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GATK4 SplitNCigarReads: fasta_fai_dict tuple is now split into separate input channels (nf-core#1076)
* 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 <[email protected]>
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modules/gatk4/splitncigarreads/main.nf

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@@ -20,7 +20,9 @@ process GATK4_SPLITNCIGARREADS {
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input:
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tuple val(meta), path(bam)
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tuple path(fasta), path(fai), path(dict)
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path fasta
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path fai
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path dict
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output:
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tuple val(meta), path('*.bam'), emit: bam

modules/gatk4/splitncigarreads/meta.yml

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

tests/modules/gatk4/splitncigarreads/main.nf

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

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