uploading saplesheet

mskcc-omics-workflows · Aug 20, 2024 · 6e99e68 · 6e99e68
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commit 6e99e68
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diff --git a/tests/resources/stub/duplex.bai b/tests/resources/stub/duplex.bai
diff --git a/tests/resources/stub/duplex.bam b/tests/resources/stub/duplex.bam
diff --git a/tests/resources/stub/genome.dict b/tests/resources/stub/genome.dict
diff --git a/tests/resources/stub/genome.fasta b/tests/resources/stub/genome.fasta
diff --git a/tests/resources/stub/genome.fasta.fai b/tests/resources/stub/genome.fasta.fai
diff --git a/tests/resources/stub/simplex.bai b/tests/resources/stub/simplex.bai
diff --git a/tests/resources/stub/simplex.bam b/tests/resources/stub/simplex.bam
diff --git a/tests/resources/stub/standard.bam b/tests/resources/stub/standard.bam
diff --git a/tests/resources/stub/stub_aux_bams.csv b/tests/resources/stub/stub_aux_bams.csv
@@ -0,0 +1,6 @@
+sample_id,normal_path,duplex_path,simplex_path,type
+sample1,${projectDir}/tests/resources/v1.0/stub/standard.bam,null,null,TYPE
+sample2,null,${projectDir}/tests/resources/v1.0/stub/duplex.bam,${projectDir}/tests/resources/v1.0/stub/simplex.bam,TYPE
+sample3,null,${projectDir}/tests/resources/v1.0/stub/duplex.bam,${projectDir}/tests/resources/v1.0/stub/simplex.bam,TYPE
+sample4,${projectDir}/tests/resources/v1.0/stub/standard.bam,null,null,TYPE
+
diff --git a/tests/resources/stub/stub_pipeline_input.csv b/tests/resources/stub/stub_pipeline_input.csv
@@ -0,0 +1,3 @@
+patient_id,sample_id,type,maf,standard_bam,standard_bai,duplex_bam,duplex_bai,simplex_bam,simplex_bai
+null,sample1,CASE,null,null,null,${projectDir}/tests/resources/v1.0/stub/duplex.bam,${projectDir}/tests/resources/v1.0/stub/duplex.bai,${projectDir}/tests/resources/v1.0/stub/simplex.bam,${projectDir}/tests/resources/v1.0/stub/simplex.bai
+null,sample2,CONTROL,null,null,null,${projectDir}/tests/resources/v1.0/stub/duplex.bam,${projectDir}/tests/resources/v1.0/stub/duplex.bai,${projectDir}/tests/resources/v1.0/stub/simplex.bam,${projectDir}/tests/resources/v1.0/stub/simplex.bai
diff --git a/tests/resources/stub/stub_rules.json b/tests/resources/stub/stub_rules.json
@@ -0,0 +1,23 @@
+[
+    {
+        "Tag_Column_Name": "null",
+        "Hugo_Symbol": "null",
+        "Variant_Classification": ["null", "null", "null", "null", "null", "null", "null", "null", "null", "null"],
+        "Start_Position": "null",
+        "End_Position": "null"
+    },
+    {
+        "Tag_Column_Name": "null",
+        "Hugo_Symbol": ["null"],
+        "Variant_Classification": ["null", "null"],
+        "Start_Position": 1,
+        "End_Position": 2
+    },
+    {
+        "Tag_Column_Name": "null",
+        "Hugo_Symbol": ["null"],
+        "Variant_Classification": ["null"],
+        "Start_Position": "null",
+        "End_Position": "null"
+    }
+]
diff --git a/tests/resources/stub/test.bed b/tests/resources/stub/test.bed
diff --git a/tests/resources/stub/test2.bed b/tests/resources/stub/test2.bed