update scripts and configs

src/template/combine_columns/config.vsh.yaml

@@ -7,11 +7,14 @@ arguments:
     type: file
     multiple: true
     required: true
+    example: [ resources_test/file1.tsv, resources_test/file2.tsv ]
+
   - name: "--output"
     alternatives: [ "-o" ]
     type: file
     required: true
     direction: output
+    example: output.tsv
 
 resources:
   - type: r_script

src/template/combine_columns/script.R

@@ -1,8 +1,8 @@
 
 ## VIASH START
 par <- list(
-    input = c("data/file1.tsv", "data/file2.tsv"),
-    output = "temp/foo.tsv"
+  input = c("resources_test/file1.tsv", "resources_test/file2.tsv"),
+  output = "temp/foo.tsv"
 )
 ## VIASH END
 

src/template/remove_comments/config.vsh.yaml

@@ -6,7 +6,7 @@ arguments:
     alternatives: [ "-i" ]
     type: file
     required: true
-    example: "file.tsv"
+    example: "resources_test/file1.tsv"
   - name: "--output"
     alternatives: [ "-o" ]
     type: file

src/template/remove_comments/script.sh

@@ -1,3 +1,3 @@
 #!/bin/bash
 
-grep -v '^#' "$par_input" > "$par_output"
+grep -v '^#' "$par_input" > "$par_output"

src/template/remove_comments/test.sh

@@ -2,6 +2,8 @@
 
 echo "Generate test tsv content"
 
+
+
 echo ">>> Running tests with only comments"
 
 cat > file1.tsv <<EOF
@@ -11,31 +13,38 @@ cat > file1.tsv <<EOF
 # contains comments
 EOF
 
-./$meta_functionality_name -i file1.tsv -o output1.tsv
+$meta_executable -i file1.tsv -o output1.tsv
 
 [[ ! -f output1.tsv ]] && echo "It seems no output is generated" && exit 1
 [[ ! `sed -n '$=' output1.tsv` == "" ]] && echo "All lines should be filtered out" && exit 1
 
+
+
+
 echo ">>> Running tests with no comments"
 
 cat > file2.tsv <<EOF
 This file contains
 no comments no
 EOF
 
-./$meta_functionality_name -i file2.tsv -o output2.tsv
+$meta_executable -i file2.tsv -o output2.tsv
 
 [[ ! -f output2.tsv ]] && echo "It seems no output is generated" && exit 1
 [[ ! `sed -n '$=' output2.tsv` == 2 ]] && echo "No lines should be filtered out" && exit 1
 
+
+
+
+
 echo ">>> Running tests mixed"
 
 cat > file3.tsv <<EOF
 # This file contains
 no comments no
 EOF
 
-./$meta_functionality_name -i file3.tsv -o output3.tsv
+$meta_executable -i file3.tsv -o output3.tsv
 
 [[ ! -f output3.tsv ]] && echo "It seems no output is generated" && exit 1
 [[ ! `sed -n '$=' output3.tsv` == 1 ]] && echo "No lines should be filtered out" && exit 1

src/template/take_column/config.vsh.yaml

@@ -6,11 +6,15 @@ arguments:
     alternatives: [ "-i" ]
     type: file
     required: true
+    example: "resources_test/file1.tsv"
+
   - name: "--output"
     alternatives: [ "-o" ]
     type: file
     required: true
     direction: output
+    example: path/to/output.tsv
+
   - name: "--column"
     type: integer
     required: false

src/template/take_column/script.py

@@ -2,9 +2,9 @@
 
 ## VIASH START
 par = {
-    "input": "data/file1.tsv",
-    "column": 2,
-    "output": "temp/foo"
+  "input": "resources_test/file1.tsv",
+  "column": 2,
+  "output": "temp/foo"
 }
 ## VIASH END
 
@@ -15,4 +15,4 @@
 tab_filt = tab.iloc[:, par["column"]-1]
 
 # write to file
-tab_filt.to_csv(par["output"], index=False)
+tab_filt.to_csv(par["output"], index=False)

src/template/workflow/config.vsh.yaml

@@ -12,12 +12,14 @@ arguments:
     type: file
     required: true
     description: Input TSV file
-    example: file1.tar.gz 
+    example: resources_test/file1.tsv
+
   - name: "--column"
     type: integer
     required: false
     default: 2
     description: The column index to extract from the TSV input file
+
   - name: "--output"
     alternatives: [ "-o" ]
     type: file

src/template/workflow/main.nf

@@ -5,52 +5,71 @@ workflow run_wf {
   main:
     output_ch = input_ch
 
-      | view{"input: $it"}
-
-      // Remove comments from each TSV input file
+      /*
+        Remove comments from each TSV input file
+        
+        Example of an element in the channel at this stage:
+        
+          [ "myid", [ input: "path/to/input.tsv", column: 3 ] ]
+      */
       | remove_comments.run(
         fromState: [ input: "input" ],
-        toState: [ output: "output" ]
+        toState: [ data_comments_removed: "output" ]
       )
 
-      | view{"after remove_comments: $it"}
-
-      // Extract a single column from each TSV
-      // The column to extract is specified in the sample sheet
+      /*
+        Extract a single column from each TSV
+        
+        Example of an element in the channel at this stage:
+        
+          [
+            "myid",
+            [
+              input: "path/to/input.tsv",
+              column: 3,
+              data_comments_removed: "work/path/to/output.tsv"
+            ]
+          ]
+      */
       | take_column.run(
         fromState: [
-          input: "output",
+          input: "data_comments_removed",
           column: "column"
         ],
-        toState: [ output: "output" ]
+        toState: [ data_one_column: "output" ]
       )
 
-      | view{"after take_column: $it"}
-
       // Combine the given tuples into one
       | toSortedList
 
       | map { state_list ->
         def new_id = "combined"
         def new_state = [
-          input: state_list.collect{ id, state -> state.output },
+          input: state_list.collect{ id, state -> state.data_one_column },
+          // store the original id in the _meta field
           _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 the TSV files into one
+        
+        Example of an element in the channel at this stage:
+        
+          [
+            "combined",
+            [
+              input: [ "path/to/output1.tsv", "path/to/output2.tsv" ],
+              _meta: [ join_id: "myid" ]
+            ]
+          ]
+      */
       | combine_columns.run(
-        auto: [ publish: true ],
         fromState: [ input: "input" ],
-        toState: ["output": "output"]
+        toState: [ output: "output" ]
       )
 
-      | view{"after combine_columns: $it"}
-
       // make sure the output state only contains
       // a value called 'output' and '_meta'
       | setState(["output", "_meta"])