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

* 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>

modules/gatk4/applybqsr/main.nf

@@ -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
 

modules/gatk4/applybqsr/meta.yml

@@ -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
+      description: BAM/CRAM file from alignment
-      pattern: "*.{bam}"
+      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

modules/gatk4/baserecalibrator/main.nf

@@ -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
 

modules/gatk4/baserecalibrator/meta.yml

@@ -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
+      description: BAM/CRAM file from alignment
-      pattern: "*.{bam}"
+      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"

modules/gatk4/haplotypecaller/main.nf

@@ -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
@@ -31,6 +34,8 @@ process GATK4_HAPLOTYPECALLER {
 
     script:
     def prefix          = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
+    def interval_option = interval ? "-L ${interval}" : ""
+    def dbsnp_option    = dbsnp ? "-D ${dbsnp}" : ""
     def avail_mem       = 3
     if (!task.memory) {
         log.info '[GATK HaplotypeCaller] Available memory not known - defaulting to 3GB. Specify process memory requirements to change this.'
@@ -42,9 +47,12 @@ process GATK4_HAPLOTYPECALLER {
         --java-options "-Xmx${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)}:

modules/gatk4/haplotypecaller/meta.yml

@@ -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
+      description: BAM/CRAM file from alignment
-      pattern: "*.bam"
+      pattern: "*.{bam,cram}"
-  - bai:
+  - input_index:
       type: file
-      description: Index of BAM file
+      description: BAI/CRAI file from alignment
-      pattern: "*.bam.bai"
+      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"

modules/gatk4/markduplicates/main.nf

@@ -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

modules/gatk4/markduplicates/meta.yml

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

modules/manta/germline/main.nf

@@ -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

modules/manta/germline/meta.yml

@@ -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}"

modules/manta/somatic/main.nf

@@ -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 \
+        --tumorBam $input_tumor \
-        --normalBam $cram_normal \
+        --normalBam $input_normal \
         --reference $fasta \
         $options_manta \
         --runDir manta

modules/manta/somatic/meta.yml

@@ -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}"

modules/manta/tumoronly/main.nf

@@ -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

modules/manta/tumoronly/meta.yml

@@ -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

modules/samtools/merge/main.nf

@@ -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("${prefix}.bam"), emit: bam
+    tuple val(meta), path("${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.*\$//')

modules/samtools/merge/meta.yml

@@ -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"

modules/samtools/stats/main.nf

@@ -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.*\$//')

modules/samtools/stats/meta.yml

@@ -22,14 +22,18 @@ input:
         description: |
             Groovy Map containing sample information
             e.g. [ id:'test', single_end:false ]
-    - bam:
+    - input:
       type: file
-        description: BAM/CRAM/SAM file
+      description: BAM/CRAM file from alignment
-        pattern: "*.{bam,cram,sam}"
+      pattern: "*.{bam,cram}"
-    - bai:
+    - input_index:
       type: file
-        description: Index for BAM/CRAM/SAM file
+      description: BAI/CRAI file from alignment
-        pattern: "*.{bai,crai,sai}"
+      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"

modules/samtools/view/main.nf

@@ -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
+    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.*\$//')

modules/samtools/view/meta.yml

@@ -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
+        description: filtered/converted BAM/SAM file
-        pattern: "*.{bam,cram,sam}"
+        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"

modules/strelka/germline/main.nf

@@ -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 \\

modules/strelka/germline/meta.yml

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

modules/strelka/somatic/main.nf

@@ -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 \\
+        --tumor $input_tumor \\
-        --normal $cram_normal \\
+        --normal $input_normal \\
         --referenceFasta $fasta \\
         $options_target_bed \\
         $options_manta \\

modules/strelka/somatic/meta.yml

@@ -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}"

subworkflows/nf-core/bam_stats_samtools/main.nf

@@ -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 )

tests/modules/gatk4/applybqsr/main.nf

@@ -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 )
+}

tests/modules/gatk4/applybqsr/test.yml

@@ -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

tests/modules/gatk4/baserecalibrator/main.nf

@@ -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),

tests/modules/gatk4/baserecalibrator/test.yml

@@ -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

tests/modules/gatk4/haplotypecaller/main.nf

@@ -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 )
 }

tests/modules/gatk4/haplotypecaller/test.yml

@@ -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

tests/modules/gatk4/markduplicates/main.nf

@@ -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 )
+}

tests/modules/gatk4/markduplicates/test.yml

@@ -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

tests/modules/samtools/merge/main.nf

@@ -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 )
 }

tests/modules/samtools/merge/test.yml

@@ -1,7 +1,15 @@
-- name: samtools merge
+- name: samtools merge test_samtools_merge
-  command: nextflow run ./tests/modules/samtools/merge -entry test_samtools_merge -c tests/config/nextflow.config
+  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

tests/modules/samtools/stats/main.nf

@@ -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 )
 }

tests/modules/samtools/stats/test.yml

@@ -1,8 +1,17 @@
-- name: samtools stats
+- name: samtools stats test_samtools_stats
-  command: nextflow run ./tests/modules/samtools/stats -entry test_samtools_stats -c tests/config/nextflow.config
+  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

tests/modules/samtools/view/main.nf

@@ -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 )
 }

tests/modules/samtools/view/test.yml

@@ -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