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Update to allow cram + update needed to use the gatk4 modules in sarek (#976)

Browse source 
* Make samtools/merge cram compliant

* samtools/stats cram compliance

* update yml file

* samtools/view to deal with crams

* Update tests to make sure cram works

* also fix tmp dir and min mem in one go

* basequalityrecal test for cram + min mem + tmpdir

* update haplotypecaller for sarek

* update haplotype yml

* update markdup to allow multiple bams, take out params to be passed with options.args

* remove TODO statement

* Remove variable md5sum

* add emtpy input to stats module in subworkflows

* subworkflows seem to work now on my side

* Apply code review

Co-authored-by: Maxime U. Garcia <maxime.garcia@scilifelab.se>

* replace bam with input to be more inclusive

* rename everywhere

* rename input

* remove variable checksum

Co-authored-by: Maxime U. Garcia <maxime.garcia@scilifelab.se>
This commit is contained in:
FriederikeHanssen 2021-10-29 13:01:05 +02:00 committed by GitHub
parent 71945a5b5f
commit ac1e6df076
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GPG key ID: 4AEE18F83AFDEB23
39 changed files with 356 additions and 109 deletions
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10
modules/gatk4/applybqsr/main.nf
View file

@ -19,7 +19,7 @@ process GATK4_APPLYBQSR {
}
input:
tuple val(meta), path(bam), path(bai), path(bqsr_table)
tuple val(meta), path(input), path(input_index), path(bqsr_table)
path fasta
path fastaidx
path dict
@ -32,12 +32,18 @@ process GATK4_APPLYBQSR {
script:
def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
def interval = intervals ? "-L ${intervals}" : ""
if (!task.memory) {
log.info '[GATK ApplyBQSR] Available memory not known - defaulting to 3GB. Specify process memory requirements to change this.'
} else {
avail_mem = task.memory.giga
}
"""
gatk ApplyBQSR \\
-R $fasta \\
-I $bam \\
-I $input \\
--bqsr-recal-file $bqsr_table \\
$interval \\
--tmp-dir . \\
-O ${prefix}.bam \\
$options.args

10
modules/gatk4/applybqsr/meta.yml
View file

@ -20,10 +20,14 @@ input:
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
- bam:
- input:
type: file
description: BAM file from alignment
pattern: "*.{bam}"
description: BAM/CRAM file from alignment
pattern: "*.{bam,cram}"
- input_index:
type: file
description: BAI/CRAI file from alignment
pattern: "*.{bai,crai}"
- bqsr_table:
type: file
description: Recalibration table from gatk4_baserecalibrator

11
modules/gatk4/baserecalibrator/main.nf
View file

@ -19,7 +19,7 @@ process GATK4_BASERECALIBRATOR {
}
input:
tuple val(meta), path(bam), path(bai)
tuple val(meta), path(input), path(input_index)
path fasta
path fastaidx
path dict
@ -35,12 +35,19 @@ process GATK4_BASERECALIBRATOR {
def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
def intervalsCommand = intervalsBed ? "-L ${intervalsBed}" : ""
def sitesCommand = knownSites.collect{"--known-sites ${it}"}.join(' ')
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 BaseRecalibrator \
-R $fasta \
-I $bam \
-I $input \
$sitesCommand \
$intervalsCommand \
--tmp-dir . \
$options.args \
-O ${prefix}.table

11
modules/gatk4/baserecalibrator/meta.yml
View file

@ -20,10 +20,14 @@ input:
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
- bam:
- input:
type: file
description: BAM file from alignment
pattern: "*.{bam}"
description: BAM/CRAM file from alignment
pattern: "*.{bam,cram}"
- input_index:
type: file
description: BAI/CRAI file from alignment
pattern: "*.{bai,crai}"
- fasta:
type: file
description: The reference fasta file
@ -57,3 +61,4 @@ output:
authors:
- "@yocra3"
- "@FriederikeHanssen"

