[GH-7778] Added matlock/bam2juicer #10305
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| --- | ||
| # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json | ||
| channels: | ||
| - conda-forge | ||
| - bioconda | ||
| dependencies: | ||
| - bioconda::matlock=20181227 | ||
| - bioconda::samtools=1.21 |
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| process MATLOCK_BAM2JUICER { | ||
| tag "$meta.id" | ||
| label 'process_single' | ||
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| // WARN: Version information not provided by tool on CLI. Please update the VERSION variable when bumping | ||
| conda "${moduleDir}/environment.yml" | ||
| container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? | ||
| 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/59/59df5236cc790cac47380a5654f39052a1cb3f9c7868ed397e4b3205a9fb2776/data': | ||
| 'community.wave.seqera.io/library/matlock_samtools:3c30bc2808902fde' }" | ||
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| input: | ||
| tuple val(meta), path(input_file) | ||
| tuple val(meta2), path(fasta), path(fai) | ||
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| output: | ||
| tuple val(meta), path("*.links.txt") , emit: links_txt | ||
| tuple val("${task.process}"), val('samtools'), eval("samtools version | sed '1!d;s/.* //'"), topic: versions, emit: versions_samtools | ||
| tuple val("${task.process}"), val('matlock'), val('20181227'), topic: versions, emit: versions_matlock | ||
| // WARN: Version information not provided by tool on CLI. Please update the VERSION variable when bumping | ||
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| when: | ||
| task.ext.when == null || task.ext.when | ||
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| script: | ||
| def prefix = task.ext.prefix ?: "${meta.id}.links" | ||
| def args2 = task.ext.args2 ?: '' | ||
| def input_ext = input_file.extension | ||
| def reference = fasta ? "--reference ${fasta}" : "" | ||
| def filter_cmd = args2 != '' ? "samtools view --threads $task.cpus $args2 -Sb $input_file $reference > ${prefix}.juicer.bam" : '' | ||
| def juicer_input = args2 != '' ? "${prefix}.juicer.${input_ext}" : "$input_file" | ||
| def bam_del_cmd = args2 != '' ? "rm ${prefix}.juicer.bam" : '' | ||
| """ | ||
| $filter_cmd | ||
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| matlock \\ | ||
| bam2 \\ | ||
| juicer \\ | ||
| $juicer_input \\ | ||
| ${prefix}.txt | ||
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| $bam_del_cmd | ||
| """ | ||
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| stub: | ||
| def prefix = task.ext.prefix ?: "${meta.id}.links" | ||
| def args2 = task.ext.args2 ?: '' | ||
| def input_ext = input_file.extension | ||
| def reference = fasta ? "--reference ${fasta}" : "" | ||
| def filter_cmd = args2 != '' ? "samtools view --threads $task.cpus $args2 -Sb $input_file $reference > ${prefix}.juicer.bam" : '' | ||
| def juicer_input = args2 != '' ? "${prefix}.juicer.${input_ext}" : "$input_file" | ||
| def bam_del_cmd = args2 != '' ? "rm ${prefix}.juicer.bam" : '' | ||
| """ | ||
| echo "filter command: $filter_cmd" | ||
| echo "juicer input: $juicer_input" | ||
| echo "bam delete command: $bam_del_cmd" | ||
|
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| touch ${prefix}.txt | ||
| """ | ||
| } |
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| # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json | ||
| name: "matlock_bam2juicer" | ||
| description: Converts a BAM file to Juicer links format | ||
| keywords: | ||
| - BAM | ||
| - HiC | ||
| - juicer | ||
| tools: | ||
| - "matlock": | ||
| description: "Simple tools for working with Hi-C data" | ||
| homepage: "https://github.com/phasegenomics/matlock" | ||
| documentation: "https://github.com/phasegenomics/matlock" | ||
| tool_dev_url: "https://github.com/phasegenomics/matlock" | ||
| licence: ["GNU Affero General Public License v3"] | ||
| identifier: "" | ||
|
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| input: | ||
