From 8a5b1de1074b44fb1fea816761320c72418e8cb6 Mon Sep 17 00:00:00 2001
From: Robrecht Cannoodt <rcannood@gmail.com>
Date: Wed, 17 Jul 2024 12:57:09 +0200
Subject: [PATCH] update wf

---
 resources_test/params.yaml    |  5 +++++
 src/template/workflow/main.nf | 24 +++++++++++++++++++-----
 2 files changed, 24 insertions(+), 5 deletions(-)
 create mode 100644 resources_test/params.yaml

diff --git a/resources_test/params.yaml b/resources_test/params.yaml
new file mode 100644
index 0000000..13c3627
--- /dev/null
+++ b/resources_test/params.yaml
@@ -0,0 +1,5 @@
+param_list:
+  - id: file1
+    input: resources_test/file1.tsv
+  - id: file2
+    input: resources_test/file2.tsv
\ No newline at end of file
diff --git a/src/template/workflow/main.nf b/src/template/workflow/main.nf
index 4c8069a..4ee4f93 100644
--- a/src/template/workflow/main.nf
+++ b/src/template/workflow/main.nf
@@ -5,12 +5,16 @@ workflow run_wf {
   main:
     output_ch = input_ch
 
+      | view{"input: $it"}
+
       // Remove comments from each TSV input file
       | remove_comments.run(
         fromState: [ input: "input" ],
         toState: [ output: "output" ]
       )
 
+      | view{"after remove_comments: $it"}
+
       // Extract a single column from each TSV
       // The column to extract is specified in the sample sheet
       | take_column.run(
@@ -21,26 +25,36 @@ workflow run_wf {
         toState: [ output: "output" ]
       )
 
+      | view{"after take_column: $it"}
+
       // Combine the given tuples into one
       | toSortedList
 
-      | map { list ->
+      | map { state_list ->
         def new_id = "combined"
         def new_state = [
-          input = list.collect{ id, state -> state.output },
-          _meta: [ join_id: list[0][1] ]
+          input: state_list.collect{ id, state -> state.output },
+          _meta: [ join_id: state_list[0][0] ]
         ]
         [ new_id, new_state ]
       }
 
+      | view{"before combine_columns: $it"}
+
       // Concatenate TSVs into one
       // and prep the output state.
       | combine_columns.run(
         auto: [ publish: true ],
-        fromState: [ input: "output" ],
-        toState: { id, result, state -> result }
+        fromState: [ input: "input" ],
+        toState: ["output": "output"]
       )
 
+      | view{"after combine_columns: $it"}
+
+      // make sure the output state only contains
+      // a value called 'output' and '_meta'
+      | setState(["output", "_meta"])
+
   emit:
     output_ch
 }
\ No newline at end of file