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GATK4 SplitNCigarReads: fasta_fai_dict tuple is now split into separate input channels (#1076)

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* fasta_fai_dict tuple is now split into separate input channels

* fix: lint errors

* fix: pytest errors

* Update modules/gatk4/splitncigarreads/meta.yml

* Update modules/gatk4/splitncigarreads/main.nf

Co-authored-by: Maxime U. Garcia <maxime.garcia@scilifelab.se>
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praveenraj2018 2021-11-16 15:09:30 +01:00 committed by GitHub
parent b50f4e3d59
commit 691feeafdc
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3 changed files with 18 additions and 10 deletions
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4
modules/gatk4/splitncigarreads/main.nf
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@ -20,7 +20,9 @@ process GATK4_SPLITNCIGARREADS {
input:
tuple val(meta), path(bam)
tuple path(fasta), path(fai), path(dict)
path fasta
path fai
path dict
output:
tuple val(meta), path('*.bam'), emit: bam

15
modules/gatk4/splitncigarreads/meta.yml
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@ -24,10 +24,17 @@ input:
description: BAM/SAM/CRAM file containing reads
pattern: "*.{bam,sam,cram}"
- fasta:
type: tuple of files
description: |
Tuple of fasta file (first), sequence dict (second) and fasta index (third)
pattern: ["*.fasta", "*.dict", "*.fai"]
type: file
description: The reference fasta file
pattern: "*.fasta"
- fai:
type: file
description: Index of reference fasta file
pattern: "*.fasta.fai"
- dict:
type: file
description: GATK sequence dictionary
pattern: "*.dict"
output:
- bam:
type: file

9
tests/modules/gatk4/splitncigarreads/main.nf
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@ -8,10 +8,9 @@ workflow test_gatk4_splitncigarreads {
input = [ [ id:'test' ], // meta map
[ file(params.test_data['sarscov2']['illumina']['test_paired_end_bam'], checkIfExists: true) ]
]
fasta = [ file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true),
file(params.test_data['sarscov2']['genome']['genome_fasta_fai'], checkIfExists: true),
file(params.test_data['sarscov2']['genome']['genome_dict'], checkIfExists: true)
]
fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
fai = file(params.test_data['sarscov2']['genome']['genome_fasta_fai'], checkIfExists: true)
dict = file(params.test_data['sarscov2']['genome']['genome_dict'], checkIfExists: true)
GATK4_SPLITNCIGARREADS ( input, fasta )
GATK4_SPLITNCIGARREADS ( input, fasta, fai, dict )
}