Adding tcoffee module

This commit is contained in:
JoseEspinosa 2020-03-05 17:18:35 +01:00
parent 17ccbce67b
commit 707d2855d6
5 changed files with 70 additions and 2 deletions

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@ -2,7 +2,7 @@ name: FastQC
on: on:
push: {} push: {}
pull_request: pull_request:
paths: tools/fastqc/* paths: tools/tcoffee/*
jobs: jobs:
run_ci_test: run_ci_test:
@ -20,4 +20,4 @@ jobs:
sudo mv nextflow /usr/local/bin/ sudo mv nextflow /usr/local/bin/
# Test the module # Test the module
- run: nextflow run ./tools/fastqc/test/ -ansi-log false - run: nextflow run ./tools/tcoffee/test/ -ansi-log false

18
tools/tcoffee/main.nf Normal file
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@ -0,0 +1,18 @@
process tcoffee {
tag {fasta}
// publishDir "${params.outdir}/tcoffee" //not working
publishDir "${baseDir}/results/tcoffee", mode: 'copy'
container 'quay.io/biocontainers/t_coffee:11.0.8--py27pl5.22.0_5'
input:
path(fasta)
output:
path("${fasta}.aln")
script:
"""
t_coffee -seq $fasta -outfile ${fasta}.aln
"""
}

28
tools/tcoffee/meta.yml Normal file
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@ -0,0 +1,28 @@
name: t-coffee
description: Run tcofee multiple sequence alignment
keywords:
- MSA
- sequence aligment
tools:
- t-coffee:
description: |
T-Coffee is a multiple sequence alignment package.
It uses a progressive approach and a consistency objective
function for alignment evaluation.
homepage: http://www.tcoffee.org/
documentation: http://www.tcoffee.org/Projects/tcoffee/index.html#DOCUMENTATION
input:
-
- fasta:
type: path
description: Input fasta file
pattern: *.{fasta,fa,tfa}
output:
-
- alignment:
type: file
description: tcoffee alignment file
pattern: *.aln
authors:
- @JoseEspinosa

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@ -0,0 +1,20 @@
#!/usr/bin/env nextflow
nextflow.preview.dsl = 2
include check_output from '../../../nf-core/module_testing/check_process_outputs.nf'
include tcoffee from '../main.nf'
// Define input channels
fasta = Channel.fromPath('../../../test-datasets/tools/tcoffee/input/BBA0001.tfa')
// Run the workflow
workflow {
tcoffee(fasta)
// .check_output()
}

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@ -0,0 +1,2 @@
docker.enabled = true
params.outdir = './results'