Update version & add intervals usage (#1214)

* Update version & add intervals usage

* Fix config when passing intervals as file

* Use proper paths

modules/deepvariant/main.nf

@@ -8,11 +8,11 @@ process DEEPVARIANT {
     }
 
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'google/deepvariant:1.2.0' :
-        'google/deepvariant:1.2.0' }"
+        'google/deepvariant:1.3.0' :
+        'google/deepvariant:1.3.0' }"
 
     input:
-    tuple val(meta), path(bam), path(bai)
+    tuple val(meta), path(input), path(index), path(intervals)
     path(fasta)
     path(fai)
 
@@ -24,14 +24,16 @@ process DEEPVARIANT {
     script:
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
+    def regions = intervals ? "--regions ${intervals}" : ""
 
     """
     /opt/deepvariant/bin/run_deepvariant \\
         --ref=${fasta} \\
-        --reads=${bam} \\
+        --reads=${input} \\
         --output_vcf=${prefix}.vcf.gz \\
         --output_gvcf=${prefix}.g.vcf.gz \\
         ${args} \\
+        ${regions} \\
         --num_shards=${task.cpus}
 
     cat <<-END_VERSIONS > versions.yml
@@ -39,5 +41,4 @@ process DEEPVARIANT {
         deepvariant: \$(echo \$(/opt/deepvariant/bin/run_deepvariant --version) | sed 's/^.*version //; s/ .*\$//' )
     END_VERSIONS
     """
-
 }

modules/deepvariant/meta.yml

@@ -18,14 +18,18 @@ 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
+      pattern: "*.bam/cram"
+  - index:
       type: file
-      description: Index of BAM file
-      pattern: "*.bai"
+      description: Index of BAM/CRAM file
+      pattern: "*.bai/crai"
+  - interval:
+      type: file
+      description: Interval file for targeted regions
+      pattern: "*.bed"
   - fasta:
       type: file
       description: The reference fasta file

tests/modules/deepvariant/main.nf

@@ -2,13 +2,16 @@
 
 nextflow.enable.dsl = 2
 
-include { DEEPVARIANT } from '../../../modules/deepvariant/main.nf'
+include { DEEPVARIANT                          } from '../../../modules/deepvariant/main.nf'
+include { DEEPVARIANT as DEEPVARIANT_INTERVALS } from '../../../modules/deepvariant/main.nf'
 
 workflow test_deepvariant {
 
-    bam_tuple_ch = Channel.of([[ id:'test', single_end:false ], // meta map
+    bam_tuple_ch = Channel.of([ [ 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']['test_paired_end_sorted_bam_bai'], checkIfExists: true)])
+                               file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true),
+                               []
+                                ])
 
     fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
 
@@ -16,3 +19,18 @@ workflow test_deepvariant {
 
     DEEPVARIANT ( bam_tuple_ch, fasta, fai)
 }
+
+workflow test_deepvariant_cram_intervals {
+
+    cram_tuple_ch = Channel.of([[ id:'test', single_end:false ], // 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']['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)
+
+    DEEPVARIANT_INTERVALS ( cram_tuple_ch, fasta, fai)
+}

tests/modules/deepvariant/nextflow.config

@@ -6,5 +6,9 @@ process {
          ext.args = ' --regions=\"chr22:0-40001\" --model_type=WGS '
          ext.prefix = { "${meta.id}_out" }
      }
+     withName: DEEPVARIANT_INTERVALS {
+         ext.args = '--model_type=WGS '
+         ext.prefix = { "${meta.id}_out" }
+     }
 
 }

tests/modules/deepvariant/test.yml

@@ -1,9 +1,23 @@
-- name: deepvariant
-  command: nextflow run ./tests/modules/deepvariant -entry test_deepvariant -c tests/config/nextflow.config
+- name: deepvariant test_deepvariant
+  command: nextflow run tests/modules/deepvariant -entry test_deepvariant -c tests/config/nextflow.config
   tags:
     - deepvariant
   files:
-    - path: output/deepvariant/test_out.vcf.gz
-      md5sum: 66d86be7a9bafe1f5c6304ebee18ee20
     - path: output/deepvariant/test_out.g.vcf.gz
-      md5sum: 4ca868f0a4fdb17a280c3ed083d228e0
+      md5sum: c4c65a3eaf62d6fbe0aba0a414318c8d
+    - path: output/deepvariant/test_out.vcf.gz
+      md5sum: ad964f68ac1d1b2720a9a4e0b6a3a389
+    - path: output/deepvariant/versions.yml
+      md5sum: 51572055ca5c07fc4001b25a9c273bf8
+
+- name: deepvariant test_deepvariant_cram_intervals
+  command: nextflow run tests/modules/deepvariant -entry test_deepvariant_cram_intervals -c tests/config/nextflow.config
+  tags:
+    - deepvariant
+  files:
+    - path: output/deepvariant/test_out.g.vcf.gz
+      md5sum: c4c65a3eaf62d6fbe0aba0a414318c8d
+    - path: output/deepvariant/test_out.vcf.gz
+      md5sum: ad964f68ac1d1b2720a9a4e0b6a3a389
+    - path: output/deepvariant/versions.yml
+      md5sum: 7d9293db0d44423b114abc7116feb967