New module: COPTR/ESTIMATE #7149
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| @@ -0,0 +1,7 @@ | ||
| --- | ||
| # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json | ||
| channels: | ||
| - conda-forge | ||
| - bioconda | ||
| dependencies: | ||
| - "bioconda::coptr=1.1.4" |
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| process COPTR_ESTIMATE { | ||
| tag "$meta.id" | ||
| label 'process_low' | ||
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| conda "${moduleDir}/environment.yml" | ||
| container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? | ||
| 'https://depot.galaxyproject.org/singularity/coptr:1.1.4--pyhdfd78af_3': | ||
| 'biocontainers/coptr:1.1.4--pyhdfd78af_3' }" | ||
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| input: | ||
| tuple val(meta), path(pkl, stageAs: "coverage_maps/*") | ||
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| output: | ||
| tuple val(meta), path("*.csv"), emit: ptr | ||
| path "versions.yml" , emit: versions | ||
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| when: | ||
| task.ext.when == null || task.ext.when | ||
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| script: | ||
| def args = task.ext.args ?: '' | ||
| def prefix = task.ext.prefix ?: "${meta.id}" | ||
| """ | ||
| coptr \\ | ||
| estimate \\ | ||
| $args \\ | ||
| coverage_maps/ \\ | ||
| ptrs.csv | ||
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| cat <<-END_VERSIONS > versions.yml | ||
| "${task.process}": | ||
| coptr: \$(coptr |& sed -E '11!d ; s/CoPTR.*?\\(v(.*?)\\).*/\\1/') | ||
| END_VERSIONS | ||
| """ | ||
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| stub: | ||
| def args = task.ext.args ?: '' | ||
| def prefix = task.ext.prefix ?: "${meta.id}" | ||
| """ | ||
| touch ${prefix}.csv | ||
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| cat <<-END_VERSIONS > versions.yml | ||
| "${task.process}": | ||
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| coptr: \$(coptr |& sed -E '11!d ; s/CoPTR.*?\\(v(.*?)\\).*/\\1/') | ||
| END_VERSIONS | ||
| """ | ||
| } | ||
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| --- | ||
| # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json | ||
| name: "coptr_estimate" | ||
| description: Calculates peak-to-through ratio (PTR) from metagenomic sequence data | ||
| keywords: | ||
| - coptr | ||
| - mapping | ||
| - ptr | ||
| tools: | ||
| - "coptr": | ||
| description: "Accurate and robust inference of microbial growth dynamics from | ||
| metagenomic sequencing reads." | ||
| homepage: "https://github.com/tyjo/coptr" | ||
| documentation: "https://coptr.readthedocs.io/" | ||
| tool_dev_url: "https://github.com/tyjo/coptr" | ||
| doi: "10.1101/gr.275533.121" | ||
| licence: ["GPL v3"] | ||
| identifier: biotools:coptr | ||
|
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| input: | ||
| - - meta: | ||
| type: map | ||
| description: | | ||
| Groovy Map containing sample information | ||
| e.g. `[ id:'sample1', single_end:false ]` | ||
| - pkl: | ||
| type: file | ||
| description: Python pickle file containing coverage maps | ||
| pattern: "*.pkl" | ||
| ontologies: | ||
| - edam: "http://edamontology.org/format_4002" | ||
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| output: | ||
| - ptr: | ||
| - meta: | ||
| type: map | ||
| description: | | ||
| Groovy Map containing sample information | ||
| e.g. `[ id:'sample1', single_end:false ]` | ||
| - "*.csv": | ||
| type: file | ||
| description: CSV table with rows as reference genomes, columns samples and entries as log2 PTR | ||
| pattern: "*.csv" | ||
| ontologies: | ||
| - edam: "http://edamontology.org/format_3752" | ||
|
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||
| - versions: | ||
