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Merge branch 'master' into maxquant

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Gregor Sturm 2022-01-02 22:36:05 +01:00 committed by GitHub
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21 changed files with 104 additions and 87 deletions
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10
modules/gatk4/applybqsr/main.nf
View file

@ -8,20 +8,22 @@ process GATK4_APPLYBQSR {
'quay.io/biocontainers/gatk4:4.2.4.0--hdfd78af_0' }"
input:
tuple val(meta), path(input), path(input_index), path(bqsr_table)
tuple val(meta), path(input), path(input_index), path(bqsr_table), path(intervals)
path fasta
path fai
path dict
path intervals
output:
tuple val(meta), path("*.bam"), emit: bam
tuple val(meta), path("*.bam"), emit: bam, optional: true
tuple val(meta), path("*.cram"), emit: cram, optional: true
path "versions.yml" , emit: versions
script:
def args = task.ext.args ?: ''
def prefix = task.ext.prefix ?: "${meta.id}"
def interval = intervals ? "-L ${intervals}" : ""
def file_type = input.getExtension()
def avail_mem = 3
if (!task.memory) {
log.info '[GATK ApplyBQSR] Available memory not known - defaulting to 3GB. Specify process memory requirements to change this.'
@ -35,7 +37,7 @@ process GATK4_APPLYBQSR {
--bqsr-recal-file $bqsr_table \\
$interval \\
--tmp-dir . \\
-O ${prefix}.bam \\
-O ${prefix}.${file_type} \\
$args
cat <<-END_VERSIONS > versions.yml

7
modules/gatk4/applybqsr/meta.yml
View file

@ -31,6 +31,9 @@ input:
- bqsr_table:
type: file
description: Recalibration table from gatk4_baserecalibrator
- intervals:
type: file
description: Bed file with the genomic regions included in the library (optional)
- fasta:
type: file
description: The reference fasta file
@ -43,9 +46,7 @@ input:
type: file
description: GATK sequence dictionary
pattern: "*.dict"
- intervalsBed:
type: file
description: Bed file with the genomic regions included in the library (optional)
output:
- meta:

7
modules/gatk4/baserecalibrator/main.nf
View file

@ -8,11 +8,10 @@ process GATK4_BASERECALIBRATOR {
'quay.io/biocontainers/gatk4:4.2.4.0--hdfd78af_0' }"
input:
tuple val(meta), path(input), path(input_index)
tuple val(meta), path(input), path(input_index), path(intervals)
path fasta
path fai
path dict
path intervalsBed
path knownSites
path knownSites_tbi
@ -23,14 +22,16 @@ process GATK4_BASERECALIBRATOR {
script:
def args = task.ext.args ?: ''
def prefix = task.ext.prefix ?: "${meta.id}"
def intervalsCommand = intervalsBed ? "-L ${intervalsBed}" : ""
def intervalsCommand = intervals ? "-L ${intervals}" : ""
def sitesCommand = knownSites.collect{"--known-sites ${it}"}.join(' ')
def avail_mem = 3
if (!task.memory) {
log.info '[GATK BaseRecalibrator] Available memory not known - defaulting to 3GB. Specify process memory requirements to change this.'
} else {
avail_mem = task.memory.giga
}
"""
gatk --java-options "-Xmx${avail_mem}g" BaseRecalibrator \
-R $fasta \

6
modules/gatk4/baserecalibrator/meta.yml
View file

@ -28,6 +28,9 @@ input:
type: file
description: BAI/CRAI file from alignment
pattern: "*.{bai,crai}"
- intervals:
type: file
description: Bed file with the genomic regions included in the library (optional)
- fasta:
type: file
description: The reference fasta file
@ -40,9 +43,6 @@ input:
type: file
description: GATK sequence dictionary
pattern: "*.dict"
- intervalsBed:
type: file
description: Bed file with the genomic regions included in the library (optional)
- knownSites:
type: file
description: Bed file with the genomic regions included in the library (optional)

