Merge branch 'master' into cnvkit/antitarget

2024-12-22 02:58:17 +00:00 · 2022-05-24 07:36:07 +02:00 · 2022-05-24 07:36:07 +02:00 · b3e2f70651
commit b3e2f70651
parent 58c5ec2f4e 91f9a0711d
8 changed files with 67 additions and 26 deletions
--- a/modules/picard/collecthsmetrics/main.nf
+++ b/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) {
--- a/modules/picard/collectmultiplemetrics/main.nf
+++ b/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}":
--- a/modules/picard/collectwgsmetrics/main.nf
+++ b/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
--- a/tests/modules/picard/collecthsmetrics/main.nf
+++ b/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 )
+}
--- a/tests/modules/picard/collecthsmetrics/test.yml
+++ b/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
--- a/tests/modules/picard/collectmultiplemetrics/main.nf
+++ b/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
-              file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true)
+    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['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, [] )
+}
--- a/tests/modules/picard/collectmultiplemetrics/test.yml
+++ b/tests/modules/picard/collectmultiplemetrics/test.yml
@ -1,17 +1,33 @@
- name: 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
+- 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
  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.insert_size_metrics
-    - path: ./output/picard/test.CollectMultipleMetrics.quality_distribution_metrics
-    - path: ./output/picard/test.CollectMultipleMetrics.quality_by_cycle_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_distribution.pdf
-    - path: ./output/picard/test.CollectMultipleMetrics.read_length_histogram.pdf
-    - path: ./output/picard/test.CollectMultipleMetrics.base_distribution_by_cycle.pdf
-    - path: ./output/picard/test.CollectMultipleMetrics.insert_size_histogram.pdf
+    - 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
+
+- 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
--- a/tests/modules/picard/collectwgsmetrics/test.yml
+++ b/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"