18
modules/gatk4/haplotypecaller/main.nf
View file

@ -19,10 +19,13 @@ process GATK4_HAPLOTYPECALLER {
}
input:
tuple val(meta), path(bam), path(bai)
tuple val(meta), path(input), path(input_index)
path fasta
path fai
path dict
path dbsnp
path dbsnp_tbi
path interval
output:
tuple val(meta), path("*.vcf.gz"), emit: vcf
@ -30,8 +33,10 @@ process GATK4_HAPLOTYPECALLER {
path "versions.yml" , emit: versions
script:
def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
def avail_mem = 3
def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
def interval_option = interval ? "-L ${interval}" : ""
def dbsnp_option = dbsnp ? "-D ${dbsnp}" : ""
def avail_mem = 3
if (!task.memory) {
log.info '[GATK HaplotypeCaller] Available memory not known - defaulting to 3GB. Specify process memory requirements to change this.'
} else {
@ -42,9 +47,12 @@ process GATK4_HAPLOTYPECALLER {
--java-options "-Xmx${avail_mem}g" \\
HaplotypeCaller \\
-R $fasta \\
-I $bam \\
-I $input \\
${dbsnp_option} \\
${interval_option} \\
-O ${prefix}.vcf.gz \\
$options.args
$options.args \\
--tmp-dir .
cat <<-END_VERSIONS > versions.yml
${getProcessName(task.process)}:

23
modules/gatk4/haplotypecaller/meta.yml
View file

@ -21,14 +21,14 @@ input:
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
- bam:
- input:
type: file
description: BAM file
pattern: "*.bam"
- bai:
description: BAM/CRAM file from alignment
pattern: "*.{bam,cram}"
- input_index:
type: file
description: Index of BAM file
pattern: "*.bam.bai"
description: BAI/CRAI file from alignment
pattern: "*.{bai,crai}"
- fasta:
type: file
description: The reference fasta file
@ -41,6 +41,16 @@ input:
type: file
description: GATK sequence dictionary
pattern: "*.dict"
- dbsnp:
type: file
description: VCF file containing known sites (optional)
- 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:
type: map
@ -62,3 +72,4 @@ output:
authors:
- "@suzannejin"
- "@FriederikeHanssen"

13
modules/gatk4/markduplicates/main.nf
View file

@ -19,21 +19,28 @@ process GATK4_MARKDUPLICATES {
}
input:
tuple val(meta), path(bam)
tuple val(meta), path(bams)
output:
tuple val(meta), path("*.bam") , emit: bam
tuple val(meta), path("*.bai") , emit: bai
tuple val(meta), path("*.metrics"), emit: metrics
path "versions.yml" , emit: versions
script:
def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
def bam_list = bams.collect(){ bam -> "--INPUT ".concat(bam.toString()) }.join(" ")
def avail_mem = 3
if (!task.memory) {
log.info '[GATK HaplotypeCaller] Available memory not known - defaulting to 3GB. Specify process memory requirements to change this.'
} else {
avail_mem = task.memory.giga
}
"""
gatk MarkDuplicates \\
--INPUT $bam \\
$bam_list \\
--METRICS_FILE ${prefix}.metrics \\
--TMP_DIR . \\
--ASSUME_SORT_ORDER coordinate \\
--CREATE_INDEX true \\
--OUTPUT ${prefix}.bam \\
$options.args

1
modules/gatk4/markduplicates/meta.yml
View file

@ -47,3 +47,4 @@ output:
authors:
- "@ajodeh-juma"
- "@FriederikeHanssen"

4
modules/manta/germline/main.nf
View file

@ -19,7 +19,7 @@ process MANTA_GERMLINE {
}
input:
tuple val(meta), path(cram), path(crai)
tuple val(meta), path(input), path(input_index)
path fasta
path fai
path target_bed
@ -39,7 +39,7 @@ process MANTA_GERMLINE {
def options_manta = target_bed ? "--exome --callRegions $target_bed" : ""
"""
configManta.py \
--bam $cram \
--bam $input \
--reference $fasta \
$options_manta \
--runDir manta

