Merge branch 'master' into new-module-gatk4/reblockgvcf

modules/ensemblvep/main.nf

@@ -13,6 +13,7 @@ process ENSEMBLVEP {
     val   species
     val   cache_version
     path  cache
+    path  fasta
     path  extra_files
 
     output:
@@ -27,6 +28,8 @@ process ENSEMBLVEP {
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
     def dir_cache = cache ? "\${PWD}/${cache}" : "/.vep"
+    def reference = fasta ? "--fasta $fasta" : ""
+
     """
     mkdir $prefix
 
@@ -34,6 +37,7 @@ process ENSEMBLVEP {
         -i $vcf \\
         -o ${prefix}.ann.vcf \\
         $args \\
+        $reference \\
         --assembly $genome \\
         --species $species \\
         --cache \\

modules/ensemblvep/meta.yml

@@ -36,6 +36,11 @@ input:
       type: file
       description: |
         path to VEP cache (optional)
+  - fasta:
+      type: file
+      description: |
+        reference FASTA file (optional)
+      pattern: "*.{fasta,fa}"
   - extra_files:
       type: tuple
       description: |

modules/gatk4/markduplicatesspark/main.nf

@@ -2,7 +2,7 @@ process GATK4_MARKDUPLICATES_SPARK {
     tag "$meta.id"
     label 'process_high'
 
-    conda (params.enable_conda ? "bioconda::gatk4=4.2.3.0" : null)
+    conda (params.enable_conda ? "bioconda::gatk4=4.2.3.0 conda-forge::openjdk=8.0.312" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/gatk4:4.2.3.0--hdfd78af_0' :
         'broadinstitute/gatk:4.2.3.0' }"
@@ -15,6 +15,7 @@ process GATK4_MARKDUPLICATES_SPARK {
 
     output:
     tuple val(meta), path("${prefix}"),     emit: output
+    tuple val(meta), path("*.metrics"),     emit: metrics, optional: true
     path "versions.yml"               ,     emit: versions
 
     when:
@@ -25,6 +26,7 @@ process GATK4_MARKDUPLICATES_SPARK {
     prefix = task.ext.prefix ?: "${meta.id}"
     def input_list = bam.collect{"--input $it"}.join(' ')
 
+
     def avail_mem = 3
     if (!task.memory) {
         log.info '[GATK MarkDuplicatesSpark] Available memory not known - defaulting to 3GB. Specify process memory requirements to change this.'
@@ -32,8 +34,6 @@ process GATK4_MARKDUPLICATES_SPARK {
         avail_mem = task.memory.giga
     }
     """
-    export SPARK_USER=spark3
-
     gatk --java-options "-Xmx${avail_mem}g" MarkDuplicatesSpark \\
         $input_list \\
         --output $prefix \\
@@ -45,6 +45,7 @@ process GATK4_MARKDUPLICATES_SPARK {
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
         gatk4: \$(echo \$(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//')
+        openjdk: \$(echo \$(java -version 2>&1) | grep version | sed 's/\"//g' | cut -f3 -d ' ')
     END_VERSIONS
     """
 }

modules/gatk4/markduplicatesspark/meta.yml

@@ -58,3 +58,4 @@ authors:
   - "@ajodeh-juma"
   - "@FriederikeHanssen"
   - "@maxulysse"
+  - "@SusiJo"

tests/modules/ensemblvep/main.nf

@@ -4,11 +4,22 @@ nextflow.enable.dsl = 2
 
 include { ENSEMBLVEP } from '../../../modules/ensemblvep/main.nf'
 
-workflow test_ensemblvep {
+workflow test_ensemblvep_fasta {
     input = [
         [ id:'test' ], // meta map
         file(params.test_data['sarscov2']['illumina']['test_vcf'], checkIfExists: true)
     ]
 
