Change intervals to be part of sample specific input (#1189)

* Change intervals to be part of sample specific input

* Fix some tests

* Update checksum

* Update intervals

* Update intervals

* Try out gavins idea for adding the file

* update test line

* update test line

* update test line

* revert contains line

modules/gatk4/applybqsr/main.nf

@@ -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

modules/gatk4/applybqsr/meta.yml

@@ -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:

modules/gatk4/baserecalibrator/main.nf

@@ -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 \

modules/gatk4/baserecalibrator/meta.yml

@@ -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)

modules/gatk4/genotypegvcfs/main.nf

@@ -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) {

modules/gatk4/genotypegvcfs/meta.yml

@@ -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:

modules/gatk4/haplotypecaller/main.nf

@@ -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) {

modules/gatk4/haplotypecaller/meta.yml

@@ -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:

tests/modules/gatk4/applybqsr/main.nf

@@ -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 )
 }

tests/modules/gatk4/applybqsr/test.yml

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

tests/modules/gatk4/baserecalibrator/main.nf

@@ -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 )
 }

tests/modules/gatk4/genotypegvcfs/main.nf

@@ -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, [], [])
-
-    GATK4_GENOTYPEGVCFS ( input, fasta, fastaIndex, fastaDict, [], [], intervalsBed )
 }
 
 // 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 )
-
-    GATK4_GENOTYPEGVCFS ( input, fasta, fastaIndex, fastaDict, dbsnp, dbsnpIndex, intervalsBed )
 }
 
 // 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 )
 }

tests/modules/gatk4/haplotypecaller/main.nf

@@ -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 )
 }