Tailfindr (#1904)
* adding tailfindr module * replacing the container * removing todo * removing todo and fixing meta.yml * Update modules/tailfindr/main.nf Co-authored-by: Jose Espinosa-Carrasco <kadomu@gmail.com> * Update modules/tailfindr/main.nf Co-authored-by: Jose Espinosa-Carrasco <kadomu@gmail.com> * Update modules/tailfindr/meta.yml Co-authored-by: Jose Espinosa-Carrasco <kadomu@gmail.com> * Update modules/tailfindr/main.nf Co-authored-by: Jose Espinosa-Carrasco <kadomu@gmail.com> * Update tests/modules/tailfindr/test.yml Co-authored-by: Jose Espinosa-Carrasco <kadomu@gmail.com> * Update modules/tailfindr/meta.yml Co-authored-by: Jose Espinosa-Carrasco <kadomu@gmail.com> * Update modules/tailfindr/meta.yml Co-authored-by: Jose Espinosa-Carrasco <kadomu@gmail.com> * Update modules/tailfindr/main.nf Co-authored-by: Jose Espinosa-Carrasco <kadomu@gmail.com> * Update modules/tailfindr/main.nf Co-authored-by: Jose Espinosa-Carrasco <kadomu@gmail.com> * Update main.nf * Update meta.yml * Update modules/tailfindr/main.nf Co-authored-by: Jose Espinosa-Carrasco <kadomu@gmail.com> * Update meta.yml * Update main.nf * adding pytest * Update main.nf * Update modules/tailfindr/main.nf Co-authored-by: Jose Espinosa-Carrasco <kadomu@gmail.com> * Update test.yml * Update main.nf * Update main.nf Co-authored-by: Jose Espinosa-Carrasco <kadomu@gmail.com>master
Luca Cozzuto
2 years ago
committed by
GitHub
parent
c9dc0a82d0
commit
a8b0fce8ce
@ -0,0 +1,38 @@
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process TAILFINDR {
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tag "$meta.id"
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label 'process_high'
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conda (params.enable_conda ? "bioconda::ont-fast5-api=0.4.1 bioconda::r-tailfindr=1.3" : null)
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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'https://depot.galaxyproject.org/singularity/mulled-v2-f24f1399a77784f913670cbb36a0f17b78e0631b:80e40d512cd5a71665e3e00e8d0ad1462fc58f76-0':
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'quay.io/biocontainers/mulled-v2-f24f1399a77784f913670cbb36a0f17b78e0631b:80e40d512cd5a71665e3e00e8d0ad1462fc58f76-0' }"
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input:
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tuple val(meta), path(fast5)
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output:
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tuple val(meta), path("*.csv.gz"), emit: csv_gz
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path("versions.yml"), emit: versions
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when:
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task.ext.when == null || task.ext.when
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script:
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def args = task.ext.args ? ", ${task.ext.args}": ''
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def prefix = task.ext.prefix ?: "${meta.id}"
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"""
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R --vanilla --slave -e "library(tailfindr);
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find_tails(fast5_dir = './' ,
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save_dir = './' ${args},
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csv_filename = \'${meta.id}.csv\',
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num_cores = ${task.cpus})";
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gzip ${meta.id}.csv
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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tailfindr: \$(Rscript -e "cat(paste(packageVersion('tailfindr'), collapse='.'))")
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ont-fast5-api: \$(pip show ont-fast5-api | grep Version | awk '{print \$2}')
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END_VERSIONS
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"""
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}
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name: "tailfindr"
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description: Estimating poly(A)-tail lengths from basecalled fast5 files produced by Nanopore sequencing of RNA and DNA
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keywords:
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- polyA
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- fast5
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tools:
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- "tailfindr":
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description: "An R package for estimating poly(A)-tail lengths in Oxford Nanopore RNA and DNA reads."
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homepage: "https://github.com/adnaniazi/tailfindr"
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documentation: "https://github.com/adnaniazi/tailfindr/blob/master/README.md"
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tool_dev_url: "https://github.com/adnaniazi/tailfindr"
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doi: "10.1261/rna.071332.119"
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licence: "['AGPL v3']"
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input:
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- meta:
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type: map
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description: |
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Groovy Map containing sample information
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e.g. [ id:'test' ]
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- fast5:
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type: file
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description: fast5 file
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pattern: "*.fast5"
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output:
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- meta:
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type: map
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description: |
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Groovy Map containing sample information
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e.g. [ id:'test' ]
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- versions:
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type: file
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description: File containing software versions
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pattern: "versions.yml"
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- csv_gz:
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type: file
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description: Compressed csv file
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pattern: "*.csv.gz"
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authors:
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- "@lucacozzuto"
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@ -0,0 +1,15 @@
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#!/usr/bin/env nextflow
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nextflow.enable.dsl = 2
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include { TAILFINDR } from '../../../modules/tailfindr/main.nf'
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workflow test_tailfindr {
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input = [
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[ id: 'test' ], // meta map
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file('https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/tailfindr/test.fast5', checkIfExists: true)
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]
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TAILFINDR ( input )
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}
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@ -0,0 +1,5 @@
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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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@ -0,0 +1,9 @@
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- name: "tailfindr"
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command: nextflow run ./tests/modules/tailfindr -entry test_tailfindr -c ./tests/config/nextflow.config -c ./tests/modules/tailfindr/nextflow.config
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tags:
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- "tailfindr"
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files:
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- path: "output/tailfindr/test.csv.gz"
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md5sum: 329e856d529dfd1ab31b0dedffc71f3c
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- path: output/tailfindr/versions.yml
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md5sum: 3a4e99bd95d9489da261b12a0ad740bb
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