udpate tutorial example config files

databio · Nov 6, 2021 · d48b089 · d48b089
1 parent 7767404
commit d48b089
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diff --git a/examples/meta/tutorial.csv b/examples/meta/tutorial.csv
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+sample_name,organism,protocol,read_type,read1,read2
+tutorial,human,PROSEQ,paired,R1,R2
diff --git a/examples/meta/tutorial.yaml b/examples/meta/tutorial.yaml
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+# Run tutorial samples through PEPPRO
+name: tutorial
+
+pep_version: 2.0.0
+sample_table: "tutorial.csv"
+
+looper:
+  output_dir: "$PROCESSED/tutorial"  # export PROCESSED="/path/to/your_output_folder/"
+  pipeline_interfaces: ["$CODEBASE/peppro/project_pipeline_interface.yaml"]  # export CODEBASE="/path/to/your_tools_folder/"
+
+sample_modifiers:
+  append:
+    pipeline_interfaces: ["$CODEBASE/peppro/sample_pipeline_interface.yaml"] 
+  derive:
+    attributes: [read1, read2]
+    sources:
+        R1: "$CODEBASE/peppro/examples/data/{sample_name}_r1.fq.gz"
+        R2: "$CODEBASE/peppro/examples/data/{sample_name}_r2.fq.gz"
+  imply:
+    - if:
+        organism: ["human", "Homo sapiens", "Human", "Homo_sapiens"]
+      then:
+        genome: "hg38"
+        prealignments: ["human_rDNA", "rCRSd"]
Original file line number	Diff line number	Diff line change
		@@ -0,0 +1,2 @@
		sample_name,organism,protocol,read_type,read1,read2
		tutorial,human,PROSEQ,paired,R1,R2