| - - meta: | ||
| type: map | ||
| description: | | ||
| Groovy Map containing sample information | ||
| e.g. `[ id:'sample1' ]` | ||
| - bam: | ||
| type: file | ||
| description: Sorted BAM/CRAM/SAM file | ||
| pattern: "*.{bam,cram,sam}" | ||
| ontologies: | ||
| - edam: "http://edamontology.org/format_25722" | ||
| - edam: "http://edamontology.org/format_2573" | ||
| - edam: "http://edamontology.org/format_3462" | ||
|
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| output: | ||
| links_txt: | ||
| - - meta: | ||
| type: map | ||
| description: | | ||
| Groovy Map containing sample information | ||
| e.g. `[ id:'sample1' ]` | ||
| - "*.links.txt": | ||
| type: file | ||
| description: Juicer links file | ||
| pattern: "*links.txt" | ||
| ontologies: [] | ||
| versions: | ||
| - versions.yml: | ||
| type: file | ||
| description: File containing software versions | ||
| pattern: "versions.yml" | ||
| ontologies: | ||
| - edam: http://edamontology.org/format_3750 # YAML | ||
| authors: | ||
| - "@GallVp" | ||
| maintainers: | ||
| - "@GallVp" | ||
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| nextflow_process { | ||
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| name "Test Process MATLOCK_BAM2JUICER" | ||
| script "../main.nf" | ||
| config "./nextflow.config" | ||
| process "MATLOCK_BAM2JUICER" | ||
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| tag "modules" | ||
| tag "modules_nfcore" | ||
| tag "matlock" | ||
| tag "matlock/bam2juicer" | ||
|
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| test("hongyang - hic - bam - filter") { | ||
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| when { | ||
| params { | ||
| filter_args = '-F 3852' | ||
| } | ||
| process { | ||
| """ | ||
| input[0] = [ | ||
| [ id:'test' ], // meta map | ||
| file('https://github.com/Plant-Food-Research-Open/assemblyqc/raw/eef371b57bda38fb0ff8167f7a547325c8211c3f/tests/hic/testdata/HYh1h2_Chr01_6000000_6015000.bam', checkIfExists: true), | ||
|
Contributor
There was a problem hiding this comment. We don't really like external data, is there not a suitable bam file in the test-datasets already?
Member
Author
There was a problem hiding this comment. Thank you @SPPearce for the review. This has to be a BAM file from HiC reads. There are HiC reads under
I guess the easier solution is 1 but that will add an unnecessary test dependency on BWA/MEM which is a widely used and regularly updated tool. Its maintainer will have to carry the burden of maintaining this module as well.
Contributor
There was a problem hiding this comment. You could just copy this bam into test-datasets, that would also work. |
||
| ] | ||
| input[1] = [ [], [], [] ] | ||
| """ | ||
| } | ||
| } | ||
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| then { | ||
| assertAll( | ||
| { assert process.success }, | ||
| { assert snapshot(process.out).match() } | ||
| ) | ||
| } | ||
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| } | ||
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| test("hongyang - hic - bam - stub") { | ||
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| options '-stub' | ||
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| when { | ||
| params { | ||
| filter_args = '' | ||
| } | ||
| process { | ||
| """ | ||
| input[0] = [ | ||
| [ id:'test' ], // meta map | ||
| file('https://github.com/Plant-Food-Research-Open/assemblyqc/raw/eef371b57bda38fb0ff8167f7a547325c8211c3f/tests/hic/testdata/HYh1h2_Chr01_6000000_6015000.bam', checkIfExists: true), | ||
| ] | ||
| input[1] = [ [], [], [] ] | ||
| """ | ||
| } | ||
| } | ||
|
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| then { | ||
| assertAll( | ||
| { assert process.success }, | ||
| { assert snapshot(process.out).match() } | ||
| ) | ||
| } | ||
|
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| } | ||
|
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| test("hongyang - hic - bam - filter - stub") { | ||
| options '-stub' | ||