4
modules/manta/germline/meta.yml
View file

@ -23,11 +23,11 @@ input:
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
- cram:
- input:
type: file
description: BAM/CRAM/SAM file
pattern: "*.{bam,cram,sam}"
- crai:
- input_index:
type: file
description: BAM/CRAM/SAM index file
pattern: "*.{bai,crai,sai}"

6
modules/manta/somatic/main.nf
View file

@ -19,7 +19,7 @@ process MANTA_SOMATIC {
}
input:
tuple val(meta), path(cram_normal), path(crai_normal), path(cram_tumor), path(crai_tumor)
tuple val(meta), path(input_normal), path(input_index_normal), path(input_tumor), path(input_index_tumor)
path fasta
path fai
path target_bed
@ -42,8 +42,8 @@ process MANTA_SOMATIC {
"""
configManta.py \
--tumorBam $cram_tumor \
--normalBam $cram_normal \
--tumorBam $input_tumor \
--normalBam $input_normal \
--reference $fasta \
$options_manta \
--runDir manta

8
modules/manta/somatic/meta.yml
View file

@ -23,19 +23,19 @@ input:
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
- cram_normal:
- input_normal:
type: file
description: BAM/CRAM/SAM file
pattern: "*.{bam,cram,sam}"
- crai_normal:
- input_index_normal:
type: file
description: BAM/CRAM/SAM index file
pattern: "*.{bai,crai,sai}"
- cram_tumor:
- input_tumor:
type: file
description: BAM/CRAM/SAM file
pattern: "*.{bam,cram,sam}"
- crai_tumor:
- input_index_tumor:
type: file
description: BAM/CRAM/SAM index file
pattern: "*.{bai,crai,sai}"

4
modules/manta/tumoronly/main.nf
View file

@ -19,7 +19,7 @@ process MANTA_TUMORONLY {
}
input:
tuple val(meta), path(cram), path(crai)
tuple val(meta), path(input), path(input_index)
path fasta
path fai
path target_bed
@ -39,7 +39,7 @@ process MANTA_TUMORONLY {
def options_manta = target_bed ? "--exome --callRegions $target_bed" : ""
"""
configManta.py \
--tumorBam $cram \
--tumorBam $input \
--reference $fasta \
$options_manta \
--runDir manta

5
modules/manta/tumoronly/meta.yml
View file

@ -23,11 +23,11 @@ input:
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
- cram:
- input:
type: file
description: BAM/CRAM/SAM file
pattern: "*.{bam,cram,sam}"
- crai:
- input_index:
type: file
description: BAM/CRAM/SAM index file
pattern: "*.{bai,crai,sai}"
@ -54,7 +54,6 @@ output:
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
- candidate_small_indels_vcf:
type: file
description: Gzipped VCF file containing variants

12
modules/samtools/merge/main.nf
View file

@ -19,16 +19,20 @@ process SAMTOOLS_MERGE {
}
input:
tuple val(meta), path(bams)
tuple val(meta), path(input_files)
path fasta
output:
tuple val(meta), path("${prefix}.bam"), emit: bam
path "versions.yml" , emit: versions
tuple val(meta), path("${prefix}.bam"), optional:true, emit: bam
tuple val(meta), path("${prefix}.cram"), optional:true, emit: cram
path "versions.yml" , emit: versions
script:
prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
def file_type = input_files[0].getExtension()
def reference = fasta ? "--reference ${fasta}" : ""
"""
samtools merge ${prefix}.bam $bams
samtools merge ${reference} ${prefix}.${file_type} $input_files
cat <<-END_VERSIONS > versions.yml
${getProcessName(task.process)}:
${getSoftwareName(task.process)}: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')

