From 06ea767aef642b8167d78521b11a012b955d4f59 Mon Sep 17 00:00:00 2001
From: Samuel Lampa <samuel.lampa@scilifelab.se>
Date: Tue, 5 Nov 2024 11:20:40 +0100
Subject: [PATCH] Format ci.yml file

---
 .github/workflows/ci.yml | 30 ++++++++++++++++--------------
 1 file changed, 16 insertions(+), 14 deletions(-)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index 353def6..be9e0d8 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -1,6 +1,6 @@
 name: CI
 # This workflow runs the pipeline with the minimal test dataset to check that
-# it completes without any syntax errors
+# it completes without errors
 on:
   push:
     branches:
@@ -61,19 +61,21 @@ jobs:
         run:
           df -h
 
-          #- name: Run pipeline with test data
-          #  run: |
-          #    nextflow  \
-          #      -log $(pwd)/nextflow.log \
-          #      run main.nf \
-          #      --outdir results \
-          #      --db $(pwd)/assets/databases/emu_database \
-          #      --seqtype map-ont \
-          #       -profile singularity,test \
-          #      --quality_filtering \
-          #      --longread_qc_qualityfilter_minlength 1200 \
-          #      --longread_qc_qualityfilter_maxlength 1800 \
-          #      --merge_fastq_pass $(pwd)/assets/test_assets/ci; \
+      # The below snippet is kept for now, if for debugging purposes you would
+      # want to run a test pipeline without nf-test
+      #- name: Run pipeline with test data
+      #  run: |
+      #    nextflow  \
+      #      -log $(pwd)/nextflow.log \
+      #      run main.nf \
+      #      --outdir results \
+      #      --db $(pwd)/assets/databases/emu_database \
+      #      --seqtype map-ont \
+      #       -profile singularity,test \
+      #      --quality_filtering \
+      #      --longread_qc_qualityfilter_minlength 1200 \
+      #      --longread_qc_qualityfilter_maxlength 1800 \
+      #      --merge_fastq_pass $(pwd)/assets/test_assets/ci; \
 
       - name: Run nf-test
         run: |