5
modules/gatk4/genotypegvcfs/main.nf
View file

@ -8,13 +8,12 @@ process GATK4_GENOTYPEGVCFS {
'quay.io/biocontainers/gatk4:4.2.4.0--hdfd78af_0' }"
input:
tuple val(meta), path(gvcf), path(gvcf_index)
tuple val(meta), path(gvcf), path(gvcf_index), path(intervals)
path fasta
path fasta_index
path fasta_dict
path dbsnp
path dbsnp_index
path intervals_bed
output:
tuple val(meta), path("*.vcf.gz"), emit: vcf
@ -25,7 +24,7 @@ process GATK4_GENOTYPEGVCFS {
def args = task.ext.args ?: ''
def prefix = task.ext.prefix ?: "${meta.id}"
def dbsnp_options = dbsnp ? "-D ${dbsnp}" : ""
def interval_options = intervals_bed ? "-L ${intervals_bed}" : ""
def interval_options = intervals ? "-L ${intervals}" : ""
def gvcf_options = gvcf.name.endsWith(".vcf") || gvcf.name.endsWith(".vcf.gz") ? "$gvcf" : "gendb://$gvcf"
def avail_mem = 3
if (!task.memory) {

7
modules/gatk4/genotypegvcfs/meta.yml
View file

@ -25,6 +25,9 @@ input:
description: |
Tuple of gVCF(.gz) file (first) and its index (second) or the path to a GenomicsDB (and empty)
pattern: ["*.{vcf,vcf.gz}", "*.{idx,tbi}"]
- intervals:
type: file
description: Bed file with the genomic regions included in the library (optional)
- fasta:
type: file
description: Reference fasta file
@ -45,10 +48,6 @@ input:
type: tuple of files
description: dbSNP VCF index file
pattern: "*.tbi"
- intervals_bed:
type: file
description: An intevals BED file
pattern: "*.bed"
output:
- meta:

5
modules/gatk4/haplotypecaller/main.nf
View file

@ -8,13 +8,12 @@ process GATK4_HAPLOTYPECALLER {
'quay.io/biocontainers/gatk4:4.2.4.0--hdfd78af_0' }"
input:
tuple val(meta), path(input), path(input_index)
tuple val(meta), path(input), path(input_index), path(intervals)
path fasta
path fai
path dict
path dbsnp
path dbsnp_tbi
path interval
output:
tuple val(meta), path("*.vcf.gz"), emit: vcf
@ -24,7 +23,7 @@ process GATK4_HAPLOTYPECALLER {
script:
def args = task.ext.args ?: ''
def prefix = task.ext.prefix ?: "${meta.id}"
def interval_option = interval ? "-L ${interval}" : ""
def interval_option = intervals ? "-L ${intervals}" : ""
def dbsnp_option = dbsnp ? "-D ${dbsnp}" : ""
def avail_mem = 3
if (!task.memory) {

6
modules/gatk4/haplotypecaller/meta.yml
View file

@ -29,6 +29,9 @@ input:
type: file
description: BAI/CRAI file from alignment
pattern: "*.{bai,crai}"
- intervals:
type: file
description: Bed file with the genomic regions included in the library (optional)
- fasta:
type: file
description: The reference fasta file
@ -47,9 +50,6 @@ input:
- dbsnp_tbi:
type: file
description: VCF index of dbsnp (optional)
- interval:
type: file
description: Bed file with the genomic regions included in the library (optional)
output:
- meta:

2
modules/kleborate/main.nf
View file

@ -21,7 +21,7 @@ process KLEBORATE {
kleborate \\
$args \\
--outfile ${prefix}.results.txt \\
--assemblies *.fasta
--assemblies $fastas
cat <<-END_VERSIONS > versions.yml
"${task.process}":

2
modules/last/postmask/main.nf
View file

@ -17,7 +17,7 @@ process LAST_POSTMASK {
script:
def args = task.ext.args ?: ''
def prefix = task.ext.prefix ?: "${meta.id}"
if( "$maf" == "${prefix}.maf.gz" ) error "Input and output names are the same, use the suffix option to disambiguate"
if( "$maf" == "${prefix}.maf.gz" ) error "Input and output names are the same, use \"task.ext.prefix\" to disambiguate!"
"""
last-postmask $args $maf | gzip --no-name > ${prefix}.maf.gz

