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Merge branch 'nf-core:master' into master

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James A. Fellows Yates 2022-03-03 17:37:04 +01:00 committed by GitHub
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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 { process MALT_RUN {
tag "$meta.id"
label 'process_high' label 'process_high'
conda (params.enable_conda ? "bioconda::malt=0.53" : null) conda (params.enable_conda ? "bioconda::malt=0.53" : null)
@ -7,15 +8,15 @@ process MALT_RUN {
'quay.io/biocontainers/malt:0.53--hdfd78af_0' }" 'quay.io/biocontainers/malt:0.53--hdfd78af_0' }"
input: input:
path fastqs tuple val(meta), path(fastqs)
val mode val mode
path index path index
output: output:
path "*.rma6" , emit: rma6 tuple val(meta), path("*.rma6") , emit: rma6
path "*.{tab,text,sam}", optional:true, emit: alignments tuple val(meta), path("*.{tab,text,sam}"), optional:true, emit: alignments
path "*.log" , emit: log tuple val(meta), path("*.log") , emit: log
path "versions.yml" , emit: versions path "versions.yml" , emit: versions
when: when:
task.ext.when == null || task.ext.when task.ext.when == null || task.ext.when

5
modules/malt/run/meta.yml
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@ -19,6 +19,11 @@ tools:
licence: ["GPL v3"] licence: ["GPL v3"]
input: input:
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
- fastqs: - fastqs:
type: file type: file
description: Input FASTQ files 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) gff = file(params.test_data['sarscov2']['genome']['genome_gff3'], checkIfExists: true)
seq_type = "DNA" seq_type = "DNA"
map_db = file("https://software-ab.informatik.uni-tuebingen.de/download/megan6/megan-nucl-Jan2021.db.zip", checkIfExists: true) 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" mode = "BlastN"
UNZIP ( map_db ) UNZIP ( map_db )
MALT_BUILD ( fastas, seq_type, gff, UNZIP.out.unzipped_archive ) MALT_BUILD ( fastas, seq_type, gff, UNZIP.out.unzipped_archive )
MALT_RUN ( input, mode, MALT_BUILD.out.index ) MALT_RUN ( input, mode, MALT_BUILD.out.index )
} }