Metadata Training

docs/side_quests/index.md

@@ -29,6 +29,8 @@ Otherwise, select a side quest from the menu below.
 ## Menu of Side Quests
 
 - [Introduction to nf-core](./nf-core.md)
+- [Metadata](./metadata.md)
+- [Splitting and Grouping](./splitting_and_grouping.md)
 - [Testing with nf-test](./nf-test.md)
 - [Workflows of workflows](./workflows_of_workflows.md)
 

docs/side_quests/orientation.md

@@ -24,9 +24,11 @@ If you run this inside `side-quests`, you should see the following output:
 
 ```console title="Directory contents"
 .
+├── metadata
 ├── nf-core
 ├── nf-test
 ├── solutions
+├── splitting_and_grouping
 └── workflows_of_workflows
 ```
 

mkdocs.yml

@@ -39,10 +39,12 @@ nav:
   - Side Quests:
       - side_quests/index.md
       - side_quests/orientation.md
-      - side_quests/workflows_of_workflows.md
-      - side_quests/splitting_and_grouping.md
+      - side_quests/metadata.md
       - side_quests/nf-test.md
       - side_quests/nf-core.md
+      - side_quests/splitting_and_grouping.md
+      - side_quests/workflows_of_workflows.md
+
   - Fundamentals Training:
       - basic_training/index.md
       - basic_training/orientation.md

side-quests/metadata/data/bonjour.txt

@@ -0,0 +1,2 @@
+Bonjour
+Salut, à demain

side-quests/metadata/data/ciao.txt

@@ -0,0 +1,2 @@
+Ciao
+Ci vediamo domani

side-quests/metadata/data/guten_tag.txt

@@ -0,0 +1,2 @@
+Guten Tag, wie geht es dir?
+Auf Wiedersehen, bis morgen

side-quests/metadata/data/hallo.txt

@@ -0,0 +1,2 @@
+Hallo
+Tschüss, bis morgen

side-quests/metadata/data/hello.txt

@@ -0,0 +1,2 @@
+Hello
+Bye, see you tomorrow

side-quests/metadata/data/hola.txt

@@ -0,0 +1,2 @@
+Hola
+Adiós, hasta mañana

side-quests/metadata/data/salut.txt

@@ -0,0 +1,2 @@
+Salut, ça va?
+à plus dans le bus

side-quests/metadata/data/samplesheet.csv

@@ -0,0 +1,8 @@
+id,character,recording
+sampleA,squirrel,/workspaces/training/side-quests/metadata/data/bonjour.txt
+sampleB,tux,/workspaces/training/side-quests/metadata/data/guten_tag.txt
+sampleC,sheep,/workspaces/training/side-quests/metadata/data/hallo.txt
+sampleD,turkey,/workspaces/training/side-quests/metadata/data/hello.txt
+sampleE,stegosaurus,/workspaces/training/side-quests/metadata/data/hola.txt
+sampleF,moose,/workspaces/training/side-quests/metadata/data/salut.txt
+sampleG,turtle,/workspaces/training/side-quests/metadata/data/ciao.txt

side-quests/metadata/main.nf

@@ -0,0 +1,3 @@
+workflow  {
+
+}

side-quests/metadata/nextflow.config

@@ -0,0 +1 @@
+docker.enabled=true

side-quests/solutions/metadata/main.nf

@@ -0,0 +1,68 @@
+/*
+ * Use langid to predict the language of each input file
+ */
+process IDENTIFY_LANGUAGE {
+
+    container 'community.wave.seqera.io/library/pip_langid:b2269f456a5629ff'
+
+    input:
+    tuple val(meta), path(file)
+
+    output:
+    tuple val(meta), stdout
+
+    script:
+    """
+    langid < ${greeting} -l en,de,fr,es,it | sed -E "s/.*\\('([a-z]+)'.*/\\1/" | tr -d '\\n'
+    """
+
+}
+
+/*
+ * Generate ASCII art with cowpy
+*/
+process COWPY {
+
+    publishDir "results/${meta.lang}", mode: 'copy'
+
+    container 'community.wave.seqera.io/library/cowpy:1.1.5--3db457ae1977a273'
+
+    input:
+    tuple val(meta), path(file)
+
+    output:
+    tuple val(meta), path("cowpy-${file}")
+
+    script:
+    """
+    cat $file | cowpy -c ${meta.character} > cowpy-${file}
+    """
+
+}
+
+workflow  {
+
+    ch_samplesheet = Channel.fromPath("./data/samplesheet.csv")
+                    .splitCsv(header: true)
+                    .map { row ->
+                        [ [id:row.id, character:row.character], row.recording ]
+                    }
+
+    ch_prediction = IDENTIFY_LANGUAGE(ch_samplesheet)
+
+    ch_languages = ch_samplesheet.join(ch_prediction)
+                                .map { meta, file, lang ->
+                                    [ meta + [lang:lang], file ]
+                                }
+                                .map{ meta, file ->
+                                    def lang_group = (meta.lang.equals('de') || meta.lang.equals('en')) ? 'germanic' : 'romanic'
+                                    [ meta + [lang_group:lang_group], file ]
+                                }
+
+    romanic_languages = ch_languages.filter { meta, file ->
+                                        meta.lang_group == 'romanic'
+                                    }
+
+    COWPY(romanic_languages)
+
+}

side-quests/solutions/metadata/nextflow.config

@@ -0,0 +1 @@
+docker.enabled=true