Get rid of meta map from bbmap/index (#700)

Got rid of meta map from bbmap/index
This commit is contained in:
Daniel Lundin 2021-09-15 12:38:56 +02:00 committed by GitHub
parent b2a6f5409e
commit 3a8bfc1d33
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GPG key ID: 4AEE18F83AFDEB23
4 changed files with 4 additions and 16 deletions

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@ -9,7 +9,7 @@ process BBMAP_INDEX {
label 'process_long'
publishDir "${params.outdir}",
mode: params.publish_dir_mode,
saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:[:], publish_by_meta:[]) }
conda (params.enable_conda ? "bioconda::bbmap=38.92" : null)
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
@ -19,10 +19,10 @@ process BBMAP_INDEX {
}
input:
tuple val(meta), path(fasta)
path fasta
output:
tuple val(meta), path('ref') , emit: index
path 'ref' , emit: index
path "*.version.txt" , emit: version
script:

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@ -14,22 +14,12 @@ tools:
licence: ['UC-LBL license (see package)']
input:
- meta:
type: map
description: |
Groovy Map containing optional parameters to bbmap.sh
e.g. [ id:'test', single_end:false ]
- fasta:
type: fasta
description: fasta formatted file with nucleotide sequences
pattern: "*.{fna,fa,fasta}"
output:
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
- version:
type: file
description: File containing software version

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@ -6,8 +6,7 @@ include { BBMAP_INDEX } from '../../../../modules/bbmap/index/main.nf' addParams
workflow test_bbmap_index {
input = [ [ id:'test' ], // meta map
file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true) ]
input = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
BBMAP_INDEX ( input )
}

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@ -7,6 +7,5 @@
- bbmap/index
files:
- path: output/bbmap/ref/genome/1/chr1.chrom.gz
md5sum: fc20702f3378836f06d4104b9cd88918
- path: output/bbmap/ref/index/1/chr1_index_k13_c15_b1.block
md5sum: 9f0d9a7413c1d2c16cc24555b2381163