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Add meta to MALT/RUN (#1372)

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* Add meta to MALT/RUN

* Update modules/malt/run/main.nf
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James A. Fellows Yates 2022-03-03 16:35:19 +01:00 committed by GitHub
parent c450b08a75
commit 76cdd46f3f
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3 changed files with 16 additions and 6 deletions
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11
modules/malt/run/main.nf
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@ -1,4 +1,5 @@
process MALT_RUN {
tag "$meta.id"
label 'process_high'
conda (params.enable_conda ? "bioconda::malt=0.53" : null)
@ -7,15 +8,15 @@ process MALT_RUN {
'quay.io/biocontainers/malt:0.53--hdfd78af_0' }"
input:
path fastqs
tuple val(meta), path(fastqs)
val mode
path index
output:
path "*.rma6" , emit: rma6
path "*.{tab,text,sam}", optional:true, emit: alignments
path "*.log" , emit: log
path "versions.yml" , emit: versions
tuple val(meta), path("*.rma6") , emit: rma6
tuple val(meta), path("*.{tab,text,sam}"), optional:true, emit: alignments
tuple val(meta), path("*.log") , emit: log
path "versions.yml" , emit: versions
when:
task.ext.when == null || task.ext.when

5
modules/malt/run/meta.yml
View file

@ -19,6 +19,11 @@ tools:
licence: ["GPL v3"]
input:
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
- fastqs:
type: file
description: Input FASTQ files

6
tests/modules/malt/run/main.nf
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@ -12,10 +12,14 @@ workflow test_malt_run {
gff = file(params.test_data['sarscov2']['genome']['genome_gff3'], checkIfExists: true)
seq_type = "DNA"
map_db = file("https://software-ab.informatik.uni-tuebingen.de/download/megan6/megan-nucl-Jan2021.db.zip", checkIfExists: true)
input = file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true)
input = [
[ id:'test', single_end:false ], // meta map
file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true)
]
mode = "BlastN"
UNZIP ( map_db )
MALT_BUILD ( fastas, seq_type, gff, UNZIP.out.unzipped_archive )
MALT_RUN ( input, mode, MALT_BUILD.out.index )
}