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reformatted input to tuple

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This commit is contained in:
kevinmenden 2021-02-22 13:31:54 +01:00
parent 43446bc37e
commit 69d7bb4fca
4 changed files with 12 additions and 13 deletions
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4
software/gatk4/splitncigarreads/main.nf
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@ -20,9 +20,7 @@ process GATK4_SPLITNCIGARREADS {
input: input:
tuple val(meta), path(bam) tuple val(meta), path(bam)
path(fasta) tuple path(fasta), path(fai), path(dict)
path(fai)
path(dict)
output: output:
tuple val(meta), path('*.split_cigar.bam'), emit: bam tuple val(meta), path('*.split_cigar.bam'), emit: bam

7
software/gatk4/splitncigarreads/meta.yml
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@ -44,9 +44,10 @@ input:
description: BAM/SAM/CRAM file containing reads description: BAM/SAM/CRAM file containing reads
pattern: "*.{bam,sam,cram}" pattern: "*.{bam,sam,cram}"
- fasta: - fasta:
type: file type: tuple of files
description: Reference sequence file description: |
pattern: "*.fasta" Tuple of fasta file (first), sequence dict (second) and fasta index (third)
pattern: ["*.fasta", "*.dict", "*.fai"]
output: output:
- bam: - bam:
type: file type: file

8
tests/software/gatk4/splitncigarreads/main.nf
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@ -10,9 +10,9 @@ workflow test_gatk4_splitncigarreads {
input = [ [ id:'test' ], // meta map input = [ [ id:'test' ], // meta map
[ file("${launchDir}/tests/data/bam/sarscov2_aln.bam", checkIfExists: true)] ] [ file("${launchDir}/tests/data/bam/sarscov2_aln.bam", checkIfExists: true)] ]
fasta = file("tests/data/fasta/sarscov2/GCA_011545545.1_ASM1154554v1_genomic.fna", checkIfExists: true) fasta = [ file("tests/data/fasta/sarscov2/GCA_011545545.1_ASM1154554v1_genomic.fna", checkIfExists: true),
fai = file("tests/data/fasta/sarscov2/GCA_011545545.1_ASM1154554v1_genomic.fna.fai", checkIfExists: true) file("tests/data/fasta/sarscov2/GCA_011545545.1_ASM1154554v1_genomic.fna.fai", checkIfExists: true),
dict = file("tests/data/fasta/sarscov2/GCA_011545545.1_ASM1154554v1_genomic.dict", checkIfExists: true) file("tests/data/fasta/sarscov2/GCA_011545545.1_ASM1154554v1_genomic.dict", checkIfExists: true)]
GATK4_SPLITNCIGARREADS ( input, fasta, fai, dict ) GATK4_SPLITNCIGARREADS ( input, fasta )
} }

6
tests/software/gatk4/splitncigarreads/test.yml
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@ -2,7 +2,7 @@
command: nextflow run ./tests/software/gatk4/splitncigarreads -entry test_gatk4_splitncigarreads -c tests/config/nextflow.config command: nextflow run ./tests/software/gatk4/splitncigarreads -entry test_gatk4_splitncigarreads -c tests/config/nextflow.config
tags: tags:
- gatk4 - gatk4
- gatk4_mergevcfs - gatk4_splitncigarreads
files: files:
- path: output/gatk4/test.merged.vcf.gz - path: output/gatk4/test.split_cigar.bam
md5sum: f25850b7bd4d362b5ea67d4453e9df55 md5sum: 9228ac79882a4929c797c891b1bd9f6d