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Update TIDDIT to 3.0.0

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This commit is contained in:
Rike 2022-06-03 10:52:50 +02:00
parent b86d792055
commit 2c9e2f5e73
2 changed files with 29 additions and 11 deletions
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13
modules/tiddit/sv/main.nf
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@ -2,15 +2,16 @@ process TIDDIT_SV {
tag "$meta.id" tag "$meta.id"
label 'process_medium' label 'process_medium'
conda (params.enable_conda ? "bioconda::tiddit=2.12.1" : null) conda (params.enable_conda ? "bioconda::tiddit=3.0.0" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/tiddit:2.12.1--py38h1773678_0' : 'https://depot.galaxyproject.org/singularity/tiddit:3.0.0--py39h59fae87_1' :
'quay.io/biocontainers/tiddit:2.12.1--py38h1773678_0' }" 'quay.io/biocontainers/tiddit:3.0.0--py39h59fae87_1' }"
input: input:
tuple val(meta), path(bam) tuple val(meta), path(input)
path fasta path fasta
path fai path fai
path bwa_index
output: output:
tuple val(meta), path("*.vcf") , emit: vcf tuple val(meta), path("*.vcf") , emit: vcf
@ -26,10 +27,12 @@ process TIDDIT_SV {
def prefix = task.ext.prefix ?: "${meta.id}" def prefix = task.ext.prefix ?: "${meta.id}"
def reference = fasta ? "--ref $fasta" : "" def reference = fasta ? "--ref $fasta" : ""
""" """
INDEX=`find -L ./ -name "*.amb" | sed 's/.amb//'`
tiddit \\ tiddit \\
--sv \\ --sv \\
$args \\ $args \\
--bam $bam \\ --bam $input \\
$reference \\ $reference \\
-o $prefix -o $prefix

17
tests/modules/tiddit/sv/main.nf
View file

@ -2,6 +2,7 @@
nextflow.enable.dsl = 2 nextflow.enable.dsl = 2
include { BWA_INDEX } from '../../../../modules/bwa/index/main.nf'
include { TIDDIT_SV } from '../../../../modules/tiddit/sv/main.nf' include { TIDDIT_SV } from '../../../../modules/tiddit/sv/main.nf'
workflow test_tiddit_sv { workflow test_tiddit_sv {
@ -13,7 +14,9 @@ workflow test_tiddit_sv {
fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], 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) fai = file(params.test_data['sarscov2']['genome']['genome_fasta_fai'], checkIfExists: true)
TIDDIT_SV ( input, fasta, fai ) BWA_INDEX( fasta )
TIDDIT_SV ( input, fasta, fai , BWA_INDEX.out.index)
} }
workflow test_tiddit_sv_no_ref { workflow test_tiddit_sv_no_ref {
@ -24,3 +27,15 @@ workflow test_tiddit_sv_no_ref {
TIDDIT_SV ( input, [], [] ) TIDDIT_SV ( input, [], [] )
} }
workflow test_tiddit_sv_cram {
input = [
[ id:'test' ], // meta map
[ file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram'], checkIfExists: true) ]
]
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)
TIDDIT_SV ( input, fasta, fai )
}