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Added module for msisensorpro/pro #8529
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3a207b4
Added module
Tuur-ds 98cacdd
updated module
Tuur-ds 1e86c7e
Updated testdata
Tuur-ds f59aa53
Merge branch 'master' into msisensorpro/pro
Tuur-ds 4c98fd0
Updated meta.yml
Tuur-ds f58f080
some small changes
Tuur-ds b9aad02
Updated meta.yml output block
Tuur-ds d66dd47
Merge branch 'master' into msisensorpro/pro
nvnieuwk 19e1072
added pattern for list in meta.yml
Tuur-ds 5c394b3
Merge branch 'msisensorpro/pro' of github.com:Tuur-ds/modules into ms…
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,7 @@ | ||
| --- | ||
| # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json | ||
| channels: | ||
| - conda-forge | ||
| - bioconda | ||
| dependencies: | ||
| - bioconda::msisensor-pro=1.3.0 |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,55 @@ | ||
| process MSISENSORPRO_PRO { | ||
| tag "$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/msisensor-pro%3A1.3.0--hfef96ef_0': | ||
| 'biocontainers/msisensor-pro:1.3.0--hfef96ef_0' }" | ||
|
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| input: | ||
| tuple val(meta), path(input), path(index) | ||
| tuple val(meta2), path(list) | ||
| tuple val(meta3), path(fasta) | ||
| tuple val(meta4), path(fai) | ||
|
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| output: | ||
| tuple val(meta), path("${prefix}") , emit: summary_msi | ||
| tuple val(meta), path("${prefix}_all") , emit: all_msi | ||
| tuple val(meta), path("${prefix}_dis") , emit: dis_msi | ||
| tuple val(meta), path("${prefix}_unstable") , emit: unstable_msi | ||
| 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 ?: '' | ||
| prefix = task.ext.prefix ?: "${meta.id}" | ||
| """ | ||
| msisensor-pro \\ | ||
| pro \\ | ||
| -d $list \\ | ||
| -t $input \\ | ||
| -g $fasta \\ | ||
| -o ${prefix} \\ | ||
| -b $task.cpus \\ | ||
| $args | ||
|
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| cat <<-END_VERSIONS > versions.yml | ||
| "${task.process}": | ||
| msisensor-pro: \$(msisensor-pro 2>&1 | sed -nE 's/Version:\\s*//p') | ||
| END_VERSIONS | ||
| """ | ||
|
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||
| stub: | ||
| prefix = task.ext.prefix ?: "${meta.id}" | ||
| """ | ||
| touch ${prefix} ${prefix}_all ${prefix}_dis ${prefix}_unstable | ||
|
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| cat <<-END_VERSIONS > versions.yml | ||
| "${task.process}": | ||
| 10000 msisensor-pro: \$(msisensor-pro 2>&1 | sed -nE 's/Version:\\s*//p') | ||
| END_VERSIONS | ||
| """ | ||
| } |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,106 @@ | ||
| --- | ||
| name: "msisensorpro_pro" | ||
| description: MSIsensor-pro/pro is a tool used to evaluate MSI using single (tumor) sample | ||
| sequencing data | ||
| keywords: | ||
| - msisensor-pro | ||
| - pro | ||
| - micro-satellite | ||
| tools: | ||
| - msisensorpro: | ||
| description: Microsatellite Instability (MSI) detection using high-throughput | ||
| sequencing data. | ||
| homepage: https://github.com/xjtu-omics/msisensor-pro | ||
| documentation: https://github.com/xjtu-omics/msisensor-pro/wiki | ||
| tool_dev_url: https://github.com/xjtu-omics/msisensor-pro | ||
| doi: "10.1016/j.gpb.2020.02.001" | ||
| licence: ["Custom Licence"] | ||
| identifier: "" | ||
|
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||
| input: | ||
| - - meta: | ||
| type: map | ||
| description: | | ||
| Groovy Map containing sample information | ||
| e.g. `[ id:'sample1', single_end:false ]` | ||
| - input: | ||
| type: file | ||
| description: sorted BAM/CRAM file | ||
| pattern: "*.{bam,cram}" | ||
| - index: | ||
| type: file | ||
| description: index file for input | ||
| pattern: "*.{bai,crai}" | ||
| - - meta2: | ||
| type: map | ||
| description: | | ||
| Groovy Map containing sample information | ||
| e.g. `[ id:'sample1', single_end:false ]` | ||
| - list: | ||
| type: file | ||
| description: micro-satellite list | ||
| pattern: "*.{list}" | ||
| - - meta3: | ||
| type: map | ||
| description: | | ||
| Groovy Map containing sample information | ||
| e.g. `[ id:'sample1', single_end:false ]` | ||
| - fasta: | ||
| type: file | ||
| description: reference genome used to create micro-satellite list | ||
| pattern: "*.{fasta}" | ||
| - - meta4: | ||
| type: map | ||
| description: | | ||
| Groovy Map containing sample information | ||
| e.g. `[ id:'sample1', single_end:false ]` | ||
| - fai: | ||
| type: file | ||
| description: index file for reference fasta | ||
| pattern: "*.{fai}" | ||
| output: | ||
| - summary_msi: | ||
| - meta: | ||
| type: map | ||
| description: | | ||
| Groovy Map containing sample information | ||
| e.g. `[ id:'sample1', single_end:false ]` | ||
| - ${prefix}: | ||
