-
Notifications
You must be signed in to change notification settings - Fork 654
Commit
This commit does not belong to any branch on this repository, and may belong to a fork outside of the repository.
Co-authored-by: Jose Espinosa-Carrasco <kadomu@gmail.com>
- Loading branch information
1 parent
b036288
commit 81232af
Showing
6 changed files
with
118 additions
and
0 deletions.
There are no files selected for viewing
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Original file line number | Diff line number | Diff line change |
---|---|---|
@@ -0,0 +1,43 @@ | ||
def VERSION = '1.0.4' // Version information not provided by tool on CLI | ||
|
||
process MCRONI { | ||
tag "$meta.id" | ||
label 'process_low' | ||
|
||
conda (params.enable_conda ? "bioconda::mcroni=1.0.4" : null) | ||
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? | ||
'https://depot.galaxyproject.org/singularity/mcroni%3A1.0.4--pyh5e36f6f_0': | ||
'quay.io/biocontainers/mcroni:1.0.4--pyh5e36f6f_0' }" | ||
|
||
input: | ||
tuple val(meta), path(fasta) | ||
|
||
output: | ||
tuple val(meta), path("*.tsv") , emit: tsv | ||
tuple val(meta), path("*.fa"), optional: true, emit: fa | ||
path "versions.yml" , emit: versions | ||
|
||
when: | ||
task.ext.when == null || task.ext.when | ||
|
||
script: | ||
def args = task.ext.args ?: '' | ||
def prefix = task.ext.prefix ?: "${meta.id}" | ||
def is_compressed = fasta.getName().endsWith(".gz") ? true : false | ||
def fasta_name = fasta.getName().replace(".gz", "") | ||
""" | ||
if [ "$is_compressed" == "true" ]; then | ||
gzip -c -d $fasta > $fasta_name | ||
fi | ||
mcroni \\ | ||
$args \\ | ||
--output $prefix \\ | ||
--fasta $fasta_name | ||
cat <<-END_VERSIONS > versions.yml | ||
"${task.process}": | ||
mcroni: $VERSION | ||
END_VERSIONS | ||
""" | ||
} |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Original file line number | Diff line number | Diff line change |
---|---|---|
@@ -0,0 +1,46 @@ | ||
name: "mcroni" | ||
description: Analysis of mcr-1 gene (mobilized colistin resistance) for sequence variation | ||
keywords: | ||
- resistance | ||
- fasta | ||
tools: | ||
- "mcroni": | ||
description: "Scripts for finding and processing promoter variants upstream of mcr-1" | ||
homepage: "https://github.com/liampshaw/mcroni" | ||
documentation: "https://github.com/liampshaw/mcroni" | ||
tool_dev_url: "https://github.com/liampshaw/mcroni" | ||
doi: "" | ||
licence: "['MIT']" | ||
|
||
input: | ||
- meta: | ||
type: map | ||
description: | | ||
Groovy Map containing sample information | ||
e.g. [ id:'test', single_end:false ] | ||
- fasta: | ||
type: file | ||
description: A fasta file. | ||
pattern: "*.{fasta.gz,fasta,fa.gz,fa,fna.gz,fna}" | ||
|
||
output: | ||
- meta: | ||
type: map | ||
description: | | ||
Groovy Map containing sample information | ||
e.g. [ id:'test', single_end:false ] | ||
- versions: | ||
type: file | ||
description: File containing software versions | ||
pattern: "versions.yml" | ||
- tsv: | ||
type: file | ||
description: mcroni results in TSV format | ||
pattern: "*.tsv" | ||
- fa: | ||
type: file | ||
description: mcr-1 matching sequences | ||
pattern: "*.fa" | ||
|
||
authors: | ||
- "@rpetit3" |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Original file line number | Diff line number | Diff line change |
---|---|---|
@@ -0,0 +1,13 @@ | ||
#!/usr/bin/env nextflow | ||
|
||
nextflow.enable.dsl = 2 | ||
|
||
include { MCRONI } from '../../../modules/mcroni/main.nf' | ||
|
||
workflow test_mcroni { | ||
|
||
input = [ [ id:'test', single_end:false ], // meta map | ||
file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) ] | ||
|
||
MCRONI ( input ) | ||
} |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Original file line number | Diff line number | Diff line change |
---|---|---|
@@ -0,0 +1,5 @@ | ||
process { | ||
|
||
publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" } | ||
|
||
} |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Original file line number | Diff line number | Diff line change |
---|---|---|
@@ -0,0 +1,7 @@ | ||
- name: mcroni test_mcroni | ||
command: nextflow run ./tests/modules/mcroni -entry test_mcroni -c ./tests/config/nextflow.config -c ./tests/modules/mcroni/nextflow.config | ||
tags: | ||
- mcroni | ||
files: | ||
- path: output/mcroni/test_table.tsv | ||
md5sum: 64f8438dcc476e8b4d762fedc2e3f69e |