millironx/nf-core_modules
1
0
Fork 0
mirror of https://github.com/MillironX/nf-core_modules.git synced 2025-01-03 04:52:09 -05:00
Code Issues Releases Packages Activity

restructure tiddit/sv + test (just one for now)

Browse source
This commit is contained in:
MaxUlysse 2022-06-03 13:00:29 +02:00
parent 40996cdbe1
commit f1a5cc07db
3 changed files with 19 additions and 51 deletions
Show stats Download patch file Download diff file Expand all files Collapse all files

19
modules/tiddit/sv/main.nf
View file

@ -8,16 +8,15 @@ process TIDDIT_SV {
'quay.io/biocontainers/tiddit:3.0.0--py39h59fae87_1' }" 'quay.io/biocontainers/tiddit:3.0.0--py39h59fae87_1' }"
input: input:
tuple val(meta), path(input) tuple val(meta), path(input), path(index)
path fasta path fasta
path fai path fai
path bwa_index path bwa_index
output: output:
tuple val(meta), path("*.vcf") , emit: vcf tuple val(meta), path("*.vcf") , emit: vcf
tuple val(meta), path("*.ploidy.tab") , emit: ploidy tuple val(meta), path("*.ploidies.tab"), emit: ploidy
tuple val(meta), path("*.signals.tab"), emit: signals path "versions.yml" , emit: versions
path "versions.yml" , emit: versions
when: when:
task.ext.when == null || task.ext.when task.ext.when == null || task.ext.when
@ -27,7 +26,11 @@ 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//'` for i in `ls ${bwa_index}`
do
ln -s ${bwa_index}/\$i ${fasta}.\${i##*.}
done
tiddit \\ tiddit \\
--sv \\ --sv \\
@ -38,7 +41,7 @@ process TIDDIT_SV {
cat <<-END_VERSIONS > versions.yml cat <<-END_VERSIONS > versions.yml
"${task.process}": "${task.process}":
tiddit: \$(echo \$(tiddit 2>&1) | sed 's/^.*TIDDIT-//; s/ .*\$//') tiddit: \$(echo \$(tiddit 2>&1) | sed 's/^.*tiddit-//; s/ .*\$//')
END_VERSIONS END_VERSIONS
""" """
@ -51,7 +54,7 @@ process TIDDIT_SV {
cat <<-END_VERSIONS > versions.yml cat <<-END_VERSIONS > versions.yml
"${task.process}": "${task.process}":
tiddit: \$(echo \$(tiddit 2>&1) | sed 's/^.*TIDDIT-//; s/ .*\$//') tiddit: \$(echo \$(tiddit 2>&1) | sed 's/^.*tiddit-//; s/ .*\$//')
END_VERSIONS END_VERSIONS
""" """
} }

26
tests/modules/tiddit/sv/main.nf
View file

@ -5,10 +5,11 @@ 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'
workflow test_tiddit_sv { workflow test_tiddit_sv_bam {
input = [ input = [
[ id:'test' ], // meta map [ 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'], 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) fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
@ -18,24 +19,3 @@ workflow test_tiddit_sv {
TIDDIT_SV ( input, fasta, fai , BWA_INDEX.out.index) TIDDIT_SV ( input, fasta, fai , BWA_INDEX.out.index)
} }
workflow test_tiddit_sv_no_ref {
input = [
[ id:'test' ], // meta map
[ file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true) ]
]
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 )
}

25
tests/modules/tiddit/sv/test.yml
View file

@ -1,25 +1,10 @@
- name: tiddit sv - name: tiddit sv test_tiddit_sv_bam
command: nextflow run ./tests/modules/tiddit/sv -entry test_tiddit_sv -c ./tests/config/nextflow.config -c ./tests/modules/tiddit/sv/nextflow.config command: nextflow run ./tests/modules/tiddit/sv -entry test_tiddit_sv_bam -c ./tests/config/nextflow.config -c ./tests/modules/tiddit/sv/nextflow.config
tags: tags:
- tiddit - tiddit
- tiddit/sv - tiddit/sv
files: files:
- path: output/tiddit/test.ploidy.tab - path: output/tiddit/test.ploidies.tab
md5sum: 45e050b0e204f0a5a3a99627cc440eaa md5sum: 6319d3611f7b6b94425a184d274b3dfc
- path: output/tiddit/test.signals.tab
md5sum: dab4b2fec4ddf8eb1c23005b0770150e
- path: output/tiddit/test.vcf - path: output/tiddit/test.vcf
md5sum: bdce14ae8292bf3deb81f6f255baf859 md5sum: 41d3f8746f0420f894104321b7e64f67
- name: tiddit sv no ref
command: nextflow run ./tests/modules/tiddit/sv -entry test_tiddit_sv_no_ref -c ./tests/config/nextflow.config -c ./tests/modules/tiddit/sv/nextflow.config
tags:
- tiddit
- tiddit/sv
files:
- path: output/tiddit/test.ploidy.tab
md5sum: 45e050b0e204f0a5a3a99627cc440eaa
- path: output/tiddit/test.signals.tab
md5sum: dab4b2fec4ddf8eb1c23005b0770150e
- path: output/tiddit/test.vcf
md5sum: 3d0e83a8199b2bdb81cfe3e6b12bf64b