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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,7 @@ | ||
| --- | ||
| # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json | ||
| channels: | ||
| - conda-forge | ||
| - bioconda | ||
| dependencies: | ||
| - "bioconda::bbmap=39.13" |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,57 @@ | ||
| process BBMAP_REPAIR { | ||
| tag "$meta.id" | ||
| label 'process_single' | ||
| conda "${moduleDir}/environment.yml" | ||
| container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? | ||
| 'https://depot.galaxyproject.org/singularity/bbmap:39.13--he5f24ec_1': | ||
| 'biocontainers/bbmap:39.13--he5f24ec_1' }" | ||
|
|
||
| input: | ||
| tuple val(meta), path(reads) | ||
| val(interleave) | ||
|
|
||
| output: | ||
| tuple val(meta), path("*_repaired.fastq.gz") , emit: repaired | ||
| tuple val(meta), path("${prefix}_singleton.fastq.gz"), emit: singleton | ||
| path "versions.yml" , emit: versions | ||
| path "*.log" , emit: log | ||
|
|
||
| when: | ||
| task.ext.when == null || task.ext.when | ||
|
|
||
| script: | ||
| def args = task.ext.args ?: '' | ||
| prefix = task.ext.prefix ?: "${meta.id}" | ||
| in_reads = ( interleave ) ? "in=${reads[0]}" : "in=${reads[0]} in2=${reads[1]}" | ||
| out_reads = ( interleave ) ? "out=${prefix}_repaired.fastq.gz outs=${prefix}_singleton.fastq.gz" | ||
| : "out=${prefix}_1_repaired.fastq.gz out2=${prefix}_2_repaired.fastq.gz outs=${prefix}_singleton.fastq.gz" | ||
| """ | ||
| maxmem=\$(echo \"$task.memory\"| sed 's/ GB/g/g') | ||
| repair.sh \\ | ||
| -Xmx\$maxmem \\ | ||
| $in_reads \\ | ||
| $out_reads \\ | ||
| threads=${task.cpus} | ||
| ${args} \\ | ||
| &> ${prefix}.repair.sh.log | ||
| cat <<-END_VERSIONS > versions.yml | ||
| "${task.process}": | ||
| repair.sh: \$(repair.sh --version |& sed '2!d ; s/BBMap version //') | ||
| END_VERSIONS | ||
| """ | ||
|
|
||
| stub: | ||
| prefix = task.ext.prefix ?: "${meta.id}" | ||
| """ | ||
| echo "" | gzip > ${prefix}_1_repaired.fastq.gz | ||
| echo "" | gzip > ${prefix}_2_repaired.fastq.gz | ||
| echo "" | gzip > ${prefix}_singleton.fastq.gz | ||
| touch ${prefix}.repair.sh.log | ||
| cat <<-END_VERSIONS > versions.yml | ||
| "${task.process}": | ||
| repair.sh: \$(repair.sh --version |& sed '2!d ; s/BBMap version //') | ||
| END_VERSIONS | ||
| """ | ||
| } |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,67 @@ | ||
| # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json | ||
| name: "bbmap_repair" | ||
| description: Re-pairs reads that became disordered or had some mates eliminated. | ||
| keywords: | ||
| - paired reads re-pairing | ||
| - fastq | ||
| - preprocessing | ||
| tools: | ||
| - repair: | ||
| description: Repair.sh is a tool that re-pairs reads that became disordered or had some mates eliminated | ||
| tools. | ||
| homepage: https://jgi.doe.gov/data-and-tools/software-tools/bbtools/ | ||
| documentation: https://jgi.doe.gov/data-and-tools/software-tools/bbtools/bb-tools-user-guide/ | ||
| licence: ["UC-LBL license (see package)"] | ||
| identifier: biotools:bbmap | ||
|
|
||
| input: | ||
| - - meta: | ||
| type: map | ||
| description: | | ||
| Groovy Map containing sample information | ||
| e.g. `[ id:'sample1', single_end:false ]` | ||
| - reads: | ||
| type: file | ||
| description: | | ||
| List of input paired end fastq files | ||
| pattern: "*.{fastq,fq}.gz" | ||
| - - interleave: | ||
| type: boolean | ||
| description: | | ||
| Indicates whether the input paired reads are interleaved or not | ||
| output: | ||
| - repaired: | ||
| - meta: | ||
| type: map | ||
| description: | | ||
| Groovy Map containing sample information | ||
| e.g. `[ id:'sample1', single_end:false ]` | ||