| type: file | ||
| description: txt file containing summary of results | ||
| - all_msi: | ||
| - meta: | ||
| type: map | ||
| description: | | ||
| Groovy Map containing sample information | ||
| e.g. `[ id:'sample1', single_end:false ]` | ||
| - ${prefix}_all: | ||
| type: file | ||
| description: txt file containing all results | ||
| - dis_msi: | ||
| - meta: | ||
| type: map | ||
| description: | | ||
| Groovy Map containing sample information | ||
| e.g. `[ id:'sample1', single_end:false ]` | ||
| - ${prefix}_dis: | ||
| type: file | ||
| description: txt file containing the allele length distribution | ||
| - unstable_msi: | ||
| - meta: | ||
| type: map | ||
| description: | | ||
| Groovy Map containing sample information | ||
| e.g. `[ id:'sample1', single_end:false ]` | ||
| - ${prefix}_unstable: | ||
| type: file | ||
| description: txt file containing unstable micro-satellite sites | ||
| - versions: | ||
| - versions.yml: | ||
| type: file | ||
| description: File containing software versions | ||
| pattern: "versions.yml" | ||
| authors: | ||
| - "@Tuur-ds" | ||
| maintainers: | ||
| - "@Tuur-ds" | ||
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| Original file line number | Diff line number | Diff line change |
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| @@ -0,0 +1,91 @@ | ||
| // TODO nf-core: Once you have added the required tests, please run the following command to build this file: | ||
| // nf-core modules test msisensorpro/pro | ||
| nextflow_process { | ||
|
|
||
| name "Test Process MSISENSORPRO_PRO" | ||
| script "../main.nf" | ||
| process "MSISENSORPRO_PRO" | ||
|
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||
| tag "modules" | ||
| tag "modules_nfcore" | ||
| tag "msisensorpro" | ||
| tag "msisensorpro/pro" | ||
| tag "msisensorpro/scan" | ||
|
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||
| test("testdata - [test, input, index], list, fasta") { | ||
| setup { | ||
| run("MSISENSORPRO_SCAN") { | ||
| script "../../scan/main.nf" | ||
| process { | ||
| """ | ||
| input[0] = [ [ id:'test' ], file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/sequence/genome.fasta', checkIfExists: true) ] | ||
| """ | ||
| } | ||
| } | ||
| } | ||
| when { | ||
| process { | ||
| """ | ||
| input[0] = [ | ||
| [ id:'test_bam' ], // meta map | ||
| file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.markduplicates.sorted.bam', checkIfExists: true), | ||
| file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.markduplicates.sorted.bam.bai', checkIfExists: true) | ||
| ] | ||
| input[1] = MSISENSORPRO_SCAN.out.list | ||
| input[2] = [ [ id:'test_fasta' ], file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/sequence/genome.fasta', checkIfExists: true) ] | ||
| input[3] = [ [ id:'test_fai' ], file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/sequence/genome.fasta.fai', checkIfExists: true) ] | ||
|
|
||
| """ | ||
| } | ||
| } | ||
|
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||
| then { | ||
| assertAll( | ||
| { assert process.success }, | ||
| { assert snapshot(process.out).match() } | ||
| ) | ||
| } | ||
|
|
||
| } | ||
|
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| test("testdata - [test, input], list, fasta - stub") { | ||
|
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| options "-stub" | ||
|
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| setup { | ||
| run("MSISENSORPRO_SCAN") { | ||
| script "../../scan/main.nf" | ||
| process { | ||
| """ | ||
| input[0] = [ [ id:'test' ], file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/sequence/genome.fasta', checkIfExists: true) ] | ||
| """ | ||
| } | ||
| } | ||
| } | ||
|
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||
| when { | ||
| process { | ||
| """ | ||
| input[0] = [ | ||
| [ id:'test_bam' ], // meta map | ||
| file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.markduplicates.sorted.bam', checkIfExists: true), | ||
| file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.markduplicates.sorted.bam.bai', checkIfExists: true) | ||
| ] | ||
| input[1] = MSISENSORPRO_SCAN.out.list | ||
| input[2] = [ [ id:'test_fasta' ], file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/sequence/genome.fasta', checkIfExists: true) ] | ||
| input[3] = [ [ id:'test_fai' ], file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/sequence/genome.fasta.fai', checkIfExists: true) ] | ||
|
|
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| """ | ||
| } | ||
| } | ||
|
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| then { | ||
| assertAll( | ||
| { assert process.success }, | ||
| { assert snapshot(process.out).match() } | ||
| ) | ||
| } | ||
|
|
||
| } | ||
|
|
||
| } |
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Can you also add
"*.list"as pattern here?