Use clusters instead of yield for rnafusion

.github/workflows/prek.yml

@@ -0,0 +1,12 @@
+name: Lint code
+on:
+  push:
+  pull_request:
+
+jobs:
+  prek:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v3
+      - uses: actions/setup-python@v3
+      - uses: pre-commit/action@v3.0.0

.gitignore

@@ -13,6 +13,7 @@ results
 *.yml
 !src/main/resources/**/*.yml
 !src/main/resources/**/*.yaml
+!.github/workflows/**.yml
 DONE
 !tests/*/*.yaml
 .nf-test*

src/main/resources/worksheets/nfcmgg_preprocessing.yml

@@ -78,12 +78,12 @@ output:
 # - id: The name of the field in the matched file that should be used as the identifier for the metric.
 # - field: The name of the field in the matched file that should be used as the value for the metric.
 metrics:
-  yield:
+  clusters:
     pattern: ".*_SAV_data$"
     subpath: "multiqc_bclconvert_bysample.txt"
     filetype: tsv
     id: Sample
-    field: yield_
+    field: clusters
 # Define which samplesheets that should be generated and what their content is.
 # This is structured as a list of maps, where each map contains the following keys:
 # - name: The name of the YAML samplesheet to generate
@@ -126,14 +126,14 @@ samplesheets:
       && data.tag?.toLowerCase() == 'rnaseqmdg'
       && data.fastq_1 != null
     filter_func: |
-      data.yield?.toLong() >= 1000000L
+      data.clusters?.toLong() >= 1000000L
     fields:
       sample:
       fastq_1:
       fastq_2:
       strandedness:
       reads:
-        source: yield
+        source: clusters
   - name: nfcmgg_vivar_samplesheet.yaml
     description: The samplesheet for the nf-cmgg/vivar pipeline
     include_func: |

tests/preprocessing_mock/main.nf

@@ -74,7 +74,7 @@ process MOCK_OUTPUT {
 
     # Creating SAV data
     mkdir multiqc_SAV_data
-    echo "Sample\tyield_" > multiqc_SAV_data/multiqc_bclconvert_bysample.txt
+    echo "Sample\tclusters" > multiqc_SAV_data/multiqc_bclconvert_bysample.txt
     ${sav_data}
     """
 }