11
modules/lima/main.nf
View file

@ -12,9 +12,7 @@ process LIMA {
path primers
output:
tuple val(meta), path("*.clips") , emit: clips
tuple val(meta), path("*.counts") , emit: counts
tuple val(meta), path("*.guess") , emit: guess
tuple val(meta), path("*.report") , emit: report
tuple val(meta), path("*.summary"), emit: summary
path "versions.yml" , emit: versions
@ -27,10 +25,18 @@ process LIMA {
tuple val(meta), path("*.fastq.gz") , optional: true, emit: fastqgz
tuple val(meta), path("*.xml") , optional: true, emit: xml
tuple val(meta), path("*.json") , optional: true, emit: json
tuple val(meta), path("*.clips") , optional: true, emit: clips
tuple val(meta), path("*.guess") , optional: true, emit: guess
script:
def args = task.ext.args ?: ''
def prefix = task.ext.prefix ?: "${meta.id}"
if( "$ccs" == "${prefix}.bam" ) error "Input and output names are the same, set prefix in module configuration"
if( "$ccs" == "${prefix}.fasta" ) error "Input and output names are the same, set prefix in module configuration"
if( "$ccs" == "${prefix}.fasta.gz" ) error "Input and output names are the same, set prefix in module configuration"
if( "$ccs" == "${prefix}.fastq" ) error "Input and output names are the same, set prefix in module configuration"
if( "$ccs" == "${prefix}.fastq.gz" ) error "Input and output names are the same, set prefix in module configuration"
"""
OUT_EXT=""
@ -46,7 +52,6 @@ process LIMA {
OUT_EXT="fastq.gz"
fi
echo \$OUT_EXT
lima \\
$ccs \\
$primers \\

2
modules/plink/extract/main.nf
View file

@ -19,7 +19,7 @@ process PLINK_EXTRACT {
script:
def args = task.ext.args ?: ''
def prefix = task.ext.prefix ?: "${meta.id}"
if( "$bed" == "${prefix}.bed" ) error "Input and output names are the same, use the suffix option to disambiguate"
if( "$bed" == "${prefix}.bed" ) error "Input and output names are the same, use \"task.ext.prefix\" to disambiguate!"
"""
plink \\
--bfile ${meta.id} \\

2
modules/pmdtools/filter/main.nf
View file

@ -22,7 +22,7 @@ process PMDTOOLS_FILTER {
def args3 = task.ext.args3 ?: ''
def split_cpus = Math.floor(task.cpus/2)
def prefix = task.ext.prefix ?: "${meta.id}"
if ("$bam" == "${prefix}.bam") error "[pmdtools/filter] Input and output names are the same, use the suffix option to disambiguate!"
if ("$bam" == "${prefix}.bam") error "[pmdtools/filter] Input and output names are the same, use \"task.ext.prefix\" to disambiguate!"
//threshold and header flags activate filtering function of pmdtools
"""
samtools \\

2
modules/samblaster/main.nf
View file

@ -19,7 +19,7 @@ process SAMBLASTER {
def args2 = task.ext.args2 ?: ''
def args3 = task.ext.args3 ?: ''
def prefix = task.ext.prefix ?: "${meta.id}"
if( "$bam" == "${prefix}.bam" ) error "Input and output names are the same, use the suffix option to disambiguate"
if( "$bam" == "${prefix}.bam" ) error "Input and output names are the same, use \"task.ext.prefix\" to disambiguate!"
"""
samtools view -h $args2 $bam | \\
samblaster $args | \\

2
modules/samtools/fixmate/main.nf
View file

@ -17,7 +17,7 @@ process SAMTOOLS_FIXMATE {
script:
def args = task.ext.args ?: ''
def prefix = task.ext.prefix ?: "${meta.id}"
if ("$bam" == "${prefix}.bam") error "Input and output names are the same, use the suffix option to disambiguate!"
if ("$bam" == "${prefix}.bam") error "Input and output names are the same, use \"task.ext.prefix\" to disambiguate!"
"""
samtools \\

