From 69d7bb4fcab79b89450c43434466858ac09411d4 Mon Sep 17 00:00:00 2001 From: kevinmenden Date: Mon, 22 Feb 2021 13:31:54 +0100 Subject: [PATCH] reformatted input to tuple --- software/gatk4/splitncigarreads/main.nf | 4 +--- software/gatk4/splitncigarreads/meta.yml | 7 ++++--- tests/software/gatk4/splitncigarreads/main.nf | 8 ++++---- tests/software/gatk4/splitncigarreads/test.yml | 6 +++--- 4 files changed, 12 insertions(+), 13 deletions(-) diff --git a/software/gatk4/splitncigarreads/main.nf b/software/gatk4/splitncigarreads/main.nf index ce3d10e3..0d7e0aa7 100644 --- a/software/gatk4/splitncigarreads/main.nf +++ b/software/gatk4/splitncigarreads/main.nf @@ -20,9 +20,7 @@ process GATK4_SPLITNCIGARREADS { input: tuple val(meta), path(bam) - path(fasta) - path(fai) - path(dict) + tuple path(fasta), path(fai), path(dict) output: tuple val(meta), path('*.split_cigar.bam'), emit: bam diff --git a/software/gatk4/splitncigarreads/meta.yml b/software/gatk4/splitncigarreads/meta.yml index c35690a6..33610180 100644 --- a/software/gatk4/splitncigarreads/meta.yml +++ b/software/gatk4/splitncigarreads/meta.yml @@ -44,9 +44,10 @@ input: description: BAM/SAM/CRAM file containing reads pattern: "*.{bam,sam,cram}" - fasta: - type: file - description: Reference sequence file - pattern: "*.fasta" + type: tuple of files + description: | + Tuple of fasta file (first), sequence dict (second) and fasta index (third) + pattern: ["*.fasta", "*.dict", "*.fai"] output: - bam: type: file diff --git a/tests/software/gatk4/splitncigarreads/main.nf b/tests/software/gatk4/splitncigarreads/main.nf index d8d7209f..27fd0c33 100644 --- a/tests/software/gatk4/splitncigarreads/main.nf +++ b/tests/software/gatk4/splitncigarreads/main.nf @@ -10,9 +10,9 @@ workflow test_gatk4_splitncigarreads { input = [ [ id:'test' ], // meta map [ file("${launchDir}/tests/data/bam/sarscov2_aln.bam", 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) - dict = file("tests/data/fasta/sarscov2/GCA_011545545.1_ASM1154554v1_genomic.dict", checkIfExists: true) + fasta = [ file("tests/data/fasta/sarscov2/GCA_011545545.1_ASM1154554v1_genomic.fna", checkIfExists: true), + file("tests/data/fasta/sarscov2/GCA_011545545.1_ASM1154554v1_genomic.fna.fai", 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 ) } diff --git a/tests/software/gatk4/splitncigarreads/test.yml b/tests/software/gatk4/splitncigarreads/test.yml index 3d52a60d..2dd9e0d5 100644 --- a/tests/software/gatk4/splitncigarreads/test.yml +++ b/tests/software/gatk4/splitncigarreads/test.yml @@ -2,7 +2,7 @@ command: nextflow run ./tests/software/gatk4/splitncigarreads -entry test_gatk4_splitncigarreads -c tests/config/nextflow.config tags: - gatk4 - - gatk4_mergevcfs + - gatk4_splitncigarreads files: - - path: output/gatk4/test.merged.vcf.gz - md5sum: f25850b7bd4d362b5ea67d4453e9df55 + - path: output/gatk4/test.split_cigar.bam + md5sum: 9228ac79882a4929c797c891b1bd9f6d