Fix up cutadapt tests

.github/workflows/cutadapt.yml

@@ -7,10 +7,11 @@ on:
 jobs:
   run_ci_test:
     runs-on: ubuntu-latest
-
+    env:
+      NXF_ANSI_LOG: false
     steps:
-      # Check out the repository
       - uses: actions/checkout@v2
+
       - name: Checkout submodules
         shell: bash
         run: |
@@ -25,10 +26,10 @@ jobs:
 
       - name: Test module with paired-end data
         run: |
-          cd software/cutadapt/test_paired/
-          nextflow run . -ansi-log false
+          cd software/cutadapt/test/
+          nextflow run .
 
       - name: Test module with single-end data
         run: |
-          cd software/cutadapt/test_single/
-          nextflow run . -ansi-log false
+          cd software/cutadapt/test/
+          nextflow run . --single_end

.github/workflows/fastqc.yml

@@ -7,7 +7,8 @@ on:
 jobs:
   run_ci_test:
     runs-on: ubuntu-latest
-
+    env:
+      NXF_ANSI_LOG: false
     steps:
 
     # Check out the repository
@@ -20,4 +21,4 @@ jobs:
         sudo mv nextflow /usr/local/bin/
 
     # Test the module
-    - run: nextflow run ./software/fastqc/test/ -ansi-log false
+    - run: nextflow run ./software/fastqc/test/

.github/workflows/samtools_index.yml

@@ -7,7 +7,8 @@ on:
 jobs:
   run_ci_test:
     runs-on: ubuntu-latest
-
+    env:
+      NXF_ANSI_LOG: false
     steps:
 
     # Check out the repository
@@ -20,4 +21,4 @@ jobs:
         sudo mv nextflow /usr/local/bin/
 
     # Test the module
-    - run: nextflow run ./software/samtools/index/test/ -ansi-log false
+    - run: nextflow run ./software/samtools/index/test/

.github/workflows/samtools_sort.yml

@@ -7,7 +7,8 @@ on:
 jobs:
   run_ci_test:
     runs-on: ubuntu-latest
-
+    env:
+      NXF_ANSI_LOG: false
     steps:
 
     # Check out the repository
@@ -20,4 +21,4 @@ jobs:
         sudo mv nextflow /usr/local/bin/
 
     # Test the module
-    - run: nextflow run ./software/samtools/sort/test/ -ansi-log false
+    - run: nextflow run ./software/samtools/sort/test/

.github/workflows/tcoffee.yml

@@ -7,7 +7,8 @@ on:
 jobs:
   run_ci_test:
     runs-on: ubuntu-latest
-
+    env:
+      NXF_ANSI_LOG: false
     steps:
 
     # Check out the repository
@@ -27,4 +28,4 @@ jobs:
     # Test the module
     - run: |
         cd software/tcoffee/test/
-        nextflow run . -ansi-log false
+        nextflow run .

.github/workflows/trim_galore.yml

@@ -7,7 +7,8 @@ on:
 jobs:
   run_ci_test:
     runs-on: ubuntu-latest
-
+    env:
+      NXF_ANSI_LOG: false
     steps:
 
     # Check out the repository
@@ -20,4 +21,4 @@ jobs:
         sudo mv nextflow /usr/local/bin/
 
     # Test the module
-    - run: nextflow run ./software/trim_galore/test/ -ansi-log false
+    - run: nextflow run ./software/trim_galore/test/

software/cutadapt/test/main.nf

@@ -3,19 +3,18 @@ nextflow.preview.dsl = 2
 include '../main.nf' params(params)
 
 // Define input channels
-paired_end_input = Channel.fromFilePairs('../../../test-datasets/tools/cutadapt/input/*_{1,2}.fastq' )
+input_fastqs = Channel.fromFilePairs('../../../test-datasets/tools/cutadapt/input/*_{1,2}.fastq' )
 
-// TODO: params.single_end is set to false in nextflow config
-// But most of this module is not functional currently anyway....
-single_end_input = Channel.from([
+if(params.single_end){
+    input_fastqs = Channel.from([
             ['SRR4238351', '../../../test-datasets/tools/cutadapt/input/SRR4238351_subsamp.fastq.gz'],
             ['SRR4238355', '../../../test-datasets/tools/cutadapt/input/SRR4238355_subsamp.fastq.gz'],
             ['SRR4238359', '../../../test-datasets/tools/cutadapt/input/SRR4238359_subsamp.fastq.gz'],
             ['SRR4238379', '../../../test-datasets/tools/cutadapt/input/SRR4238379_subsamp.fastq.gz']
         ]).map { row -> [ row[0], [ file(row[1]) ] ] }
+}
 
 // Run the workflow
 workflow {
-    cutadapt(paired_end_input)
-    cutadapt(single_end_input)
+    cutadapt(input_fastqs)
 }