| - "*_repaired.fastq.gz": | ||
| type: file | ||
| description: re-paired reads | ||
| pattern: "*_repaired.fastq.gz" | ||
| - singleton: | ||
| - meta: | ||
| type: map | ||
| description: | | ||
| Groovy Map containing sample information | ||
| e.g. `[ id:'sample1', single_end:false ]` | ||
| - "${prefix}_singleton.fastq.gz": | ||
| type: file | ||
| description: singleton reads | ||
| pattern: "*singleton.fastq.gz" | ||
| - versions: | ||
| - versions.yml: | ||
| type: file | ||
| description: File containing software versions | ||
| pattern: "versions.yml" | ||
| - log: | ||
| - "*.log": | ||
| type: file | ||
| description: log file containing stdout and stderr from repair.sh | ||
| pattern: "*.log" | ||
| authors: | ||
| - "@mazzalab" | ||
| maintainers: | ||
| - "@mazzalab" | ||
| - "@tm4zza" |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,115 @@ | ||
| nextflow_process { | ||
|
|
||
| name "Test Process BBMAP_REPAIR" | ||
| script "../main.nf" | ||
| process "BBMAP_REPAIR" | ||
|
|
||
| tag "modules" | ||
| tag "modules_nfcore" | ||
| tag "bbmap" | ||
| tag "bbmap/repair" | ||
|
|
||
| test("sarscov2_illumina_paired - fastq_gz") { | ||
| config "./nextflow.config" | ||
|
|
||
| when { | ||
| params { | ||
| module_args = 'qin=33' | ||
| } | ||
| process { | ||
| """ | ||
| input[0] = [ | ||
| [ id:'test', single_end:false ], // meta map | ||
| [file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true), | ||
| file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_2.fastq.gz', checkIfExists: true)] | ||
| ] | ||
| input[1] = false | ||
| """ | ||
| } | ||
| } | ||
| then { | ||
| assertAll( | ||
| { assert process.success }, | ||
| { assert snapshot(process.out.versions).match() } | ||
| ) | ||
| } | ||
| } | ||
|
|
||
| test("sarscov2_illumina_interleaved - fastq_gz") { | ||
| config "./nextflow.config" | ||
|
|
||
| when { | ||
| params { | ||
| module_args = 'qin=33' | ||
| } | ||
| process { | ||
| """ | ||
| input[0] = [ | ||
| [ id:'test', single_end:false ], // meta map | ||
| [file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_interleaved.fastq.gz', checkIfExists: true)] | ||
| ] | ||
| input[1] = true | ||
| """ | ||
| } | ||
| } | ||
| then { | ||
| assertAll( | ||
| { assert process.success }, | ||
| { assert snapshot(process.out.versions).match() } | ||
| ) | ||
| } | ||
| } | ||
|
|
||
| test("sarscov2_illumina_paired - fastq_gz - stub") { | ||
| config "./nextflow.config" | ||
| options "-stub" | ||
|
|
||
| when { | ||
| params { | ||
| module_args = 'qin=33' | ||
| } | ||
| process { | ||
| """ | ||
| input[0] = [ | ||
| [ id:'test', single_end:false ], // meta map | ||
| [file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true), | ||
| file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_2.fastq.gz', checkIfExists: true)] | ||
| ] | ||
| input[1] = false | ||
| """ | ||
| } | ||
| } | ||
| then { | ||
| assertAll( | ||
| { assert process.success }, | ||
| { assert snapshot(process.out).match() } | ||
| ) | ||
| } | ||
| } | ||
|
|
||
| test("sarscov2_illumina_interleaved - fastq_gz - stub") { | ||
| config "./nextflow.config" | ||
| options "-stub" | ||
|
|
||
| when { | ||
| params { | ||
| module_args = 'qin=33' | ||
| } | ||
| process { | ||
| """ | ||
| input[0] = [ | ||
| [ id:'test', single_end:false ], // meta map | ||
| [file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_interleaved.fastq.gz', checkIfExists: true)] | ||
| ] | ||
| input[1] = true | ||
| """ | ||
| } | ||
| } | ||
| then { | ||
| assertAll( | ||
| { assert process.success }, | ||
| { assert snapshot(process.out).match() } | ||
| ) | ||
| } | ||
| } | ||
| } |
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