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

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

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

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

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

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

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

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@ -7,28 +7,30 @@ include { MANTA_GERMLINE } from '../../../../modules/manta/germline/main.nf'
workflow test_manta_germline { workflow test_manta_germline {
input = [ input = [
[ id:'test'], // meta map [ 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'], 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_crai'], checkIfExists: true)]
[],[]
] ]
fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], 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) 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 { workflow test_manta_germline_target_bed {
input = [ input = [
[ id:'test'], // meta map [ 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'], 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_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)
] ]
fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], 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) 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 { 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']['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']['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']['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']['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)
] ]
fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], 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) 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 )
} }