|
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| when { | ||
| params { | ||
| filter_args = '-F 3852' | ||
| } | ||
| process { | ||
| """ | ||
| input[0] = [ | ||
| [ id:'test' ], // meta map | ||
| file('https://github.com/Plant-Food-Research-Open/assemblyqc/raw/eef371b57bda38fb0ff8167f7a547325c8211c3f/tests/hic/testdata/HYh1h2_Chr01_6000000_6015000.bam', checkIfExists: true), | ||
| ] | ||
| input[1] = [ [], [], [] ] | ||
| """ | ||
| } | ||
| } | ||
|
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| then { | ||
| assertAll( | ||
| { assert process.success }, | ||
| { assert snapshot(process.out).match() } | ||
| ) | ||
| } | ||
|
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||
| } | ||
|
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||
| } | ||
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,167 @@ | ||
| { | ||
| "hongyang - hic - bam - filter - stub": { | ||
| "content": [ | ||
| { | ||
| "0": [ | ||
| [ | ||
| { | ||
| "id": "test" | ||
| }, | ||
| "test.links.txt:md5,d41d8cd98f00b204e9800998ecf8427e" | ||
| ] | ||
| ], | ||
| "1": [ | ||
| [ | ||
| "MATLOCK_BAM2JUICER", | ||
| "samtools", | ||
| "1.21" | ||
| ] | ||
| ], | ||
| "2": [ | ||
| [ | ||
| "MATLOCK_BAM2JUICER", | ||
| "matlock", | ||
| "20181227" | ||
| ] | ||
| ], | ||
| "links_txt": [ | ||
| [ | ||
| { | ||
| "id": "test" | ||
| }, | ||
| "test.links.txt:md5,d41d8cd98f00b204e9800998ecf8427e" | ||
| ] | ||
| ], | ||
| "versions_matlock": [ | ||
| [ | ||
| "MATLOCK_BAM2JUICER", | ||
| "matlock", | ||
| "20181227" | ||
| ] | ||
| ], | ||
| "versions_samtools": [ | ||
| [ | ||
| "MATLOCK_BAM2JUICER", | ||
| "samtools", | ||
| "1.21" | ||
| ] | ||
| ] | ||
| } | ||
| ], | ||
| "meta": { | ||
| "nf-test": "0.9.3", | ||
| "nextflow": "25.10.4" | ||
| }, | ||
| "timestamp": "2026-03-04T12:27:35.175427" | ||
| }, | ||
| "hongyang - hic - bam - filter": { | ||
| "content": [ | ||
| { | ||
| "0": [ | ||
| [ | ||
| { | ||
| "id": "test" | ||
| }, | ||
| "test.links.txt:md5,567eac1531683649c20d6ed2ef3fa711" | ||
| ] | ||
| ], | ||
| "1": [ | ||
| [ | ||
| "MATLOCK_BAM2JUICER", | ||
| "samtools", | ||
| "1.21" | ||
| ] | ||
| ], | ||
| "2": [ | ||
| [ | ||
| "MATLOCK_BAM2JUICER", | ||
| "matlock", | ||
| "20181227" | ||
| ] | ||
| ], | ||
| "links_txt": [ | ||
| [ | ||
| { | ||
| "id": "test" | ||
| }, | ||
| "test.links.txt:md5,567eac1531683649c20d6ed2ef3fa711" | ||
| ] | ||
| ], | ||
| "versions_matlock": [ | ||
| [ | ||
| "MATLOCK_BAM2JUICER", | ||
| "matlock", | ||
| "20181227" | ||
| ] | ||
| ], | ||
| "versions_samtools": [ | ||
| [ | ||
| "MATLOCK_BAM2JUICER", | ||
| "samtools", | ||
| "1.21" | ||
| ] | ||
| ] | ||
| } | ||
| ], | ||
| "meta": { | ||
| "nf-test": "0.9.3", | ||
| "nextflow": "25.10.4" | ||
| }, | ||
| "timestamp": "2026-03-04T12:25:18.772447" | ||
| }, | ||
| "hongyang - hic - bam - stub": { | ||
| "content": [ | ||
| { | ||
| "0": [ | ||
| [ | ||
| { | ||
| "id": "test" | ||
| }, | ||
| "test.links.txt:md5,d41d8cd98f00b204e9800998ecf8427e" | ||
| ] | ||
| ], | ||
| "1": [ | ||
| [ | ||
| "MATLOCK_BAM2JUICER", | ||
| "samtools", | ||
| "1.21" | ||
| ] | ||
| ], | ||
| "2": [ | ||
| [ | ||
| "MATLOCK_BAM2JUICER", | ||
| "matlock", | ||
| "20181227" | ||
| ] | ||
| ], | ||
| "links_txt": [ | ||
| [ | ||
| { | ||
| "id": "test" | ||
| }, | ||
| "test.links.txt:md5,d41d8cd98f00b204e9800998ecf8427e" | ||
| ] | ||
| ], | ||
| "versions_matlock": [ | ||
| [ | ||
| "MATLOCK_BAM2JUICER", | ||
| "matlock", | ||
| "20181227" | ||
| ] | ||
| ], | ||
| "versions_samtools": [ | ||
| [ | ||
| "MATLOCK_BAM2JUICER", | ||
| "samtools", | ||
| "1.21" | ||
| ] | ||
| ] | ||
| } | ||
| ], | ||
| "meta": { | ||
| "nf-test": "0.9.3", | ||
| "nextflow": "25.10.4" | ||
| }, | ||
| "timestamp": "2026-03-04T12:27:29.566833" | ||
| } | ||
| } |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,5 @@ | ||
| process { | ||
| withName: 'MATLOCK_BAM2JUICER' { | ||
| ext.args2 = params.filter_args | ||
| } | ||
| } |
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