From 0f5f68df93179f5c51f066dd01ed2c5b9852d7a8 Mon Sep 17 00:00:00 2001
From: simonleandergrimm <simonleandergrimm@gmail.com>
Date: Thu, 16 Jan 2025 00:07:25 +0000
Subject: [PATCH] Fixed tag in end-to-end-se.yml for the ont test run. Added a
 manual parameter for data being ONT. Added adapters to the ONT file so it
 doesn't break.

---
 .github/workflows/end-to-end-se.yml | 2 +-
 configs/run.config                  | 3 +++
 configs/run_dev_se.config           | 3 +++
 test-data/nextflow.config           | 5 +++--
 tests/run_dev_ont.config            | 4 ++++
 tests/run_dev_se.config             | 3 +++
 6 files changed, 17 insertions(+), 3 deletions(-)

diff --git a/.github/workflows/end-to-end-se.yml b/.github/workflows/end-to-end-se.yml
index 66b41924..ac04e944 100644
--- a/.github/workflows/end-to-end-se.yml
+++ b/.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
\ No newline at end of file
+        run: nf-test test --tag run_dev_ont --verbose
\ No newline at end of file
diff --git a/configs/run.config b/configs/run.config
index 09cbd5d3..34777c3a 100644
--- a/configs/run.config
+++ b/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)
diff --git a/configs/run_dev_se.config b/configs/run_dev_se.config
index 7414ea35..58371e4e 100644
--- a/configs/run_dev_se.config
+++ b/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)
diff --git a/test-data/nextflow.config b/test-data/nextflow.config
index 191f7a20..34777c3a 100644
--- a/test-data/nextflow.config
+++ b/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
diff --git a/tests/run_dev_ont.config b/tests/run_dev_ont.config
index 9ab5031d..e36229cc 100644
--- a/tests/run_dev_ont.config
+++ b/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
diff --git a/tests/run_dev_se.config b/tests/run_dev_se.config
index 34b72954..4d7ff50e 100644
--- a/tests/run_dev_se.config
+++ b/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)