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🔀 Merge pull request #34 from cnr-ibba/issue-33
new module: ESTSFS
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,48 @@ | ||
| process ESTSFS { | ||
| tag "$meta.id" | ||
| label 'process_single' | ||
| label 'process_long' | ||
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| // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions. | ||
| container "docker.io/bunop/est-sfs:2.0.5" | ||
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| input: | ||
| tuple val(meta), path(e_config), path(data), path(seed) | ||
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| output: | ||
| tuple val(meta), path("${prefix}_sfs.txt") , emit: sfs_out | ||
| tuple val(meta), path("${prefix}_pvalues.txt") , emit: pvalues_out | ||
| tuple val(meta), path("${prefix}.seed") , emit: seed | ||
| 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 VERSION = '2.05' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions. | ||
| prefix = task.ext.prefix ?: "${meta.id}" | ||
| """ | ||
| cp ${seed} ${prefix}.seed | ||
| est-sfs ${e_config} ${data} ${prefix}.seed ${prefix}_sfs.txt ${prefix}_pvalues.txt | ||
| cat <<-END_VERSIONS > versions.yml | ||
| "${task.process}": | ||
| est-sfs: $VERSION | ||
| END_VERSIONS | ||
| """ | ||
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| stub: | ||
| def args = task.ext.args ?: '' | ||
| def prefix = task.ext.prefix ?: "${meta.id}" | ||
| """ | ||
| touch ${prefix}_sfs.txt | ||
| touch ${prefix}_pvalues.txt | ||
| touch ${prefix}.seed | ||
| cat <<-END_VERSIONS > versions.yml | ||
| "${task.process}": | ||
| est-sfs: $VERSION | ||
| END_VERSIONS | ||
| """ | ||
| } |
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| --- | ||
| name: "estsfs" | ||
| description: estimation of the unfolded site frequency spectrum | ||
| keywords: | ||
| - site frequency spectrum | ||
| - ancestral alleles | ||
| - derived alleles | ||
| tools: | ||
| - "estsfs": | ||
| description: "est-sfs ( Keightley and Jackson, 2018) is a stand-alone implementation of a method to infer the unfolded site frequency spectrum (the uSFS) and ancestral state probabilities by maximum likelihood (ML)." | ||
| homepage: "https://sourceforge.net/projects/est-usfs/" | ||
| documentation: "https://sourceforge.net/projects/est-usfs/" | ||
| tool_dev_url: "https://sourceforge.net/projects/est-usfs/files/est-sfs-release-2.04.tar.gz" | ||
| doi: "10.1534/genetics.118.301120" | ||
| licence: "['Free for Academic Use']" | ||
| input: | ||
| - meta: | ||
| type: map | ||
| description: | | ||
| Groovy Map containing sample information | ||
| e.g. `[ id:'test']` | ||
| - e_config: | ||
| type: file | ||
| description: config file for est-sfs | ||
| pattern: "*.txt" | ||
| - data: | ||
| type: file | ||
| description: input data file for est-sfs | ||
| pattern: "*.txt" | ||
| - seed: | ||
| type: file | ||
| description: text file containing random number seed | ||
| pattern: "*.txt" | ||
| output: | ||
| - meta: | ||
| type: map | ||
| description: | | ||
| Groovy Map containing sample information | ||
| e.g. `[ id:'test']` | ||
| - versions: | ||
| type: file | ||
| description: File containing software versions | ||
| pattern: "versions.yml" | ||
| - sfs_out: | ||
| type: file | ||
| description: output file consists of the comma-separated estimated uSFS vector | ||
| pattern: "*.txt" | ||
| - pvalues_out: | ||
| type: file | ||
| description: this file contains the estimated ancestral state probabilities for each site | ||
| pattern: "*.txt" | ||
| authors: | ||
| - "@BioInf2305" |
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| Original file line number | Diff line number | Diff line change |
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| @@ -0,0 +1,15 @@ | ||
| #!/usr/bin/env nextflow | ||
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| nextflow.enable.dsl = 2 | ||
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| include { ESTSFS } from '../../../../modules/cnr-ibba/estsfs/main.nf' | ||
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| workflow test_estsfs { | ||
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| input = [ | ||
| [ id:'test' ], // meta map | ||
| file(params.test_data['generic']['estsfs']['config_file'], checkIfExists: true), file(params.test_data['generic']['estsfs']['data_file'], checkIfExists: true), file(params.test_data['generic']['estsfs']['seed_file'], checkIfExists: true) | ||
| ] | ||
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| ESTSFS ( input ) | ||
| } |
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| Original file line number | Diff line number | Diff line change |
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| process { | ||
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| publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" } | ||
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| } |
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| Original file line number | Diff line number | Diff line change |
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| @@ -0,0 +1,11 @@ | ||
| - name: estsfs test_estsfs | ||
| command: nextflow run ./tests/modules/cnr-ibba/estsfs -entry test_estsfs -c ./tests/config/nextflow.config | ||
| tags: | ||
| - estsfs | ||
| files: | ||
| - path: output/estsfs/test_pvalues.txt | ||
| md5sum: 63f370e9f2d08591b52c0ea05c8b45a0 | ||
| - path: output/estsfs/test_sfs.txt | ||
| md5sum: 5da246e273d22b177f0683b44fe6d80a | ||
| - path: output/estsfs/test.seed | ||
| - path: output/estsfs/versions.yml |