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add extra output from snap aligner (#1826)

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Matthias De Smet 2022-06-29 12:37:38 +02:00 committed by GitHub
parent 0f1e736212
commit e2755cb039
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5 changed files with 24 additions and 15 deletions
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1
modules/snapaligner/align/main.nf
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@ -13,6 +13,7 @@ process SNAPALIGNER_ALIGN {
output: output:
tuple val(meta), path("*.bam"), emit: bam tuple val(meta), path("*.bam"), emit: bam
tuple val(meta), path("*.bai"), optional: true, emit: bai
path "versions.yml" , emit: versions path "versions.yml" , emit: versions
when: when:

5
modules/snapaligner/align/meta.yml
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@ -43,6 +43,9 @@ output:
type: file type: file
description: Aligned BAM file description: Aligned BAM file
pattern: "*.{bam}" pattern: "*.{bam}"
- bai:
type: file
description: Optional aligned BAM file index
pattern: "*.{bai}"
authors: authors:
- "@matthdsm" - "@matthdsm"

7
tests/modules/snapaligner/align/main.nf
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@ -3,8 +3,7 @@
nextflow.enable.dsl = 2 nextflow.enable.dsl = 2
include { SNAPALIGNER_INDEX } from '../../../../modules/snapaligner/index/main.nf' include { SNAPALIGNER_INDEX } from '../../../../modules/snapaligner/index/main.nf'
include { SNAPALIGNER_ALIGN as SNAPALIGNER_SINGLE } from '../../../../modules/snapaligner/align/main.nf' include { SNAPALIGNER_ALIGN } from '../../../../modules/snapaligner/align/main.nf'
include { SNAPALIGNER_ALIGN as SNAPALIGNER_PAIRED } from '../../../../modules/snapaligner/align/main.nf'
workflow test_snapaligner_single { workflow test_snapaligner_single {
@ -14,7 +13,7 @@ workflow test_snapaligner_single {
] ]
SNAPALIGNER_INDEX ( file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true),[],[],[]) SNAPALIGNER_INDEX ( file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true),[],[],[])
SNAPALIGNER_SINGLE ( input, SNAPALIGNER_INDEX.out.index ) SNAPALIGNER_ALIGN ( input, SNAPALIGNER_INDEX.out.index )
} }
workflow test_snapaligner_paired { workflow test_snapaligner_paired {
@ -25,5 +24,5 @@ workflow test_snapaligner_paired {
] ]
SNAPALIGNER_INDEX ( file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true),[],[],[]) SNAPALIGNER_INDEX ( file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true),[],[],[])
SNAPALIGNER_PAIRED ( input, SNAPALIGNER_INDEX.out.index ) SNAPALIGNER_ALIGN ( input, SNAPALIGNER_INDEX.out.index )
} }

8
tests/modules/snapaligner/align/nextflow.config
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@ -1,5 +1,9 @@
process { process {
publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" } publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
withName: SNAPALIGNER_INDEX {
publishDir = [ enabled: false ]
}
withName: SNAPALIGNER_ALIGN {
ext.args = "-so"
}
} }

14
tests/modules/snapaligner/align/test.yml
View file

@ -1,19 +1,21 @@
- name: snapaligner align test_snapaligner_single - name: snapaligner align test_snapaligner_single
command: nextflow run tests/modules/snapaligner/align -entry test_snapaligner_single -c tests/config/nextflow.config command: nextflow run ./tests/modules/snapaligner/align -entry test_snapaligner_single -c ./tests/config/nextflow.config -c ./tests/modules/snapaligner/align/nextflow.config
tags: tags:
- snapaligner/align - snapaligner/align
- snapaligner - snapaligner
files: files:
- path: output/snapaligner/test.bam - path: output/snapaligner/test.bam
md5sum: 5d95594e4ef1ee23ce56e6a7cb64f0f2 md5sum: 2dea536f28c041c1108add3523879243
- path: output/snapaligner/versions.yml - path: output/snapaligner/test.bam.bai
md5sum: 3f5cd1e8379b06554778a59b179ccc10
- name: snapaligner align test_snapaligner_paired - name: snapaligner align test_snapaligner_paired
command: nextflow run tests/modules/snapaligner/align -entry test_snapaligner_paired -c tests/config/nextflow.config command: nextflow run ./tests/modules/snapaligner/align -entry test_snapaligner_paired -c ./tests/config/nextflow.config -c ./tests/modules/snapaligner/align/nextflow.config
tags: tags:
- snapaligner/align - snapaligner/align
- snapaligner - snapaligner
files: files:
- path: output/snapaligner/test.bam - path: output/snapaligner/test.bam
md5sum: a1405da5876f15dbe8a81516b94c2a15 md5sum: 941bf870355dd34ebe2ef43ea41abcc4
- path: output/snapaligner/versions.yml - path: output/snapaligner/test.bam.bai
md5sum: ce7fd5bc6f0196e6ad70d3710e17e559