17
modules/samtools/merge/meta.yml
View file

@ -1,5 +1,5 @@
name: samtools_merge
description: Merge BAM file
description: Merge BAM or CRAM file
keywords:
- merge
- bam
@ -21,20 +21,28 @@ input:
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
- bam:
- input_files:
type: file
description: BAM file
description: BAM/CRAM file
pattern: "*.{bam,cram,sam}"
- fasta:
type: optional file
description: Reference file the CRAM was created with
pattern: "*.{fasta,fa}"
output:
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
- merged_bam:
- bam:
type: file
description: BAM file
pattern: "*.{bam}"
- cram:
type: file
description: CRAM file
pattern: "*.{cram}"
- versions:
type: file
description: File containing software versions
@ -43,3 +51,4 @@ authors:
- "@drpatelh"
- "@yuukiiwa "
- "@maxulysse"
- "@FriederikeHanssen"

6
modules/samtools/stats/main.nf
View file

@ -19,15 +19,17 @@ process SAMTOOLS_STATS {
}
input:
tuple val(meta), path(bam), path(bai)
tuple val(meta), path(input), path(input_index)
path fasta
output:
tuple val(meta), path("*.stats"), emit: stats
path "versions.yml" , emit: versions
script:
def reference = fasta ? "--reference ${fasta}" : ""
"""
samtools stats $bam > ${bam}.stats
samtools stats ${reference} ${input} > ${input}.stats
cat <<-END_VERSIONS > versions.yml
${getProcessName(task.process)}:
${getSoftwareName(task.process)}: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')

21
modules/samtools/stats/meta.yml
View file

@ -22,14 +22,18 @@ input:
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
- bam:
type: file
description: BAM/CRAM/SAM file
pattern: "*.{bam,cram,sam}"
- bai:
type: file
description: Index for BAM/CRAM/SAM file
pattern: "*.{bai,crai,sai}"
- input:
type: file
description: BAM/CRAM file from alignment
pattern: "*.{bam,cram}"
- input_index:
type: file
description: BAI/CRAI file from alignment
pattern: "*.{bai,crai}"
- fasta:
type: optional file
description: Reference file the CRAM was created with
pattern: "*.{fasta,fa}"
output:
- meta:
type: map
@ -46,3 +50,4 @@ output:
pattern: "versions.yml"
authors:
- "@drpatelh"
- "@FriederikeHanssen"

12
modules/samtools/view/main.nf
View file

@ -19,16 +19,20 @@ process SAMTOOLS_VIEW {
}
input:
tuple val(meta), path(bam)
tuple val(meta), path(input)
path fasta
output:
tuple val(meta), path("*.bam"), emit: bam
path "versions.yml" , emit: versions
tuple val(meta), path("*.bam") , optional: true, emit: bam
tuple val(meta), path("*.cram"), optional: true, emit: cram
path "versions.yml" , emit: versions
script:
def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
def reference = fasta ? "--reference ${fasta} -C" : ""
def file_type = input.getExtension()
"""
samtools view $options.args $bam > ${prefix}.bam
samtools view ${reference} $options.args $input > ${prefix}.${file_type}
cat <<-END_VERSIONS > versions.yml
${getProcessName(task.process)}:
${getSoftwareName(task.process)}: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')

15
modules/samtools/view/meta.yml
View file

@ -21,10 +21,14 @@ input:
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
- bam:
- input:
type: file
description: BAM/CRAM/SAM file
pattern: "*.{bam,cram,sam}"
- fasta:
type: optional file
description: Reference file the CRAM was created with
pattern: "*.{fasta,fa}"
output:
- meta:
type: map
@ -33,8 +37,12 @@ output:
e.g. [ id:'test', single_end:false ]
- bam:
type: file
description: filtered/converted BAM/CRAM/SAM file
pattern: "*.{bam,cram,sam}"
description: filtered/converted BAM/SAM file
pattern: "*.{bam,sam}"
- cram:
type: file
description: filtered/converted CRAM file
pattern: "*.cram"
- versions:
type: file
description: File containing software versions
@ -42,3 +50,4 @@ output:
authors:
- "@drpatelh"
- "@joseespinosa"
- "@FriederikeHanssen"

