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Revert recent changes made to some of the modules (#1463)

Browse source 
* revert changes to modules

* fix tests

* fix kraken2

* fix untar

* fix cat

* add blank lines

* fix typo
This commit is contained in:
Ramprasad Neethiraj 2022-03-30 20:21:06 +02:00 committed by GitHub
parent a973b68200
commit fd5f6f5f4f
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GPG key ID: 4AEE18F83AFDEB23
7 changed files with 27 additions and 23 deletions
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2
modules/cat/cat/main.nf
View file

@ -30,7 +30,7 @@ process CAT_CAT {
// | ungzipped | gzipped | cat | pigz |
// Use input file ending as default
prefix = task.ext.prefix ?: "${meta.id}${file_list[0].substring(file_list[0].lastIndexOf('.'))}"
prefix = task.ext.prefix ?: "${meta.id}${file_list[0].substring(file_list[0].lastIndexOf('.'))}"
out_zip = prefix.endsWith('.gz')
in_zip = file_list[0].endsWith('.gz')
command1 = (in_zip && !out_zip) ? 'zcat' : 'cat'

2
modules/deepvariant/main.nf
View file

@ -46,7 +46,7 @@ process DEEPVARIANT {
"""
stub:
def prefix = task.ext.prefix ?: "${meta.id}"
prefix = task.ext.prefix ?: "${meta.id}"
"""
touch ${prefix}.vcf.gz
touch ${prefix}.g.vcf.gz

3
modules/gatk4/createsequencedictionary/main.nf
View file

@ -39,9 +39,8 @@ process GATK4_CREATESEQUENCEDICTIONARY {
"""
stub:
def prefix = task.ext.prefix ?: "${meta.id}"
"""
touch ${prefix}.dict
touch test.dict
cat <<-END_VERSIONS > versions.yml
"${task.process}":

3
modules/manta/germline/main.nf
View file

@ -8,9 +8,10 @@ process MANTA_GERMLINE {
'quay.io/biocontainers/manta:1.6.0--h9ee0642_1' }"
input:
tuple val(meta), path(input), path(index), path(target_bed), path(target_bed_tbi)
tuple val(meta), path(input), path(index)
path fasta
path fasta_fai
tuple path(target_bed), path(target_bed_tbi)
output:

4
modules/tiddit/cov/main.nf
View file

@ -40,8 +40,8 @@ process TIDDIT_COV {
stub:
def prefix = task.ext.prefix ?: "${meta.id}"
"""
touch $prefix.wig
touch $prefix.tab
touch ${prefix}.wig
touch ${prefix}.tab
cat <<-END_VERSIONS > versions.yml
"${task.process}":

6
modules/tiddit/sv/main.nf
View file

@ -42,9 +42,9 @@ process TIDDIT_SV {
stub:
def prefix = task.ext.prefix ?: "${meta.id}"
"""
touch $prefix.vcf
touch $prefix.ploidy.tab
touch $prefix.signals.tab
touch ${prefix}.vcf
touch ${prefix}.ploidy.tab
touch ${prefix}.signals.tab
cat <<-END_VERSIONS > versions.yml
"${task.process}":

30
tests/modules/manta/germline/main.nf
View file

@ -7,28 +7,30 @@ include { MANTA_GERMLINE } from '../../../../modules/manta/germline/main.nf'
workflow test_manta_germline {
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),
[],[]
[ 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)
fai = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true)
bed = [[],[]]
MANTA_GERMLINE ( input, fasta, fai )
MANTA_GERMLINE ( input, fasta, fai, bed )
}
workflow test_manta_germline_target_bed {
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),
file(params.test_data['homo_sapiens']['genome']['genome_bed_gz'], checkIfExists: true),
file(params.test_data['homo_sapiens']['genome']['genome_bed_gz_tbi'], checkIfExists: true)
[ 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)
fai = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true)
bed = [
file(params.test_data['homo_sapiens']['genome']['genome_bed_gz'], checkIfExists: true),
file(params.test_data['homo_sapiens']['genome']['genome_bed_gz_tbi'], checkIfExists: true),
]
MANTA_GERMLINE ( input, fasta, fai )
MANTA_GERMLINE ( input, fasta, fai, bed )
}
workflow test_manta_germline_target_bed_jointcalling {
@ -37,12 +39,14 @@ workflow test_manta_germline_target_bed_jointcalling {
[file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram'], checkIfExists: true),
file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_sorted_cram'], checkIfExists: true)],
[file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram_crai'], checkIfExists: true),
file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_sorted_cram_crai'], checkIfExists: true),],
file(params.test_data['homo_sapiens']['genome']['genome_bed_gz'], checkIfExists: true),
file(params.test_data['homo_sapiens']['genome']['genome_bed_gz_tbi'], checkIfExists: true)
file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_sorted_cram_crai'], 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)
bed = [
file(params.test_data['homo_sapiens']['genome']['genome_bed_gz'], checkIfExists: true),
file(params.test_data['homo_sapiens']['genome']['genome_bed_gz_tbi'], checkIfExists: true),
]
MANTA_GERMLINE ( input, fasta, fai )
MANTA_GERMLINE ( input, fasta, fai, bed )
}