Fix formatting

Author: vdauwera

docs/side_quests/metadata.md

@@ -870,53 +870,53 @@ Applying this pattern in your own work will enable you to build robust, maintain
 
 ### Key patterns
 
-1.  **Reading and Structuring Metadata:** Reading CSV files and creating organized metadata maps that stay associated with your data files.
-
-    ```groovy
-    channel.fromPath('samplesheet.csv')
-      .splitCsv(header: true)
-      .map { row ->
-          [ [id:row.id, character:row.character], row.recording ]
-      }
-    ```
+1. **Reading and Structuring Metadata:** Reading CSV files and creating organized metadata maps that stay associated with your data files.
 
-2.  **Expanding Metadata During Workflow** Adding new information to your metadata as your pipeline progresses by adding process outputs and deriving values through conditional logic
+   ```groovy
+   channel.fromPath('samplesheet.csv')
+     .splitCsv(header: true)
+     .map { row ->
+         [ [id:row.id, character:row.character], row.recording ]
+     }
+   ```
 
-    - Adding new keys based on process output
+2. **Expanding Metadata During Workflow** Adding new information to your metadata as your pipeline progresses by adding process outputs and deriving values through conditional logic
 
-    ```groovy
-    .map { meta, file, lang ->
-      [ meta + [lang:lang], file ]
-    }
-    ```
+   - Adding new keys based on process output
 
-    - Adding new keys using a conditional clause
+   ```groovy
+   .map { meta, file, lang ->
+     [ meta + [lang:lang], file ]
+   }
+   ```
 
-    ```groovy
-    .map{ meta, file ->
-        if ( meta.lang.equals("de") || meta.lang.equals('en') ){
-            lang_group = "germanic"
-        } else if ( meta.lang in ["fr", "es", "it"] ) {
-            lang_group = "romance"
-        } else {
-            lang_group = "unknown"
-        }
-    }
-    ```
+   - Adding new keys using a conditional clause
 
-3.  **Customizing Process Behavior:** Using metadata to adapt how processes handle different files
+   ```groovy
+   .map{ meta, file ->
+       if ( meta.lang.equals("de") || meta.lang.equals('en') ){
+           lang_group = "germanic"
+       } else if ( meta.lang in ["fr", "es", "it"] ) {
+           lang_group = "romance"
+       } else {
+           lang_group = "unknown"
+       }
+   }
+   ```
 
-    - Using meta values in Process Directives
+3. **Customizing Process Behavior:** Using metadata to adapt how processes handle different files
 
-    ```groovy
-    publishDir "results/${meta.lang_group}", mode: 'copy'
-    ```
+   - Using meta values in Process Directives
 
-    - Adapting tool parameters for individual files
+   ```groovy
+   publishDir "results/${meta.lang_group}", mode: 'copy'
+   ```
 
-    ```groovy
-    cat $input_file | cowpy -c ${meta.character} > cowpy-${input_file}
-    ```
+   - Adapting tool parameters for individual files
+
+   ```groovy
+   cat $input_file | cowpy -c ${meta.character} > cowpy-${input_file}
+   ```
 
 ### Additional resources
 

docs/side_quests/splitting_and_grouping.md

@@ -1110,7 +1110,7 @@ Mastering these channel operations will enable you to build flexible, scalable p
 
 ### Key patterns
 
-1. **Creating structured input data**: Starting from a CSV file with meta maps (building on patterns from [Metadata in workflows](./metadata.md))
+1. **Creating structured input data:** Starting from a CSV file with meta maps (building on patterns from [Metadata in workflows](./metadata.md))
 
    ```groovy
    ch_samples = channel.fromPath("./data/samplesheet.csv")
@@ -1120,14 +1120,13 @@ Mastering these channel operations will enable you to build flexible, scalable p
        }
    ```
 
-2. **Splitting data into separate channels**: We used `filter` to divide data into independent streams based on the `type` field
+2. **Splitting data into separate channels:** We used `filter` to divide data into independent streams based on the `type` field
 
    ```groovy
-   // Filter channel based on condition
    channel.filter { it.type == 'tumor' }
    ```
 
-3. **Joining matched samples**: We used `join` to recombine related samples based on `id` and `repeat` fields
+3. **Joining matched samples:** We used `join` to recombine related samples based on `id` and `repeat` fields
 
    - Join two channels by key (first element of tuple)
 
@@ -1153,33 +1152,32 @@ Mastering these channel operations will enable you to build flexible, scalable p
        )
    ```
 
-4. **Distributing across intervals**: We used `combine` to create Cartesian products of samples with genomic intervals for parallel processing
+4. **Distributing across intervals:** We used `combine` to create Cartesian products of samples with genomic intervals for parallel processing
 
    ```groovy
    samples_ch.combine(intervals_ch)
    ```
 
-5. **Aggregating by grouping keys**: We used `groupTuple` to group by the first element in each tuple, thereby collecting samples sharing `id` and `interval` fields and merging technical replicates
+5. **Aggregating by grouping keys:** We used `groupTuple` to group by the first element in each tuple, thereby collecting samples sharing `id` and `interval` fields and merging technical replicates
 
    ```groovy
-   //
    channel.groupTuple()
    ```
 
-- **Optimizing the data structure:** We used `subMap` to extract specific fields and created a named closure for making transformations reusable
+6. **Optimizing the data structure:** We used `subMap` to extract specific fields and created a named closure for making transformations reusable
 
-  - Extract specific fields from a map
+   - Extract specific fields from a map
 
-  ```groovy
-  meta.subMap(['id', 'repeat'])
-  ```
+   ```groovy
+   meta.subMap(['id', 'repeat'])
+   ```
 
-  - Named closure for reusable transformations
+   - Named closure for reusable transformations
 
-  ```groovy
-  getSampleIdAndReplicate = { meta, file -> [meta.subMap(['id', 'repeat']), file] }
-  channel.map(getSampleIdAndReplicate)
-  ```
+   ```groovy
+   getSampleIdAndReplicate = { meta, file -> [meta.subMap(['id', 'repeat']), file] }
+   channel.map(getSampleIdAndReplicate)
+   ```
 
 ## Additional resources