4
modules/strelka/germline/main.nf
View file

@ -19,7 +19,7 @@ process STRELKA_GERMLINE {
}
input:
tuple val(meta), path(bam), path(bai)
tuple val(meta), path(input), path(input_index)
path fasta
path fai
path target_bed
@ -38,7 +38,7 @@ process STRELKA_GERMLINE {
def regions = target_bed ? "--exome --callRegions ${target_bed}" : ""
"""
configureStrelkaGermlineWorkflow.py \\
--bam $bam \\
--bam $input \\
--referenceFasta $fasta \\
$regions \\
$options.args \\

12
modules/strelka/germline/meta.yml
View file

@ -21,14 +21,14 @@ input:
description: |
Groovy Map containing sample information
e.g. [ id:'test']
- bam:
- input:
type: file
description: BAM file
pattern: "*.{bam}"
- bai:
description: BAM/CRAM file
pattern: "*.{bam,cram}"
- input_index:
type: file
description: BAM index file
pattern: "*.{bai}"
description: BAM/CRAI index file
pattern: "*.{bai,crai}"
- target_bed:
type: file
description: An optional bed file

6
modules/strelka/somatic/main.nf
View file

@ -19,7 +19,7 @@ process STRELKA_SOMATIC {
}
input:
tuple val(meta), path(cram_normal), path(crai_normal), path(cram_tumor), path(crai_tumor), path(manta_candidate_small_indels), path(manta_candidate_small_indels_tbi)
tuple val(meta), path(input_normal), path(input_index_normal), path(input_tumor), path(input_index_tumor), path(manta_candidate_small_indels), path(manta_candidate_small_indels_tbi)
path fasta
path fai
path target_bed
@ -38,8 +38,8 @@ process STRELKA_SOMATIC {
def options_manta = manta_candidate_small_indels ? "--indelCandidates ${manta_candidate_small_indels}" : ""
"""
configureStrelkaSomaticWorkflow.py \\
--tumor $cram_tumor \\
--normal $cram_normal \\
--tumor $input_tumor \\
--normal $input_normal \\
--referenceFasta $fasta \\
$options_target_bed \\
$options_manta \\

8
modules/strelka/somatic/meta.yml
View file

@ -21,19 +21,19 @@ input:
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
- cram_normal:
- input_normal:
type: file
description: BAM/CRAM/SAM file
pattern: "*.{bam,cram,sam}"
- crai_normal:
- input_index_normal:
type: file
description: BAM/CRAM/SAM index file
pattern: "*.{bai,crai,sai}"
- cram_tumor:
- input_tumor:
type: file
description: BAM/CRAM/SAM file
pattern: "*.{bam,cram,sam}"
- crai_tumor:
- input_index_tumor:
type: file
description: BAM/CRAM/SAM index file
pattern: "*.{bai,crai,sai}"

2
subworkflows/nf-core/bam_stats_samtools/main.nf
View file

@ -15,7 +15,7 @@ workflow BAM_STATS_SAMTOOLS {
main:
ch_versions = Channel.empty()
SAMTOOLS_STATS ( ch_bam_bai )
SAMTOOLS_STATS ( ch_bam_bai, [] )
ch_versions = ch_versions.mix(SAMTOOLS_STATS.out.versions.first())
SAMTOOLS_FLAGSTAT ( ch_bam_bai )

14
tests/modules/gatk4/applybqsr/main.nf
View file

@ -30,3 +30,17 @@ workflow test_gatk4_applybqsr_intervals {
GATK4_APPLYBQSR ( input, fasta, fai, dict, intervals )
}
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)
]
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 )
}