17
tests/modules/gatk4/applybqsr/main.nf
View file

@ -8,39 +8,40 @@ workflow test_gatk4_applybqsr {
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),
file(params.test_data['sarscov2']['illumina']['test_baserecalibrator_table'], checkIfExists: true)
file(params.test_data['sarscov2']['illumina']['test_baserecalibrator_table'], 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)
dict = file(params.test_data['sarscov2']['genome']['genome_dict'], checkIfExists: true)
GATK4_APPLYBQSR ( input, fasta, fai, dict, [] )
GATK4_APPLYBQSR ( input, fasta, fai, dict )
}
workflow test_gatk4_applybqsr_intervals {
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),
file(params.test_data['sarscov2']['illumina']['test_baserecalibrator_table'], checkIfExists: true)
file(params.test_data['sarscov2']['illumina']['test_baserecalibrator_table'], checkIfExists: true),
file(params.test_data['sarscov2']['genome']['test_bed'], 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)
dict = file(params.test_data['sarscov2']['genome']['genome_dict'], checkIfExists: true)
intervals = file(params.test_data['sarscov2']['genome']['test_bed'], checkIfExists: true)
GATK4_APPLYBQSR ( input, fasta, fai, dict, intervals )
GATK4_APPLYBQSR ( input, fasta, fai, dict )
}
workflow test_gatk4_applybqsr_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),
file(params.test_data['homo_sapiens']['illumina']['test_baserecalibrator_table'], checkIfExists: true)
file(params.test_data['homo_sapiens']['illumina']['test_baserecalibrator_table'], checkIfExists: true),
file(params.test_data['homo_sapiens']['genome']['genome_bed'], 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)
dict = file(params.test_data['homo_sapiens']['genome']['genome_dict'], checkIfExists: true)
intervals = file(params.test_data['homo_sapiens']['genome']['genome_bed'], checkIfExists: true)
GATK4_APPLYBQSR ( input, fasta, fai, dict, intervals )
GATK4_APPLYBQSR ( input, fasta, fai, dict )
}

4
tests/modules/gatk4/applybqsr/test.yml
View file

@ -26,7 +26,7 @@
- gatk4
- gatk4/applybqsr
files:
- path: output/gatk4/test.bam
md5sum: a333f80284a89a8daab28d3686a0b365
- path: output/gatk4/test.cram
md5sum: b7659b3b2adaabbe73658dc059dbfdf6
- path: output/gatk4/versions.yml
md5sum: 57933f27b3a31b05af3f7c248d365396

20
tests/modules/gatk4/baserecalibrator/main.nf
View file

@ -7,7 +7,8 @@ include { GATK4_BASERECALIBRATOR } from '../../../../modules/gatk4/baserecalibra
workflow test_gatk4_baserecalibrator {
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)
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)
fai = file(params.test_data['sarscov2']['genome']['genome_fasta_fai'], checkIfExists: true)
@ -15,14 +16,14 @@ workflow test_gatk4_baserecalibrator {
sites = file(params.test_data['sarscov2']['illumina']['test_vcf_gz'], checkIfExists: true)
sites_tbi = file(params.test_data['sarscov2']['illumina']['test_vcf_gz_tbi'], checkIfExists: true)
GATK4_BASERECALIBRATOR ( input, fasta, fai, dict, [], sites, sites_tbi )
GATK4_BASERECALIBRATOR ( input, fasta, fai, dict, sites, sites_tbi )
}
workflow test_gatk4_baserecalibrator_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),
file(params.test_data['homo_sapiens']['illumina']['test_baserecalibrator_table'], 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)
@ -30,28 +31,29 @@ workflow test_gatk4_baserecalibrator_cram {
sites = file(params.test_data['homo_sapiens']['genome']['dbsnp_146_hg38_vcf_gz'], checkIfExists: true)
sites_tbi = file(params.test_data['homo_sapiens']['genome']['dbsnp_146_hg38_vcf_gz_tbi'], checkIfExists: true)
GATK4_BASERECALIBRATOR ( input, fasta, fai, dict, [], sites, sites_tbi )
GATK4_BASERECALIBRATOR ( input, fasta, fai, dict, sites, sites_tbi )
}
workflow test_gatk4_baserecalibrator_intervals {
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)
file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true),
file(params.test_data['sarscov2']['genome']['test_bed'], 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)
dict = file(params.test_data['sarscov2']['genome']['genome_dict'], checkIfExists: true)
intervals = file(params.test_data['sarscov2']['genome']['test_bed'], checkIfExists: true)
sites = file(params.test_data['sarscov2']['illumina']['test_vcf_gz'], checkIfExists: true)
sites_tbi = file(params.test_data['sarscov2']['illumina']['test_vcf_gz_tbi'], checkIfExists: true)
GATK4_BASERECALIBRATOR ( input, fasta, fai, dict, intervals, sites, sites_tbi )
GATK4_BASERECALIBRATOR ( input, fasta, fai, dict, sites, sites_tbi )
}
workflow test_gatk4_baserecalibrator_multiple_sites {
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)
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)
fai = file(params.test_data['sarscov2']['genome']['genome_fasta_fai'], checkIfExists: true)
@ -63,5 +65,5 @@ workflow test_gatk4_baserecalibrator_multiple_sites {
file(params.test_data['sarscov2']['illumina']['test2_vcf_gz_tbi'], checkIfExists: true)
]
GATK4_BASERECALIBRATOR ( input, fasta, fai, dict, [], sites, sites_tbi )
GATK4_BASERECALIBRATOR ( input, fasta, fai, dict, sites, sites_tbi )
}

