add tests

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 +1,17 @@
 - 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
   tags:
-    - picard
     - picard/collecthsmetrics
+    - picard
   files:
-    # The file can't be md5'd consistently
     - path: output/picard/test.CollectHsMetrics.coverage_metrics
+      contains: '[ # TODO nf-core: file md5sum was variable, please replace this text with a string found in the file instead ]'
+
+- 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:
+    - path: output/picard/test.CollectHsMetrics.coverage_metrics
+      contains: '[ # TODO nf-core: file md5sum was variable, please replace this text with a string found in the file instead ]'

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 = [
+                [ 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 +1,53 @@
-- 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
   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
+      contains: '[ # TODO nf-core: file md5sum was variable, please replace this text with a string found in the file instead ]'
-    - path: ./output/picard/test.CollectMultipleMetrics.insert_size_metrics
+    - path: output/picard/test.CollectMultipleMetrics.base_distribution_by_cycle.pdf
-    - path: ./output/picard/test.CollectMultipleMetrics.quality_distribution_metrics
+      contains: '[ # TODO nf-core: file md5sum was variable, please replace this text with a string found in the file instead ]'
-    - path: ./output/picard/test.CollectMultipleMetrics.quality_by_cycle_metrics
+    - path: output/picard/test.CollectMultipleMetrics.base_distribution_by_cycle_metrics
-    - path: ./output/picard/test.CollectMultipleMetrics.base_distribution_by_cycle_metrics
+      contains: '[ # TODO nf-core: file md5sum was variable, please replace this text with a string found in the file instead ]'
-    - path: ./output/picard/test.CollectMultipleMetrics.quality_by_cycle.pdf
+    - path: output/picard/test.CollectMultipleMetrics.insert_size_histogram.pdf
-    - path: ./output/picard/test.CollectMultipleMetrics.quality_distribution.pdf
+      contains: '[ # TODO nf-core: file md5sum was variable, please replace this text with a string found in the file instead ]'
-    - path: ./output/picard/test.CollectMultipleMetrics.read_length_histogram.pdf
+    - path: output/picard/test.CollectMultipleMetrics.insert_size_metrics
-    - path: ./output/picard/test.CollectMultipleMetrics.base_distribution_by_cycle.pdf
+      contains: '[ # TODO nf-core: file md5sum was variable, please replace this text with a string found in the file instead ]'
-    - path: ./output/picard/test.CollectMultipleMetrics.insert_size_histogram.pdf
+    - path: output/picard/test.CollectMultipleMetrics.quality_by_cycle.pdf
+      contains: '[ # TODO nf-core: file md5sum was variable, please replace this text with a string found in the file instead ]'
+    - path: output/picard/test.CollectMultipleMetrics.quality_by_cycle_metrics
+      contains: '[ # TODO nf-core: file md5sum was variable, please replace this text with a string found in the file instead ]'
+    - path: output/picard/test.CollectMultipleMetrics.quality_distribution.pdf
+      contains: '[ # TODO nf-core: file md5sum was variable, please replace this text with a string found in the file instead ]'
+    - path: output/picard/test.CollectMultipleMetrics.quality_distribution_metrics
+      contains: '[ # TODO nf-core: file md5sum was variable, please replace this text with a string found in the file instead ]'
+    - path: output/picard/test.CollectMultipleMetrics.read_length_histogram.pdf
+      contains: '[ # TODO nf-core: file md5sum was variable, please replace this text with a string found in the file instead ]'
+
+- 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
+      contains: '[ # TODO nf-core: file md5sum was variable, please replace this text with a string found in the file instead ]'
+    - path: output/picard/test.CollectMultipleMetrics.base_distribution_by_cycle.pdf
+      contains: '[ # TODO nf-core: file md5sum was variable, please replace this text with a string found in the file instead ]'
+    - path: output/picard/test.CollectMultipleMetrics.base_distribution_by_cycle_metrics
+      contains: '[ # TODO nf-core: file md5sum was variable, please replace this text with a string found in the file instead ]'
+    - path: output/picard/test.CollectMultipleMetrics.insert_size_histogram.pdf
+      contains: '[ # TODO nf-core: file md5sum was variable, please replace this text with a string found in the file instead ]'
+    - path: output/picard/test.CollectMultipleMetrics.insert_size_metrics
+      contains: '[ # TODO nf-core: file md5sum was variable, please replace this text with a string found in the file instead ]'
+    - path: output/picard/test.CollectMultipleMetrics.quality_by_cycle.pdf
+      contains: '[ # TODO nf-core: file md5sum was variable, please replace this text with a string found in the file instead ]'
+    - path: output/picard/test.CollectMultipleMetrics.quality_by_cycle_metrics
+      contains: '[ # TODO nf-core: file md5sum was variable, please replace this text with a string found in the file instead ]'
+    - path: output/picard/test.CollectMultipleMetrics.quality_distribution.pdf
+      contains: '[ # TODO nf-core: file md5sum was variable, please replace this text with a string found in the file instead ]'
+    - path: output/picard/test.CollectMultipleMetrics.quality_distribution_metrics
+      contains: '[ # TODO nf-core: file md5sum was variable, please replace this text with a string found in the file instead ]'
+    - path: output/picard/test.CollectMultipleMetrics.read_length_histogram.pdf
+      contains: '[ # TODO nf-core: file md5sum was variable, please replace this text with a string found in the file instead ]'