17
tests/modules/gatk4/applybqsr/test.yml
View file

@ -1,17 +1,26 @@
- name: gatk4 applybqsr test_gatk4_applybqsr
command: nextflow run tests/modules/gatk4/applybqsr -entry test_gatk4_applybqsr -c tests/config/nextflow.config
tags:
- gatk4
- gatk4/applybqsr
- gatk4
files:
- path: output/gatk4/test.bam
md5sum: dac716c394db5e83c12b44355c098ca7
md5sum: 87a2eabae2b7b41574f966612b5addae
- name: gatk4 applybqsr test_gatk4_applybqsr_intervals
command: nextflow run tests/modules/gatk4/applybqsr -entry test_gatk4_applybqsr_intervals -c tests/config/nextflow.config
tags:
- gatk4
- gatk4/applybqsr
- gatk4
files:
- path: output/gatk4/test.bam
md5sum: 400441dbe5344658580ba0a24ba57069
md5sum: 9c015d3c1dbd9eee793b7386f432b6aa
- name: gatk4 applybqsr test_gatk4_applybqsr_cram
command: nextflow run tests/modules/gatk4/applybqsr -entry test_gatk4_applybqsr_cram -c tests/config/nextflow.config
tags:
- gatk4/applybqsr
- gatk4
files:
- path: output/gatk4/test.bam
md5sum: 02f84815fdbc99c21c8d42ebdcabbbf7

15
tests/modules/gatk4/baserecalibrator/main.nf
View file

@ -18,6 +18,21 @@ workflow test_gatk4_baserecalibrator {
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)
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)
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),

15
tests/modules/gatk4/baserecalibrator/test.yml
View file

@ -1,17 +1,26 @@
- name: gatk4 baserecalibrator test_gatk4_baserecalibrator
command: nextflow run tests/modules/gatk4/baserecalibrator -entry test_gatk4_baserecalibrator -c tests/config/nextflow.config
tags:
- gatk4/baserecalibrator
- gatk4
- gatk4/baserecalibrator
files:
- path: output/gatk4/test.table
md5sum: e2e43abdc0c943c1a54dae816d0b9ea7
- name: gatk4 baserecalibrator test_gatk4_baserecalibrator_cram
command: nextflow run tests/modules/gatk4/baserecalibrator -entry test_gatk4_baserecalibrator_cram -c tests/config/nextflow.config
tags:
- gatk4
- gatk4/baserecalibrator
files:
- path: output/gatk4/test.table
md5sum: 35d89a3811aa31711fc9815b6b80e6ec
- name: gatk4 baserecalibrator test_gatk4_baserecalibrator_intervals
command: nextflow run tests/modules/gatk4/baserecalibrator -entry test_gatk4_baserecalibrator_intervals -c tests/config/nextflow.config
tags:
- gatk4/baserecalibrator
- gatk4
- gatk4/baserecalibrator
files:
- path: output/gatk4/test.table
md5sum: 9ecb5f00a2229291705addc09c0ec231
@ -19,8 +28,8 @@
- name: gatk4 baserecalibrator test_gatk4_baserecalibrator_multiple_sites
command: nextflow run tests/modules/gatk4/baserecalibrator -entry test_gatk4_baserecalibrator_multiple_sites -c tests/config/nextflow.config
tags:
- gatk4/baserecalibrator
- gatk4
- gatk4/baserecalibrator
files:
- path: output/gatk4/test.table
md5sum: e2e43abdc0c943c1a54dae816d0b9ea7

30
tests/modules/gatk4/haplotypecaller/main.nf
View file

@ -13,5 +13,33 @@ workflow test_gatk4_haplotypecaller {
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)
]
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, [], [], [] )
}
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)
]
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)
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 )
}

