + + tag "modules" + tag "modules_nfcore" + tag "picard" + tag "picard/addorreplacereadgroups" + + test("sarscov2 - bam") { + config "./bam.config" + + when { + process { + """ + input[0] = [ [:], file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true) ] + input[1] = [ [:], [] ] + input[2] = [ [:], [] ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(file(process.out.bam[0][1]).name).match("bam_name") }, + { assert snapshot(file(process.out.bai[0][1]).name).match("bai_name") }, + ) + } + + } + + test("homo_sapiens - cram") { + config "./cram.config" + + when { + process { + """ + input[0] = [ + [ id:'test' ], // meta map + [ + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram', checkIfExists: true), ] + ] + input[1] = [ [:], file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) ] + input[2] = [ [:], file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists: true) ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(file(process.out.cram[0][1]).name).match("cram_name") }, + { assert snapshot(process.out.versions).match("versions") }, + ) + } + + } + + test("sarscov2 - bam - stub") { + config "./bam.config" + options "-stub" + + when { + process { + """ + input[0] = [ [:], file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true) ] + input[1] = [ [:], [] ] + input[2] = [ [:], [] ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + + } + +} diff --git a/modules/nf-core/picard/addorreplacereadgroups/tests/main.nf.test.snap b/modules/nf-core/picard/addorreplacereadgroups/tests/main.nf.test.snap new file mode 100644 index 00000000000..f80eaba047d --- /dev/null +++ b/modules/nf-core/picard/addorreplacereadgroups/tests/main.nf.test.snap @@ -0,0 +1,99 @@ +{ + "bam_name": { + "content": [ + "null.replaced.bam" + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-03-20T12:05:21.587215" + }, + "sarscov2 - bam - stub": { + "content": [ + { + "0": [ + [ + { + + }, + "null.replaced.bam:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "1": [ + [ + { + + }, + "null.replaced.bam.bai:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "2": [ + + ], + "3": [ + "versions.yml:md5,0a6f049f94501dcf23aabfbc0e272891" + ], + "bai": [ + [ + { + + }, + "null.replaced.bam.bai:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "bam": [ + [ + { + + }, + "null.replaced.bam:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "cram": [ + + ], + "versions": [ + "versions.yml:md5,0a6f049f94501dcf23aabfbc0e272891" + ] + } + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-03-20T12:54:03.639457" + }, + "versions": { + "content": [ + [ + "versions.yml:md5,0a6f049f94501dcf23aabfbc0e272891" + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-03-19T17:32:24.906639" + }, + "cram_name": { + "content": [ + "test.replaced.cram" + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-03-20T12:06:05.10743" + }, + "bai_name": { + "content": [ + "null.replaced.bai" + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-03-20T12:05:21.604866" + } +} \ No newline at end of file diff --git a/modules/nf-core/picard/addorreplacereadgroups/tests/tags.yml b/modules/nf-core/picard/addorreplacereadgroups/tests/tags.yml new file mode 100644 index 00000000000..733010d625d --- /dev/null +++ b/modules/nf-core/picard/addorreplacereadgroups/tests/tags.yml @@ -0,0 +1,2 @@ +picard/addorreplacereadgroups: + - "modules/nf-core/picard/addorreplacereadgroups/**" diff --git a/tests/config/pytest_modules.yml b/tests/config/pytest_modules.yml index d72dc4ddf8a..0c348689f96 100644 --- a/tests/config/pytest_modules.yml +++ b/tests/config/pytest_modules.yml @@ -1573,9 +1573,6 @@ phispy: phyloflash: - modules/nf-core/phyloflash/** - tests/modules/nf-core/phyloflash/** -picard/addorreplacereadgroups: - - modules/nf-core/picard/addorreplacereadgroups/** - - tests/modules/nf-core/picard/addorreplacereadgroups/** picard/bedtointervallist: - modules/nf-core/picard/bedtointervallist/** - tests/modules/nf-core/picard/bedtointervallist/** diff --git a/tests/modules/nf-core/picard/addorreplacereadgroups/main.nf b/tests/modules/nf-core/picard/addorreplacereadgroups/main.nf deleted file mode 100644 index e0196f34016..00000000000 --- a/tests/modules/nf-core/picard/addorreplacereadgroups/main.nf +++ /dev/null @@ -1,15 +0,0 @@ -#!/usr/bin/env nextflow - -nextflow.enable.dsl = 2 - -include { PICARD_ADDORREPLACEREADGROUPS } from '../../../../../modules/nf-core/picard/addorreplacereadgroups/main.nf' - -workflow test_picard_addorreplacereadgroups { - - input = [ - [ id:'test', single_end:false ], // meta map - file(params.test_data['sarscov2']['illumina']['test_paired_end_bam'], checkIfExists: true) - ] - - PICARD_ADDORREPLACEREADGROUPS ( input ) -} diff --git a/tests/modules/nf-core/picard/addorreplacereadgroups/test.yml b/tests/modules/nf-core/picard/addorreplacereadgroups/test.yml deleted file mode 100644 index 4ffe7234bd7..00000000000 --- a/tests/modules/nf-core/picard/addorreplacereadgroups/test.yml +++ /dev/null @@ -1,17 +0,0 @@ -- name: picard addorreplacereadgroups test_picard_addorreplacereadgroups - command: nextflow run ./tests/modules/nf-core/picard/addorreplacereadgroups -entry test_picard_addorreplacereadgroups -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/picard/addorreplacereadgroups/nextflow.config - tags: - - picard/addorreplacereadgroups - - picard - files: - - path: output/picard/test.replaced.bam - md5sum: 9068e93d318470f8ab34ccbbbbb15b2b - - path: output/picard/versions.yml -- name: picard addorreplacereadgroups test_picard_addorreplacereadgroups stub - command: nextflow run ./tests/modules/nf-core/picard/addorreplacereadgroups -entry test_picard_addorreplacereadgroups -c ./tests/config/nextflow.config -stub-run - tags: - - picard - - picard/addorreplacereadgroups - files: - - path: output/picard/test.replaced.bam - - path: output/picard/versions.yml