Merge pull request #4675 from khaled196/freec

update the control freec tutorial

topics/variant-analysis/tutorials/somatic-variant-discovery/workflows/Somatic-Variant-Discovery-from-WES-Data-Using-Control-FREEC-tests.yml

@@ -0,0 +1,47 @@
+- doc: Test outline for Somatic-Variant-Discovery-from-WES-Data-Using-Control-FREEC
+  job:
+    Normal_r1.fastq.gz:
+      class: File
+      path: test-data/Normal_r1.fastq.gz.fastqsanger.gz
+      filetype: fastqsanger.gz
+    Normal_r2.fastq.gz:
+      class: File
+      path: test-data/Normal_r2.fastq.gz.fastqsanger.gz
+      filetype: fastqsanger.gz
+    Tumor_r1.fastq.gz:
+      class: File
+      path: test-data/Tumor_r1.fastq.gz.fastqsanger.gz
+      filetype: fastqsanger.gz
+    Tumor_r2.fastq.gz:
+      class: File
+      path: test-data/Tumor_r2.fastq.gz.fastqsanger.gz
+      filetype: fastqsanger.gz
+    capture_targets_chr5_12_17.bed:
+      class: File
+      path: test-data/capture_targets_chr5_12_17.bed.bed
+      filetype: bed
+  outputs:
+    out_ratio_log2_circos:
+      path: test-data/out_ratio_log2_circos.tabular
+    out_chr_sorted_circos:
+      path: test-data/out_chr_sorted_circos.tabular
+    out_gc_profile:
+      path: test-data/out_gc_profile.tabular
+    out_mg_log2_png:
+      path: test-data/out_mg_log2_png.png
+    out_mg_png:
+      path: test-data/out_mg_png.png
+    out_sample_subclones:
+      path: test-data/out_sample_subclones.txt
+    out_sample_ratio:
+      path: test-data/out_sample_ratio.tabular
+    out_sample_info:
+      path: test-data/out_sample_info.txt
+    out_sample_coord:
+      path: test-data/out_sample_coord.tabular
+    out_control_raw:
+      path: test-data/out_control_raw.tabular
+    out_sample_raw:
+      path: test-data/out_sample_raw.tabular
+    output_png:
+      path: test-data/output_png.png