✅ Add Picard tests

tests/tasks/picard/collectalignmentsummarymetrics/inputs.json

@@ -0,0 +1,7 @@
+{
+    "alignment": "alignment.cram",
+    "alignment_index": "alignment.cram.crai",
+    "reference_fasta": "reference.fasta",
+    "reference_fasta_index": "reference.fasta.fai",
+    "stub": true
+}

tests/tasks/picard/collectalignmentsummarymetrics/run.sh

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+touch alignment.cram alignment.cram.crai reference.fasta reference.fasta.fai
+
+miniwdl run --task CollectAlignmentSummaryMetrics -i tests/tasks/picard/collectalignmentsummarymetrics/inputs.json tasks/picard/collectalignmentsummarymetrics.wdl

tests/tasks/picard/collectalignmentsummarymetrics/test_collect_alignment_summary_metrics_task.yaml

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+- name: Check if CollectAlignmentSummaryMetrics produces the expected outputs
+  tags:
+  - picard
+  - picard/collectalignmentsummarymetrics
+  command: bash tests/tasks/picard/collectalignmentsummarymetrics/run.sh
+  files:
+  - path: _LAST/out/metrics/alignment_alignment_metrics.txt
+  - path: _LAST/out/version/version.txt

tests/tasks/picard/markduplicates/inputs.json

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+{
+    "input_bams": [
+        "alignment1.bam",
+        "alignment2.bam"
+    ],
+    "output_bam_basename": "MERGED",
+    "metrics_filename": "metrics.txt",
+    "stub": true
+}

tests/tasks/picard/markduplicates/run.sh

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+touch alignment1.bam alignment2.bam
+miniwdl run --task MarkDuplicates -i tests/tasks/picard/markduplicates/inputs.json tasks/picard/markduplicates.wdl

tests/tasks/picard/markduplicates/test_mark_duplicates_task.yaml

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+- name: Check if MarkDuplicates produces the expected outputs
+  tags:
+  - picard
+  - picard/markduplicates
+  command: bash tests/tasks/picard/markduplicates/run.sh
+  files:
+  - path: _LAST/out/output_bam/MERGED.bam
+  - path: _LAST/out/version/version.txt
+  - path: _LAST/outputs.json
+    contains:
+    - '"MarkDuplicates.duplicates": 0.0'