25
tests/modules/gatk4/haplotypecaller/test.yml
View file

@ -1,13 +1,26 @@
- name: gatk4 haplotypecaller test_gatk4_haplotypecaller
command: nextflow run tests/modules/gatk4/haplotypecaller -entry test_gatk4_haplotypecaller -c tests/config/nextflow.config
tags:
- gatk4
- gatk4/haplotypecaller
- gatk4
files:
- path: output/gatk4/test.vcf.gz
- path: output/gatk4/test.vcf.gz.tbi
- name: gatk4 haplotypecaller test_gatk4_haplotypecaller_cram
command: nextflow run tests/modules/gatk4/haplotypecaller -entry test_gatk4_haplotypecaller_cram -c tests/config/nextflow.config
tags:
- gatk4/haplotypecaller
- gatk4
files:
- path: output/gatk4/test.vcf.gz
- path: output/gatk4/test.vcf.gz.tbi
- name: gatk4 haplotypecaller test_gatk4_haplotypecaller_intervals_dbsnp
command: nextflow run tests/modules/gatk4/haplotypecaller -entry test_gatk4_haplotypecaller_intervals_dbsnp -c tests/config/nextflow.config
tags:
- gatk4/haplotypecaller
- gatk4
files:
- path: output/gatk4/test.vcf.gz
should_exist: true
contains:
- 'MT192765.1'
- '54.60'
- '37.32'
- path: output/gatk4/test.vcf.gz.tbi

9
tests/modules/gatk4/markduplicates/main.nf
View file

@ -11,3 +11,12 @@ workflow test_gatk4_markduplicates {
GATK4_MARKDUPLICATES ( input )
}
workflow test_gatk4_markduplicates_multiple_bams {
input = [ [ id:'test', single_end:false ], // meta map
file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true),
file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_sorted_bam'], checkIfExists: true)
]
GATK4_MARKDUPLICATES ( input )
}

19
tests/modules/gatk4/markduplicates/test.yml
View file

@ -1,8 +1,23 @@
- name: gatk4 markduplicates test_gatk4_markduplicates
command: nextflow run tests/modules/gatk4/markduplicates -entry test_gatk4_markduplicates -c tests/config/nextflow.config
tags:
- gatk4
- gatk4/markduplicates
- gatk4
files:
- path: output/gatk4/test.bai
md5sum: e9c125e82553209933883b4fe2b8d7c2
- path: output/gatk4/test.bam
md5sum: 3b6facab3afbacfa08a7a975efbd2c6b
md5sum: bda9a7bf5057f2288ed70be3eb8a753f
- path: output/gatk4/test.metrics
- name: gatk4 markduplicates test_gatk4_markduplicates_multiple_bams
command: nextflow run tests/modules/gatk4/markduplicates -entry test_gatk4_markduplicates_multiple_bams -c tests/config/nextflow.config
tags:
- gatk4/markduplicates
- gatk4
files:
- path: output/gatk4/test.bai
md5sum: 93cebe29e7cca2064262b739235cca9b
- path: output/gatk4/test.bam
md5sum: dcd6f584006b04141fb787001a8ecacc
- path: output/gatk4/test.metrics

12
tests/modules/samtools/merge/main.nf
View file

@ -11,5 +11,15 @@ workflow test_samtools_merge {
file(params.test_data['sarscov2']['illumina']['test_single_end_sorted_bam'], checkIfExists: true)]
]
SAMTOOLS_MERGE ( input )
SAMTOOLS_MERGE ( input, [] )
}
workflow test_samtools_merge_cram {
input = [ [ id: 'test' ], // meta map
[ file(params.test_data['homo_sapiens']['illumina']['test_paired_end_recalibrated_sorted_cram'], checkIfExists: true),
file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_recalibrated_sorted_cram'], checkIfExists: true),
]
]
fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
SAMTOOLS_MERGE ( input, fasta )
}