-    ENSEMBLVEP ( input, "WBcel235", "caenorhabditis_elegans", "104", [], [] )
+    fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
+
+    ENSEMBLVEP ( input, "WBcel235", "caenorhabditis_elegans", "104", [], fasta, [] )
+}
+
+workflow test_ensemblvep_no_fasta {
+    input = [
+        [ id:'test' ], // meta map
+        file(params.test_data['sarscov2']['illumina']['test_vcf'], checkIfExists: true)
+    ]
+
+    ENSEMBLVEP ( input, "WBcel235", "caenorhabditis_elegans", "104", [], [], [] )
 }

tests/modules/ensemblvep/test.yml

@@ -1,5 +1,13 @@
-- name: ensemblvep test_ensemblvep
-  command: nextflow run ./tests/modules/ensemblvep -entry test_ensemblvep -c ./tests/config/nextflow.config -c ./tests/modules/ensemblvep/nextflow.config
+- name: ensemblvep test_ensemblvep_fasta
+  command: nextflow run ./tests/modules/ensemblvep -entry test_ensemblvep_fasta -c ./tests/config/nextflow.config -c ./tests/modules/ensemblvep/nextflow.config
+  tags:
+    - ensemblvep
+  files:
+    - path: output/ensemblvep/test.ann.vcf
+    - path: output/ensemblvep/test.summary.html
+
+- name: ensemblvep test_ensemblvep_no_fasta
+  command: nextflow run ./tests/modules/ensemblvep -entry test_ensemblvep_no_fasta -c ./tests/config/nextflow.config -c ./tests/modules/ensemblvep/nextflow.config
   tags:
     - ensemblvep
   files:

tests/modules/gatk4/markduplicatesspark/main.nf

@@ -3,26 +3,55 @@
 nextflow.enable.dsl = 2
 
 include { GATK4_MARKDUPLICATES_SPARK } from '../../../../modules/gatk4/markduplicatesspark/main.nf'
+include { GATK4_MARKDUPLICATES_SPARK as GATK4_MARKDUPLICATES_SPARK_CRAM } from '../../../../modules/gatk4/markduplicatesspark/main.nf'
+include { GATK4_MARKDUPLICATES_SPARK as GATK4_MARKDUPLICATES_SPARK_METRICS } from '../../../../modules/gatk4/markduplicatesspark/main.nf'
 
 workflow test_gatk4_markduplicates_spark {
     input = [ [ id:'test', single_end:false ], // meta map
             file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true)
             ]
-    fasta = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta'], checkIfExists: true)
-    fai = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta_fai'], checkIfExists: true)
-    dict = file(params.test_data['homo_sapiens']['genome']['genome_21_dict'], 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_MARKDUPLICATES_SPARK ( input, fasta, fai, dict )
 }
 
+// chr 22
 workflow test_gatk4_markduplicates_spark_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)
+            [   file(params.test_data['homo_sapiens']['illumina']['test_paired_end_name_sorted_bam'], checkIfExists: true),
+                file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_name_sorted_bam'], checkIfExists: true)
             ] ]
-    fasta = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta'], checkIfExists: true)
-    fai = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta_fai'], checkIfExists: true)
-    dict = file(params.test_data['homo_sapiens']['genome']['genome_21_dict'], 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_MARKDUPLICATES_SPARK ( input, fasta, fai, dict )
 }
+
+// chr 22
+workflow test_gatk4_markduplicates_spark_multiple_bams_cram_out {
+    input = [ [ id:'test', single_end:false ], // meta map
+            [   file(params.test_data['homo_sapiens']['illumina']['test_paired_end_name_sorted_bam'], checkIfExists: true),
+                file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_name_sorted_bam'], 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_MARKDUPLICATES_SPARK_CRAM ( input, fasta, fai, dict )
+}
+
+// chr 22
+workflow test_gatk4_markduplicates_spark_multiple_bams_metrics {
+    input = [ [ id:'test', single_end:false ], // meta map
+            [   file(params.test_data['homo_sapiens']['illumina']['test_paired_end_name_sorted_bam'], checkIfExists: true),
+                file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_name_sorted_bam'], 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_MARKDUPLICATES_SPARK_METRICS ( input, fasta, fai, dict )
+}

tests/modules/gatk4/markduplicatesspark/nextflow.config

@@ -2,4 +2,18 @@ process {
 
     publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
 
+    withName: GATK4_MARKDUPLICATES_SPARK {
+        ext.prefix = { "${meta.id}.bam" }
     }
+    withName: GATK4_MARKDUPLICATES_SPARK_CRAM {
+        ext.prefix = { "${meta.id}.cram" }
+    }
+    withName: GATK4_MARKDUPLICATES_SPARK_METRICS {
+        ext.args = '--metrics-file test.metrics'
+        ext.prefix = { "${meta.id}.bam" }
+    }
+
+}
+// override tests/config/nextflow.config
+docker.userEmulation = false
+

