Merge pull request #1683 from matthdsm/update/picard

picard: make reference sequence optional

modules/picard/collecthsmetrics/main.nf

@@ -24,7 +24,7 @@ process PICARD_COLLECTHSMETRICS {
     script:
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
-    def reference = fasta ? "-R $fasta" : ""
+    def reference = fasta ? "--REFERENCE_SEQUENCE ${fasta}" : ""
 
     def avail_mem = 3
     if (!task.memory) {

modules/picard/collectmultiplemetrics/main.nf

@@ -22,6 +22,7 @@ process PICARD_COLLECTMULTIPLEMETRICS {
     script:
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
+    def reference = fasta ? "--REFERENCE_SEQUENCE ${fasta}" : ""
     def avail_mem = 3
     if (!task.memory) {
         log.info '[Picard CollectMultipleMetrics] Available memory not known - defaulting to 3GB. Specify process memory requirements to change this.'
@@ -35,7 +36,7 @@ process PICARD_COLLECTMULTIPLEMETRICS {
         $args \\
         --INPUT $bam \\
         --OUTPUT ${prefix}.CollectMultipleMetrics \\
-        --REFERENCE_SEQUENCE $fasta
+        $reference
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":

modules/picard/collectwgsmetrics/main.nf

@@ -34,7 +34,7 @@ process PICARD_COLLECTWGSMETRICS {
         $args \\
         --INPUT $bam \\
         --OUTPUT ${prefix}.CollectWgsMetrics.coverage_metrics \\
-        --REFERENCE_SEQUENCE $fasta
+        --REFERENCE_SEQUENCE ${fasta}
 
 
     cat <<-END_VERSIONS > versions.yml

tests/modules/picard/collecthsmetrics/main.nf

@@ -16,3 +16,14 @@ workflow test_picard_collecthsmetrics {
 
     PICARD_COLLECTHSMETRICS ( input, fasta, fai, bait_intervals, target_intervals )
 }
+
+workflow test_picard_collecthsmetrics_nofasta {
+
+    input = [ [ id:'test', single_end:false ], // meta map
+            file(params.test_data['sarscov2']['illumina']['test_paired_end_bam'], checkIfExists: true) ]
+
+    bait_intervals = file(params.test_data['sarscov2']['genome']['baits_interval_list'], checkIfExists: true)
+    target_intervals = file(params.test_data['sarscov2']['genome']['targets_interval_list'], checkIfExists: true)
+
+    PICARD_COLLECTHSMETRICS ( input, [], [], bait_intervals, target_intervals )
+}

tests/modules/picard/collecthsmetrics/test.yml

@@ -1,8 +1,15 @@
 - name: picard collecthsmetrics test_picard_collecthsmetrics
-  command: nextflow run ./tests/modules/picard/collecthsmetrics -entry test_picard_collecthsmetrics -c ./tests/config/nextflow.config -c ./tests/modules/picard/collecthsmetrics/nextflow.config
+  command: nextflow run ./tests/modules/picard/collecthsmetrics -entry test_picard_collecthsmetrics -c ./tests/config/nextflow.config  -c ./tests/modules/picard/collecthsmetrics/nextflow.config
   tags:
-    - picard
     - picard/collecthsmetrics
+    - picard
+  files:
+    - path: output/picard/test.CollectHsMetrics.coverage_metrics
+
+- name: picard collecthsmetrics test_picard_collecthsmetrics_nofasta
+  command: nextflow run ./tests/modules/picard/collecthsmetrics -entry test_picard_collecthsmetrics_nofasta -c ./tests/config/nextflow.config  -c ./tests/modules/picard/collecthsmetrics/nextflow.config
+  tags:
+    - picard/collecthsmetrics
+    - picard
   files:
-    # The file can't be md5'd consistently
     - path: output/picard/test.CollectHsMetrics.coverage_metrics

tests/modules/picard/collectmultiplemetrics/main.nf

@@ -5,10 +5,20 @@ nextflow.enable.dsl = 2
 include { PICARD_COLLECTMULTIPLEMETRICS } from '../../../../modules/picard/collectmultiplemetrics/main.nf'
 
 workflow test_picard_collectmultiplemetrics {
-    input = [ [ id:'test', single_end:false ], // meta map
+    input = [
-              file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true)
+                [ 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['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
 
