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small update to samtools/merge (#1896)

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nvnieuwk 2022-07-18 11:37:45 +02:00 committed by GitHub
parent ffe0375048
commit 720027275c
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5 changed files with 23 additions and 18 deletions
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3
modules/samtools/merge/main.nf
View file

@ -8,8 +8,9 @@ process SAMTOOLS_MERGE {
'quay.io/biocontainers/samtools:1.15.1--h1170115_0' }" 'quay.io/biocontainers/samtools:1.15.1--h1170115_0' }"
input: input:
tuple val(meta), path(input_files) tuple val(meta), path(input_files, stageAs: "?/*")
path fasta path fasta
path fai
output: output:
tuple val(meta), path("${prefix}.bam") , optional:true, emit: bam tuple val(meta), path("${prefix}.bam") , optional:true, emit: bam

4
modules/samtools/merge/meta.yml
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@ -29,6 +29,10 @@ input:
type: optional file type: optional file
description: Reference file the CRAM was created with description: Reference file the CRAM was created with
pattern: "*.{fasta,fa}" pattern: "*.{fasta,fa}"
- fai:
type: optional file
description: Index of the reference file the CRAM was created with
pattern: "*.fai"
output: output:
- meta: - meta:
type: map type: map

26
tests/modules/samtools/merge/main.nf
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@ -6,20 +6,24 @@ include { SAMTOOLS_MERGE } from '../../../../modules/samtools/merge/main.nf'
workflow test_samtools_merge { workflow test_samtools_merge {
input = [ [ id: 'test' ], // meta map input = [ [ id: 'test' ], // meta map
[ file(params.test_data['sarscov2']['illumina']['test_paired_end_methylated_sorted_bam'], checkIfExists: true), [
file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true), file(params.test_data['sarscov2']['illumina']['test_paired_end_methylated_sorted_bam'], checkIfExists: true),
file(params.test_data['sarscov2']['illumina']['test_single_end_sorted_bam'], checkIfExists: true)] file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true),
] file(params.test_data['sarscov2']['illumina']['test_single_end_sorted_bam'], checkIfExists: true)
]
]
SAMTOOLS_MERGE ( input, [] ) SAMTOOLS_MERGE ( input, [], [] )
} }
workflow test_samtools_merge_cram { workflow test_samtools_merge_cram {
input = [ [ id: 'test' ], // meta map input = [ [ id: 'test' ], // meta map
[ file(params.test_data['homo_sapiens']['illumina']['test_paired_end_recalibrated_sorted_cram'], checkIfExists: true), [
file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_recalibrated_sorted_cram'], checkIfExists: true), file(params.test_data['homo_sapiens']['illumina']['test_paired_end_recalibrated_sorted_cram'], checkIfExists: true),
] file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_recalibrated_sorted_cram'], checkIfExists: true),
] ]
fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true) ]
SAMTOOLS_MERGE ( input, fasta ) fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
fai = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true)
SAMTOOLS_MERGE ( input, fasta, fai )
} }

4
tests/modules/samtools/merge/nextflow.config
View file

@ -2,8 +2,4 @@ process {
publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" } publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
withName: SAMTOOLS_MERGE {
ext.prefix = { "${meta.id}_merged" }
}
} }

4
tests/modules/samtools/merge/test.yml
View file

@ -4,7 +4,7 @@
- samtools - samtools
- samtools/merge - samtools/merge
files: files:
- path: output/samtools/test_merged.bam - path: output/samtools/test.bam
- name: samtools merge test_samtools_merge_cram - name: samtools merge test_samtools_merge_cram
command: nextflow run ./tests/modules/samtools/merge -entry test_samtools_merge_cram -c ./tests/config/nextflow.config -c ./tests/modules/samtools/merge/nextflow.config command: nextflow run ./tests/modules/samtools/merge -entry test_samtools_merge_cram -c ./tests/config/nextflow.config -c ./tests/modules/samtools/merge/nextflow.config
@ -12,4 +12,4 @@
- samtools - samtools
- samtools/merge - samtools/merge
files: files:
- path: output/samtools/test_merged.cram - path: output/samtools/test.cram