50
tests/modules/gatk4/genotypegvcfs/main.nf
View file

@ -10,13 +10,15 @@ workflow test_gatk4_genotypegvcfs_vcf_input {
input = [ [ id:'test' ], // meta map
file(params.test_data['homo_sapiens']['illumina']['test_genome_vcf'], checkIfExists: true),
file(params.test_data['homo_sapiens']['illumina']['test_genome_vcf_idx'], checkIfExists: true) ]
file(params.test_data['homo_sapiens']['illumina']['test_genome_vcf_idx'], checkIfExists: true),
[]
]
fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
fastaIndex = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true)
fastaDict = file(params.test_data['homo_sapiens']['genome']['genome_dict'], checkIfExists: true)
GATK4_GENOTYPEGVCFS ( input, fasta, fastaIndex, fastaDict, [], [], [] )
GATK4_GENOTYPEGVCFS ( input, fasta, fastaIndex, fastaDict, [], [])
}
// Basic parameters with compressed VCF input
@ -24,13 +26,15 @@ workflow test_gatk4_genotypegvcfs_gz_input {
input = [ [ id:'test' ], // meta map
file(params.test_data['homo_sapiens']['illumina']['test_genome_vcf_gz'], checkIfExists: true),
file(params.test_data['homo_sapiens']['illumina']['test_genome_vcf_gz_tbi'], checkIfExists: true) ]
file(params.test_data['homo_sapiens']['illumina']['test_genome_vcf_gz_tbi'], checkIfExists: true),
[]
]
fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
fastaIndex = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true)
fastaDict = file(params.test_data['homo_sapiens']['genome']['genome_dict'], checkIfExists: true)
GATK4_GENOTYPEGVCFS ( input, fasta, fastaIndex, fastaDict, [], [], [] )
GATK4_GENOTYPEGVCFS ( input, fasta, fastaIndex, fastaDict, [], [])
}
// Basic parameters + optional dbSNP
@ -38,7 +42,9 @@ workflow test_gatk4_genotypegvcfs_gz_input_dbsnp {
input = [ [ id:'test' ], // meta map
file(params.test_data['homo_sapiens']['illumina']['test_genome_vcf_gz'], checkIfExists: true),
file(params.test_data['homo_sapiens']['illumina']['test_genome_vcf_gz_tbi'], checkIfExists: true) ]
file(params.test_data['homo_sapiens']['illumina']['test_genome_vcf_gz_tbi'], checkIfExists: true),
[]
]
fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
fastaIndex = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true)
@ -47,7 +53,7 @@ workflow test_gatk4_genotypegvcfs_gz_input_dbsnp {
dbsnp = file(params.test_data['homo_sapiens']['genome']['dbsnp_146_hg38_vcf_gz'], checkIfExists: true)
dbsnpIndex = file(params.test_data['homo_sapiens']['genome']['dbsnp_146_hg38_vcf_gz_tbi'], checkIfExists: true)
GATK4_GENOTYPEGVCFS ( input, fasta, fastaIndex, fastaDict, dbsnp, dbsnpIndex, [] )
GATK4_GENOTYPEGVCFS ( input, fasta, fastaIndex, fastaDict, dbsnp, dbsnpIndex)
}
// Basic parameters + optional intervals
@ -55,15 +61,14 @@ workflow test_gatk4_genotypegvcfs_gz_input_intervals {
input = [ [ id:'test' ], // meta map
file(params.test_data['homo_sapiens']['illumina']['test_genome_vcf_gz'], checkIfExists: true),
file(params.test_data['homo_sapiens']['illumina']['test_genome_vcf_gz_tbi'], checkIfExists: true) ]
file(params.test_data['homo_sapiens']['illumina']['test_genome_vcf_gz_tbi'], checkIfExists: true),
file(params.test_data['homo_sapiens']['genome']['genome_bed'], checkIfExists: true) ]
fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
fastaIndex = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true)
fastaDict = file(params.test_data['homo_sapiens']['genome']['genome_dict'], checkIfExists: true)
intervalsBed = file(params.test_data['homo_sapiens']['genome']['genome_bed'], checkIfExists: true)
GATK4_GENOTYPEGVCFS ( input, fasta, fastaIndex, fastaDict, [], [], intervalsBed )
GATK4_GENOTYPEGVCFS ( input, fasta, fastaIndex, fastaDict, [], [])
}
// Basic parameters + optional dbSNP + optional intervals
@ -71,7 +76,9 @@ workflow test_gatk4_genotypegvcfs_gz_input_dbsnp_intervals {