     PICARD_COLLECTMULTIPLEMETRICS ( input, fasta )
 }
+
+workflow test_picard_collectmultiplemetrics_nofasta {
+    input = [
+                [ id:'test', single_end:false ], // meta map
+                file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true)
+            ]
+
+    PICARD_COLLECTMULTIPLEMETRICS ( input, [] )
+}

tests/modules/picard/collectmultiplemetrics/test.yml

@@ -1,17 +1,33 @@
-- name: picard collectmultiplemetrics
+- name: picard collectmultiplemetrics test_picard_collectmultiplemetrics
-  command: nextflow run ./tests/modules/picard/collectmultiplemetrics -entry test_picard_collectmultiplemetrics -c ./tests/config/nextflow.config -c ./tests/modules/picard/collectmultiplemetrics/nextflow.config
+  command: nextflow run ./tests/modules/picard/collectmultiplemetrics -entry test_picard_collectmultiplemetrics -c ./tests/config/nextflow.config  -c ./tests/modules/picard/collectmultiplemetrics/nextflow.config
   tags:
     - picard
     - picard/collectmultiplemetrics
   files:
-    # These can't be md5'd consistently
+    - path: output/picard/test.CollectMultipleMetrics.alignment_summary_metrics
-    - path: ./output/picard/test.CollectMultipleMetrics.alignment_summary_metrics
+    - path: output/picard/test.CollectMultipleMetrics.base_distribution_by_cycle.pdf
-    - path: ./output/picard/test.CollectMultipleMetrics.insert_size_metrics
+    - path: output/picard/test.CollectMultipleMetrics.base_distribution_by_cycle_metrics
-    - path: ./output/picard/test.CollectMultipleMetrics.quality_distribution_metrics
+    - path: output/picard/test.CollectMultipleMetrics.insert_size_histogram.pdf
-    - path: ./output/picard/test.CollectMultipleMetrics.quality_by_cycle_metrics
+    - path: output/picard/test.CollectMultipleMetrics.insert_size_metrics
-    - path: ./output/picard/test.CollectMultipleMetrics.base_distribution_by_cycle_metrics
+    - path: output/picard/test.CollectMultipleMetrics.quality_by_cycle.pdf
-    - path: ./output/picard/test.CollectMultipleMetrics.quality_by_cycle.pdf
+    - path: output/picard/test.CollectMultipleMetrics.quality_by_cycle_metrics
-    - path: ./output/picard/test.CollectMultipleMetrics.quality_distribution.pdf
+    - path: output/picard/test.CollectMultipleMetrics.quality_distribution.pdf
-    - path: ./output/picard/test.CollectMultipleMetrics.read_length_histogram.pdf
+    - path: output/picard/test.CollectMultipleMetrics.quality_distribution_metrics
-    - path: ./output/picard/test.CollectMultipleMetrics.base_distribution_by_cycle.pdf
+    - path: output/picard/test.CollectMultipleMetrics.read_length_histogram.pdf
-    - path: ./output/picard/test.CollectMultipleMetrics.insert_size_histogram.pdf
+
+- name: picard collectmultiplemetrics test_picard_collectmultiplemetrics_nofasta
+  command: nextflow run ./tests/modules/picard/collectmultiplemetrics -entry test_picard_collectmultiplemetrics_nofasta -c ./tests/config/nextflow.config  -c ./tests/modules/picard/collectmultiplemetrics/nextflow.config
+  tags:
+    - picard
+    - picard/collectmultiplemetrics
+  files:
+    - path: output/picard/test.CollectMultipleMetrics.alignment_summary_metrics
+    - path: output/picard/test.CollectMultipleMetrics.base_distribution_by_cycle.pdf
+    - path: output/picard/test.CollectMultipleMetrics.base_distribution_by_cycle_metrics
+    - path: output/picard/test.CollectMultipleMetrics.insert_size_histogram.pdf
+    - path: output/picard/test.CollectMultipleMetrics.insert_size_metrics
+    - path: output/picard/test.CollectMultipleMetrics.quality_by_cycle.pdf
+    - path: output/picard/test.CollectMultipleMetrics.quality_by_cycle_metrics
+    - path: output/picard/test.CollectMultipleMetrics.quality_distribution.pdf
+    - path: output/picard/test.CollectMultipleMetrics.quality_distribution_metrics
+    - path: output/picard/test.CollectMultipleMetrics.read_length_histogram.pdf

tests/modules/picard/collectwgsmetrics/test.yml

@@ -1,11 +1,7 @@
 - name: picard collectwgsmetrics test_picard_collectwgsmetrics
-  command: nextflow run ./tests/modules/picard/collectwgsmetrics -entry test_picard_collectwgsmetrics -c ./tests/config/nextflow.config -c ./tests/modules/picard/collectwgsmetrics/nextflow.config
+  command: nextflow run ./tests/modules/picard/collectwgsmetrics -entry test_picard_collectwgsmetrics -c ./tests/config/nextflow.config  -c ./tests/modules/picard/collectwgsmetrics/nextflow.config
   tags:
     - picard/collectwgsmetrics
     - picard
   files:
     - path: output/picard/test.CollectWgsMetrics.coverage_metrics
-      contains:
-        - "GENOME_TERRITORY"
-        - "29829"
-        - "17554"