| - "versions.yml": | ||
| type: file | ||
| description: File containing software versions | ||
| pattern: "versions.yml" | ||
|
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||
| authors: | ||
| - "@ramirobarrantes" | ||
| maintainers: | ||
| - "@ramirobarrantes" |
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| nextflow_process { | ||
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| name "Test Process COPTR_ESTIMATE" | ||
| script "../main.nf" | ||
| process "COPTR_ESTIMATE" | ||
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| tag "modules" | ||
| tag "modules_nfcore" | ||
| tag "coptr" | ||
| tag "coptr/extract" | ||
| tag "coptr/estimate" | ||
|
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| setup { | ||
| run("COPTR_EXTRACT") { | ||
| script "../../extract/main.nf" | ||
| process { | ||
| """ | ||
| input[0] = [ | ||
| [id:'test_0'], | ||
| [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true) | ||
| ] | ||
| ] | ||
| """ | ||
| } | ||
| } | ||
| } | ||
|
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| test("coptr estimate from coverage maps file") { | ||
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| when { | ||
| process { | ||
| """ | ||
| input[0] = COPTR_EXTRACT.out.coverage | ||
| """ | ||
| } | ||
| } | ||
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| then { | ||
| assertAll( | ||
| { assert process.success }, | ||
| { assert snapshot(process.out).match() | ||
| } | ||
| ) | ||
| } | ||
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| } | ||
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| test("coptr estimate from coverage maps file - stub") { | ||
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| options "-stub" | ||
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| when { | ||
| process { | ||
| """ | ||
| input[0] = COPTR_EXTRACT.out.coverage | ||
| """ | ||
| } | ||
| } | ||
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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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| } |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,68 @@ | ||
| { | ||
| "coptr estimate from coverage maps file - stub": { | ||
| "content": [ | ||
| { | ||
| "0": [ | ||
| [ | ||
| { | ||
| "id": "test_0" | ||
| }, | ||
| "test_0.csv:md5,d41d8cd98f00b204e9800998ecf8427e" | ||
| ] | ||
| ], | ||
| "1": [ | ||
| "versions.yml:md5,5400eb14b9d1287f174065acd6c0c6a4" | ||
| ], | ||
| "ptr": [ | ||
| [ | ||
| { | ||
| "id": "test_0" | ||
| }, | ||
| "test_0.csv:md5,d41d8cd98f00b204e9800998ecf8427e" | ||
| ] | ||
| ], | ||
| "versions": [ | ||
| "versions.yml:md5,5400eb14b9d1287f174065acd6c0c6a4" | ||
| ] | ||
| } | ||
| ], | ||
| "meta": { | ||
| "nf-test": "0.9.2", | ||
| "nextflow": "24.10.2" | ||
| }, | ||
| "timestamp": "2024-12-03T13:46:59.155895" | ||
| }, | ||
| "coptr estimate from coverage maps file": { | ||
| "content": [ | ||
| { | ||
| "0": [ | ||
| [ | ||
| { | ||
| "id": "test_0" | ||
| }, | ||
| "ptrs.csv:md5,e94546e830fd9fdcd50e0e6c459f78e5" | ||
| ] | ||
| ], | ||
| "1": [ | ||
| "versions.yml:md5,5400eb14b9d1287f174065acd6c0c6a4" | ||
| ], | ||
| "ptr": [ | ||
| [ | ||
| { | ||
| "id": "test_0" | ||
| }, | ||
| "ptrs.csv:md5,e94546e830fd9fdcd50e0e6c459f78e5" | ||
| ] | ||
| ], | ||
| "versions": [ | ||
| "versions.yml:md5,5400eb14b9d1287f174065acd6c0c6a4" | ||
| ] | ||
| } | ||
| ], | ||
| "meta": { | ||
| "nf-test": "0.9.2", | ||
| "nextflow": "24.10.2" | ||
| }, | ||
| "timestamp": "2024-11-29T18:28:40.680244" | ||
| } | ||
| } |
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Does this have to be a directory?
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It does, this tool is a bit particular that way...
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OK