From b2bb786038006e4a56d6821425d4e3f8228376bf Mon Sep 17 00:00:00 2001
From: Kevin Lewis <kl2@sanger.ac.uk>
Date: Thu, 8 Feb 2024 16:48:41 +0000
Subject: [PATCH] first try at adding stage2 preprocessing options

---
 .../vtlib/alignment_wtsi_stage2_template.json | 29 ++++++--------
 data/vtlib/crammerge.json                     | 40 +++++++++++++++++++
 2 files changed, 52 insertions(+), 17 deletions(-)
 create mode 100644 data/vtlib/crammerge.json

diff --git a/data/vtlib/alignment_wtsi_stage2_template.json b/data/vtlib/alignment_wtsi_stage2_template.json
index 306b4f649..e623f5a22 100644
--- a/data/vtlib/alignment_wtsi_stage2_template.json
+++ b/data/vtlib/alignment_wtsi_stage2_template.json
@@ -95,24 +95,19 @@
 ],
 "nodes":[
 	{
-		"id":"crammerge",
-		"type":"EXEC",
-		"use_STDIN": false,
-		"use_STDOUT": true,
-		"cmd": [
-			"samtools",
-			"merge",
-			"-n",
-			"-O", "BAM",
-			"-l", "0",
-			{"select":"s2_input_format", "default":"cram", "select_range":[1], "cases":{
-				"cram":["--input-fmt-option", "no_ref=1"],
-				"bam":["--input-fmt", "bam"]
+		"id":"preprocess_inputs",
+		"type":"VTFILE",
+		"name":{"subst":"s2_preprocess_inputs_method", "required":true,
+			"ifnull":{
+				"select":"s2_ppi_switch", "default":"crammerge","select_range":[1],
+				"cases":{
+					"crammerge":"crammerge.json",
+					"aviti":"elembio_nanoseq_2_pi.json"}
 			}},
-			"-",
-			{"subst":"incrams"}
-		],
-		"description":"merge individual cram files from a sample into one bam file"
+                "subst_map":{"input_format":{"subst":"s2_input_format"}},
+		"comment":"inputs: NONE; outputs: _stdout_ (bam), subst_map_parameters:[input_format]",
+		"node_prefix":"ppi_",
+		"description":"subgraph to preprocess inputs. Default: merge individual cram files from a sample into one bam file"
 	},
 	{
 		"id":"spatial_filter",
diff --git a/data/vtlib/crammerge.json b/data/vtlib/crammerge.json
new file mode 100644
index 000000000..3eeca9a51
--- /dev/null
+++ b/data/vtlib/crammerge.json
@@ -0,0 +1,40 @@
+{
+"version":"2.0",
+"description":"run bwa mem to to align input bam to supplied reference genome",
+"subgraph_io":{
+	"ports":{
+		"inputs":{
+		},
+		"outputs":{
+			"_stdout_":"crammerge"
+		}
+	}
+},
+"subst_params":[],
+"nodes":[
+	{
+		"id":"crammerge",
+		"type":"EXEC",
+		"use_STDIN": false,
+		"use_STDOUT": true,
+		"cmd": [
+			"samtools",
+			"merge",
+			"-n",
+			"-O", "BAM",
+			"-l", "0",
+			{"select":"input_format", "default":"cram", "select_range":[1], "cases":{
+				"cram":["--input-fmt-option", "no_ref=1"],
+				"bam":["--input-fmt", "bam"]
+			}},
+			"-",
+			{"subst":"incrams", "required":true}
+		],
+		"description":"merge individual cram files from a sample into one bam file"
+	}
+],
+"edges":[
+	{ "id":"bamtofastq_to_int_fq", "from":"bamtofastq", "to":"bwa_mem:fq" },
+	{ "id":"bwa_mem_to_s2b", "from":"bwa_mem", "to":"samtobam" }
+]
+}