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Get rid of meta map from bbmap/index (#700)
Got rid of meta map from bbmap/index
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b2a6f5409e
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4 changed files with 4 additions and 16 deletions
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@ -9,7 +9,7 @@ process BBMAP_INDEX {
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label 'process_long'
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publishDir "${params.outdir}",
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mode: params.publish_dir_mode,
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saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
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saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:[:], publish_by_meta:[]) }
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conda (params.enable_conda ? "bioconda::bbmap=38.92" : null)
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if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
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@ -19,10 +19,10 @@ process BBMAP_INDEX {
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}
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input:
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tuple val(meta), path(fasta)
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path fasta
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output:
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tuple val(meta), path('ref') , emit: index
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path 'ref' , emit: index
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path "*.version.txt" , emit: version
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script:
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@ -14,22 +14,12 @@ tools:
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licence: ['UC-LBL license (see package)']
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input:
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- meta:
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type: map
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description: |
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Groovy Map containing optional parameters to bbmap.sh
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e.g. [ id:'test', single_end:false ]
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- fasta:
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type: fasta
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description: fasta formatted file with nucleotide sequences
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pattern: "*.{fna,fa,fasta}"
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output:
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- meta:
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type: map
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description: |
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Groovy Map containing sample information
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e.g. [ id:'test', single_end:false ]
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- version:
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type: file
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description: File containing software version
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@ -6,8 +6,7 @@ include { BBMAP_INDEX } from '../../../../modules/bbmap/index/main.nf' addParams
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workflow test_bbmap_index {
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input = [ [ id:'test' ], // meta map
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file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true) ]
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input = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
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BBMAP_INDEX ( input )
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}
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@ -7,6 +7,5 @@
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- bbmap/index
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files:
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- path: output/bbmap/ref/genome/1/chr1.chrom.gz
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md5sum: fc20702f3378836f06d4104b9cd88918
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- path: output/bbmap/ref/index/1/chr1_index_k13_c15_b1.block
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md5sum: 9f0d9a7413c1d2c16cc24555b2381163
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