14
tests/modules/samtools/merge/test.yml
View file

@ -1,7 +1,15 @@
- name: samtools merge
command: nextflow run ./tests/modules/samtools/merge -entry test_samtools_merge -c tests/config/nextflow.config
- name: samtools merge test_samtools_merge
command: nextflow run tests/modules/samtools/merge -entry test_samtools_merge -c tests/config/nextflow.config
tags:
- samtools
- samtools/merge
- samtools
files:
- path: output/samtools/test_merged.bam
- name: samtools merge test_samtools_merge_cram
command: nextflow run tests/modules/samtools/merge -entry test_samtools_merge_cram -c tests/config/nextflow.config
tags:
- samtools/merge
- samtools
files:
- path: output/samtools/test_merged.cram

12
tests/modules/samtools/stats/main.nf
View file

@ -10,5 +10,15 @@ workflow test_samtools_stats {
file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true)
]
SAMTOOLS_STATS ( input )
SAMTOOLS_STATS ( input, [])
}
workflow test_samtools_stats_cram {
input = [ [ id: 'test' ], // meta map
file(params.test_data['homo_sapiens']['illumina']['test_paired_end_recalibrated_sorted_cram'], checkIfExists: true),
file(params.test_data['homo_sapiens']['illumina']['test_paired_end_recalibrated_sorted_cram_crai'], checkIfExists: true)
]
fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
SAMTOOLS_STATS ( input, fasta )
}

15
tests/modules/samtools/stats/test.yml
View file

@ -1,8 +1,17 @@
- name: samtools stats
command: nextflow run ./tests/modules/samtools/stats -entry test_samtools_stats -c tests/config/nextflow.config
- name: samtools stats test_samtools_stats
command: nextflow run tests/modules/samtools/stats -entry test_samtools_stats -c tests/config/nextflow.config
tags:
- samtools
- samtools/stats
files:
- path: ./output/samtools/test.paired_end.sorted.bam.stats
- path: output/samtools/test.paired_end.sorted.bam.stats
md5sum: a7f36cf11fd3bf97e0a0ae29c0627296
- name: samtools stats test_samtools_stats_cram
command: nextflow run tests/modules/samtools/stats -entry test_samtools_stats_cram -c tests/config/nextflow.config
tags:
- samtools
- samtools/stats
files:
- path: output/samtools/test.paired_end.recalibrated.sorted.cram.stats
md5sum: bd55a1da30028403f4b66dacf7a2a20e

13
tests/modules/samtools/view/main.nf
View file

@ -7,8 +7,17 @@ include { SAMTOOLS_VIEW } from '../../../../modules/samtools/view/main.nf' addPa
workflow test_samtools_view {
input = [ [ id:'test', single_end:false ], // meta map
file(params.test_data['sarscov2']['illumina']['test_paired_end_bam'], checkIfExists: true)
]
SAMTOOLS_VIEW ( input )
SAMTOOLS_VIEW ( input, [] )
}
workflow test_samtools_view_cram {
input = [ [ id: 'test' ], // meta map
file(params.test_data['homo_sapiens']['illumina']['test_paired_end_recalibrated_sorted_cram'], checkIfExists: true),
file(params.test_data['homo_sapiens']['illumina']['test_paired_end_recalibrated_sorted_cram_crai'], checkIfExists: true)
]
fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
SAMTOOLS_VIEW ( input, fasta )
}

12
tests/modules/samtools/view/test.yml
View file

@ -1,8 +1,16 @@
- name: samtools view
- name: samtools view test_samtools_view
command: nextflow run tests/modules/samtools/view -entry test_samtools_view -c tests/config/nextflow.config
tags:
- samtools
- samtools/view
- samtools
files:
- path: output/samtools/test.bam
md5sum: 8fb1e82f76416e9e30fc6b2357e2cf13
- name: samtools view test_samtools_view_cram
command: nextflow run tests/modules/samtools/view -entry test_samtools_view_cram -c tests/config/nextflow.config
tags:
- samtools/view
- samtools
files:
- path: output/samtools/test.cram