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TIDDIT - add --skip_assembly when no bwa specified (#1769)

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add --skip_assembly when no bwa specified
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Maxime U. Garcia 2022-06-13 17:02:59 +02:00 committed by GitHub
parent 680b6c5b04
commit b689b8ed88
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GPG key ID: 4AEE18F83AFDEB23
4 changed files with 56 additions and 3 deletions
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4
modules/tiddit/sv/main.nf
View file

@ -23,8 +23,10 @@ process TIDDIT_SV {
script: script:
def args = task.ext.args ?: '' def args = task.ext.args ?: ''
def prefix = task.ext.prefix ?: "${meta.id}" def prefix = task.ext.prefix ?: "${meta.id}"
def bwa_command = bwa_index ? "[[ -d $bwa_index ]] && for i in $bwa_index/*; do [[ -f $fasta && ! \"\$i\" =~ .*\"$fasta\".* ]] && ln -s \$i ${fasta}.\${i##*.} || ln -s \$i .; done" : ""
""" """
[[ -d $bwa_index ]] && for i in $bwa_index/*; do [[ -f $fasta && ! "\$i" =~ .*"$fasta".* ]] && ln -s \$i ${fasta}.\${i##*.} || ln -s \$i .; done $bwa_command
tiddit \\ tiddit \\
--sv \\ --sv \\

25
tests/modules/tiddit/sv/main.nf
View file

@ -4,6 +4,7 @@ nextflow.enable.dsl = 2
include { BWA_INDEX } from '../../../../modules/bwa/index/main.nf' 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'
include { TIDDIT_SV as TIDDIT_SV_NOBWA } from '../../../../modules/tiddit/sv/main.nf'
workflow test_tiddit_sv_bam { workflow test_tiddit_sv_bam {
input = [ input = [
@ -32,3 +33,27 @@ workflow test_tiddit_sv_cram {
TIDDIT_SV ( input, fasta, BWA_INDEX.out.index) TIDDIT_SV ( input, fasta, BWA_INDEX.out.index)
} }
workflow test_tiddit_sv_nobwa_bam {
input = [
[ id:'test' ], // meta map
[ file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true) ],
[ file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true) ]
]
fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
TIDDIT_SV_NOBWA ( input, fasta, [])
}
workflow test_tiddit_sv_nobwa_cram {
input = [
[ id:'test' ], // meta map
[ file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram'], checkIfExists: true) ],
[ file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram_crai'], checkIfExists: true) ]
]
fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
TIDDIT_SV_NOBWA ( input, fasta, [])
}

4
tests/modules/tiddit/sv/nextflow.config
View file

@ -2,4 +2,8 @@ process {
publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" } publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
withName: TIDDIT_SV_NOBWA {
ext.args = '--skip_assembly'
}
} }

22
tests/modules/tiddit/sv/test.yml
View file

@ -19,3 +19,25 @@
md5sum: f1162a940ddc8b963f6e0e506bb5c136 md5sum: f1162a940ddc8b963f6e0e506bb5c136
- path: output/tiddit/test.vcf - path: output/tiddit/test.vcf
md5sum: 56687eeffa452f78f18d54a69dd17c78 md5sum: 56687eeffa452f78f18d54a69dd17c78
- name: tiddit sv test_tiddit_sv_nobwa_bam
command: nextflow run ./tests/modules/tiddit/sv -entry test_tiddit_sv_nobwa_bam -c ./tests/config/nextflow.config -c ./tests/modules/tiddit/sv/nextflow.config
tags:
- tiddit
- tiddit/sv
files:
- path: output/tiddit/test.ploidies.tab
md5sum: 6319d3611f7b6b94425a184d274b3dfc
- path: output/tiddit/test.vcf
md5sum: ddac94f9cd4f991b6ce2052d7f78a525
- name: tiddit sv test_tiddit_sv_nobwa_cram
command: nextflow run ./tests/modules/tiddit/sv -entry test_tiddit_sv_nobwa_cram -c ./tests/config/nextflow.config -c ./tests/modules/tiddit/sv/nextflow.config
tags:
- tiddit
- tiddit/sv
files:
- path: output/tiddit/test.ploidies.tab
md5sum: f1162a940ddc8b963f6e0e506bb5c136
- path: output/tiddit/test.vcf
md5sum: 680e60574cc28d38c9673a916ecd675c