tests/modules/gatk4/markduplicatesspark/test.yml

@@ -1,25 +1,41 @@
-- name: gatk4 markduplicates test_gatk4_markduplicates_spark
-  command: nextflow run tests/modules/gatk4/markduplicatesspark -entry test_gatk4_markduplicates_spark -c tests/config/nextflow.config -c ./tests/modules/gatk4/markduplicatesspark/nextflow.config
+- name: gatk4 markduplicatesspark test_gatk4_markduplicates_spark
+  command: nextflow run ./tests/modules/gatk4/markduplicatesspark -entry test_gatk4_markduplicates_spark -c ./tests/config/nextflow.config  -c ./tests/modules/gatk4/markduplicatesspark/nextflow.config
   tags:
     - gatk4
     - gatk4/markduplicatesspark
   files:
-    - path: output/gatk4/test.bai
-      md5sum: e9c125e82553209933883b4fe2b8d7c2
     - path: output/gatk4/test.bam
-      md5sum: 2efd50b2e6b7fd9bdf242cd9e266cfa9
-    - path: output/gatk4/test.metrics
+      md5sum: dc1a09ac6371aab7c50d1a554baa06d3
     - path: output/gatk4/versions.yml
 
-- name: gatk4 markduplicates test_gatk4_markduplicates_spark_multiple_bams
-  command: nextflow run tests/modules/gatk4/markduplicatesspark -entry test_gatk4_markduplicates_spark_multiple_bams -c tests/config/nextflow.config -c ./tests/modules/gatk4/markduplicatesspark/nextflow.config
+- name: gatk4 markduplicatesspark test_gatk4_markduplicates_spark_multiple_bams
+  command: nextflow run ./tests/modules/gatk4/markduplicatesspark -entry test_gatk4_markduplicates_spark_multiple_bams -c ./tests/config/nextflow.config  -c ./tests/modules/gatk4/markduplicatesspark/nextflow.config
   tags:
     - gatk4
     - gatk4/markduplicatesspark
   files:
-    - path: output/gatk4/test.bai
-      md5sum: bad71df9c876e72a5bc0a3e0fd755f92
     - path: output/gatk4/test.bam
-      md5sum: 8187febc6108ffef7f907e89b9c091a4
-    - path: output/gatk4/test.metrics
+      md5sum: 898cb0a6616897d8ada90bab53bf0837
+    - path: output/gatk4/versions.yml
+
+- name: gatk4 markduplicatesspark test_gatk4_markduplicates_spark_multiple_bams_cram_out
+  command: nextflow run ./tests/modules/gatk4/markduplicatesspark -entry test_gatk4_markduplicates_spark_multiple_bams_cram_out -c ./tests/config/nextflow.config  -c ./tests/modules/gatk4/markduplicatesspark/nextflow.config
+  tags:
+    - gatk4
+    - gatk4/markduplicatesspark
+  files:
+    - path: output/gatk4/test.cram
+      md5sum: 2271016de5e4199736598f39d12d7587
+    - path: output/gatk4/versions.yml
+
+- name: gatk4 markduplicatesspark test_gatk4_markduplicates_spark_multiple_bams_metrics
+  command: nextflow run ./tests/modules/gatk4/markduplicatesspark -entry test_gatk4_markduplicates_spark_multiple_bams_metrics -c ./tests/config/nextflow.config  -c ./tests/modules/gatk4/markduplicatesspark/nextflow.config
+  tags:
+    - gatk4
+    - gatk4/markduplicatesspark
+  files:
+    - path: output/gatk4/test.bam
+      md5sum: 898cb0a6616897d8ada90bab53bf0837
+    - path: output/gatk4/test.metrics
+      contains: ["## METRICS CLASS", "org.broadinstitute.hellbender.utils.read.markduplicates.GATKDuplicationMetrics"]
     - path: output/gatk4/versions.yml