input = [ [ id:'test' ], // meta map
file(params.test_data['homo_sapiens']['illumina']['test_genome_vcf_gz'], checkIfExists: true),
file(params.test_data['homo_sapiens']['illumina']['test_genome_vcf_gz_tbi'], checkIfExists: true) ]
file(params.test_data['homo_sapiens']['illumina']['test_genome_vcf_gz_tbi'], checkIfExists: true),
file(params.test_data['homo_sapiens']['genome']['genome_bed'], checkIfExists: true)
]
fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
fastaIndex = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true)
@ -80,9 +87,7 @@ workflow test_gatk4_genotypegvcfs_gz_input_dbsnp_intervals {
dbsnp = file(params.test_data['homo_sapiens']['genome']['dbsnp_146_hg38_vcf_gz'], checkIfExists: true)
dbsnpIndex = file(params.test_data['homo_sapiens']['genome']['dbsnp_146_hg38_vcf_gz_tbi'], checkIfExists: true)
intervalsBed = file(params.test_data['homo_sapiens']['genome']['genome_bed'], checkIfExists: true)
GATK4_GENOTYPEGVCFS ( input, fasta, fastaIndex, fastaDict, dbsnp, dbsnpIndex, intervalsBed )
GATK4_GENOTYPEGVCFS ( input, fasta, fastaIndex, fastaDict, dbsnp, dbsnpIndex )
}
// Basic parameters with GenomicsDB input
@ -97,9 +102,11 @@ workflow test_gatk4_genotypegvcfs_gendb_input {
UNTAR ( test_genomicsdb )
gendb = UNTAR.out.untar.collect()
gendb.add([])
gendb.add([])
input = Channel.of([ id:'test' ]).combine(gendb)
GATK4_GENOTYPEGVCFS ( input, fasta, fastaIndex, fastaDict, [], [], [] )
GATK4_GENOTYPEGVCFS ( input, fasta, fastaIndex, fastaDict, [], [])
}
// Basic parameters with GenomicsDB + optional dbSNP
@ -117,9 +124,10 @@ workflow test_gatk4_genotypegvcfs_gendb_input_dbsnp {
UNTAR ( test_genomicsdb )
gendb = UNTAR.out.untar.collect()
gendb.add([])
gendb.add([])
input = Channel.of([ id:'test' ]).combine(gendb)
GATK4_GENOTYPEGVCFS ( input, fasta, fastaIndex, fastaDict, dbsnp, dbsnpIndex, [] )
GATK4_GENOTYPEGVCFS ( input, fasta, fastaIndex, fastaDict, dbsnp, dbsnpIndex)
}
// Basic parameters with GenomicsDB + optional intervals
@ -129,16 +137,15 @@ workflow test_gatk4_genotypegvcfs_gendb_input_intervals {
fastaIndex = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true)
fastaDict = file(params.test_data['homo_sapiens']['genome']['genome_dict'], checkIfExists: true)
intervalsBed = file(params.test_data['homo_sapiens']['genome']['genome_bed'], checkIfExists: true)
test_genomicsdb = file(params.test_data['homo_sapiens']['illumina']['test_genomicsdb_tar_gz'], checkIfExists: true)
UNTAR ( test_genomicsdb )
gendb = UNTAR.out.untar.collect()
gendb.add([])
gendb.add([file(params.test_data['homo_sapiens']['genome']['genome_bed'], checkIfExists: true)])
input = Channel.of([ id:'test' ]).combine(gendb)
GATK4_GENOTYPEGVCFS ( input, fasta, fastaIndex, fastaDict, [], [], intervalsBed )
GATK4_GENOTYPEGVCFS ( input, fasta, fastaIndex, fastaDict, [], [] )
}
// Basic parameters with GenomicsDB + optional dbSNP + optional intervals
@ -151,14 +158,13 @@ workflow test_gatk4_genotypegvcfs_gendb_input_dbsnp_intervals {
dbsnp = file(params.test_data['homo_sapiens']['genome']['dbsnp_146_hg38_vcf_gz'], checkIfExists: true)
dbsnpIndex = file(params.test_data['homo_sapiens']['genome']['dbsnp_146_hg38_vcf_gz_tbi'], checkIfExists: true)
intervalsBed = file(params.test_data['homo_sapiens']['genome']['genome_bed'], checkIfExists: true)
test_genomicsdb = file(params.test_data['homo_sapiens']['illumina']['test_genomicsdb_tar_gz'], checkIfExists: true)
UNTAR ( test_genomicsdb )
gendb = UNTAR.out.untar.collect()
gendb.add([])
gendb.add([file(params.test_data['homo_sapiens']['genome']['genome_bed'], checkIfExists: true)])
input = Channel.of([ id:'test' ]).combine(gendb)
GATK4_GENOTYPEGVCFS ( input, fasta, fastaIndex, fastaDict, dbsnp, dbsnpIndex, intervalsBed )
GATK4_GENOTYPEGVCFS ( input, fasta, fastaIndex, fastaDict, dbsnp, dbsnpIndex )
}

