Fixed tag in end-to-end-se.yml for the ont test run. Added a manual p…

…arameter for data being ONT. Added adapters to the ONT file so it doesn't break.

.github/workflows/end-to-end-se.yml

@@ -32,4 +32,4 @@ jobs:
         run: nf-test test --tag run_dev_se --verbose
 
       - name: Run run_dev_se workflow on ONT data
-        run: nf-test test --tag run_dev_se_ont --verbose
+        run: nf-test test --tag run_dev_ont --verbose

configs/run.config

@@ -5,6 +5,9 @@
 params {
     mode = "run"
 
+    // Sequencing platform
+    ont = false // Whether the sequencing is ONT (true) or Illumina (false)
+
     // Directories
     base_dir = "s3://nao-mgs-wb/test-batch" // Parent for working and output directories (can be S3)
     ref_dir = "s3://nao-mgs-wb/index/20241209/output" // Reference/index directory (generated by index workflow)

configs/run_dev_se.config

@@ -5,6 +5,9 @@
 params {
     mode = "run_dev_se"
 
+    // Sequencing platform
+    ont = false // Whether the sequencing is ONT (true) or Illumina (false)
+
     // Directories
     base_dir = "s3://nao-mgs-simon/test_single_read" // Parent for working and output directories (can be S3)
     ref_dir = "s3://nao-mgs-wb/index/20241209/output" // Reference/index directory (generated by index workflow)

test-data/nextflow.config

@@ -5,12 +5,13 @@
 params {
     mode = "run"
 
+    // Sequencing platform
+    ont = false // Whether the sequencing is ONT (true) or Illumina (false)
+
     // Directories
     base_dir = "s3://nao-mgs-wb/test-batch" // Parent for working and output directories (can be S3)
     ref_dir = "s3://nao-mgs-wb/index/20241209/output" // Reference/index directory (generated by index workflow)
 
-
-
     // Files
     sample_sheet = "${launchDir}/samplesheet.csv" // Path to library TSV
     adapters = "${projectDir}/ref/adapters.fasta" // Path to adapter file for adapter trimming

tests/run_dev_ont.config

@@ -5,12 +5,16 @@
 params {
     mode = "run_dev_se"
 
+    // Sequencing platform
+    ont = true // Whether the sequencing is ONT (true) or Illumina (false)
+
     // Directories
     base_dir = "./" // Parent for working and output directories (can be S3)
     ref_dir = "s3://nao-testing/index-test/output" // Reference/index directory (generated by index workflow)
 
     // Files
     sample_sheet = "${projectDir}/test-data/ont-samplesheet.csv" // Path to library TSV
+    adapters = "${projectDir}/ref/adapters.fasta" // Path to adapter file for adapter trimming. Not used for ONT.
 
     // Numerical
     human_read_filtering = true // Whether to filter human reads

tests/run_dev_se.config

@@ -5,6 +5,9 @@
 params {
     mode = "run_dev_se"
 
+    // Sequencing platform
+    ont = false // Whether the sequencing is ONT (true) or Illumina (false)
+
     // Directories
     base_dir = "./" // Parent for working and output directories (can be S3)
     ref_dir = "s3://nao-testing/index-test/output" // Reference/index directory (generated by index workflow)