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Update combine bracken outputs to include meta for publishing purposes

This commit is contained in:
James Fellows Yates 2022-12-12 10:10:24 +01:00
parent 8939ce3e20
commit 3df0a383da
4 changed files with 19 additions and 8 deletions

View file

@ -330,12 +330,12 @@ process {
]
}
withName: KRAKENTOOLS_COMBINEKREPORTS {
withName: KRAKENTOOLS_COMBINEKREPORTS_KRAKEN {
ext.prefix = { "kraken2_${meta.id}_combined_reports" }
publishDir = [
path: { "${params.outdir}/kraken2/" },
mode: params.publish_dir_mode,
pattern: '*.{txt}'
pattern: '*.txt'
]
}

View file

@ -32,7 +32,7 @@
},
"bracken/combinebrackenoutputs": {
"branch": "master",
"git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905",
"git_sha": "9c87d5fdad182590a370ea43a4ecebd200a6f6fb",
"installed_by": ["modules"]
},
"cat/fastq": {

View file

@ -1,4 +1,5 @@
process BRACKEN_COMBINEBRACKENOUTPUTS {
tag "$meta.id"
label 'process_low'
conda (params.enable_conda ? "bioconda::bracken=2.7" : null)
@ -7,18 +8,18 @@ process BRACKEN_COMBINEBRACKENOUTPUTS {
'quay.io/biocontainers/bracken:2.7--py39hc16433a_0' }"
input:
path input
tuple val(meta), path(input)
output:
path "*.txt" , emit: txt
path "versions.yml", emit: versions
tuple val(meta), path("*.txt"), emit: txt
path "versions.yml" , emit: versions
when:
task.ext.when == null || task.ext.when
script:
def args = task.ext.args ?: ''
def prefix = task.ext.prefix ?: "bracken_combined.txt"
def prefix = task.ext.prefix ?: "${meta.id}"
// WARN: Version information not provided by tool on CLI.
// Please update version string below when bumping container versions.
def VERSION = '2.7'
@ -26,7 +27,7 @@ process BRACKEN_COMBINEBRACKENOUTPUTS {
combine_bracken_outputs.py \\
$args \\
--files ${input} \\
-o ${prefix}
-o ${prefix}.txt
cat <<-END_VERSIONS > versions.yml
"${task.process}":

View file

@ -12,12 +12,22 @@ tools:
licence: ["GPL v3"]
input:
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
- input:
type: file
description: List of output files from bracken
pattern: "*"
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