16
tests/modules/gatk4/haplotypecaller/main.nf
View file

@ -7,31 +7,34 @@ include { GATK4_HAPLOTYPECALLER } from '../../../../modules/gatk4/haplotypecalle
workflow test_gatk4_haplotypecaller {
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)
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)
fai = file(params.test_data['sarscov2']['genome']['genome_fasta_fai'], checkIfExists: true)
dict = file(params.test_data['sarscov2']['genome']['genome_dict'], checkIfExists: true)
GATK4_HAPLOTYPECALLER ( input, fasta, fai, dict, [], [], [] )
GATK4_HAPLOTYPECALLER ( input, fasta, fai, dict, [], [])
}
workflow test_gatk4_haplotypecaller_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)
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)
dict = file(params.test_data['homo_sapiens']['genome']['genome_dict'], checkIfExists: true)
GATK4_HAPLOTYPECALLER ( input, fasta, fai, dict, [], [], [] )
GATK4_HAPLOTYPECALLER ( input, fasta, fai, dict, [], [])
}
workflow test_gatk4_haplotypecaller_intervals_dbsnp {
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_crai'], checkIfExists: true),
file(params.test_data['homo_sapiens']['genome']['genome_bed'], checkIfExists: true)
]
fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
@ -39,7 +42,6 @@ workflow test_gatk4_haplotypecaller_intervals_dbsnp {
dict = file(params.test_data['homo_sapiens']['genome']['genome_dict'], checkIfExists: true)
sites = file(params.test_data['homo_sapiens']['genome']['dbsnp_146_hg38_vcf_gz'], checkIfExists: true)
sites_tbi = file(params.test_data['homo_sapiens']['genome']['dbsnp_146_hg38_vcf_gz_tbi'], checkIfExists: true)
intervals = file(params.test_data['homo_sapiens']['genome']['genome_bed'], checkIfExists: true)
GATK4_HAPLOTYPECALLER ( input, fasta, fai, dict, sites, sites_tbi, intervals )
GATK4_HAPLOTYPECALLER ( input, fasta, fai, dict, sites, sites_tbi )
}

2
tests/modules/kleborate/test.yml
View file

@ -4,4 +4,4 @@
- kleborate
files:
- path: output/kleborate/test.results.txt
md5sum: b7979a71170736098fb8403cd92748f5
contains: ['strain', 'genome', 'scaffolds']