Revert "fix: disable ont actions (#555)"

This reverts commit 56e46ef.
IKIM-Essen · Aug 10, 2022 · f558e2c · f558e2c
1 parent a4951a6
commit f558e2c
Showing 1 changed file with 14 additions and 13 deletions.
diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml
@@ -67,9 +67,7 @@ jobs:
     strategy:
       matrix:
         rule: [all, all -npr]
-        # disable ont actions
-        # technology: [all, illumina, ont, ion]
-        technology: [all, illumina, ion]
+        technology: [all, illumina, ont, ion]
         seq_method: [shotgun, amplicon]
     steps:
       - uses: actions/checkout@v2
@@ -87,9 +85,11 @@ jobs:
           mkdir -p .tests/data
           curl -L https://github.com/thomasbtf/small-kraken-db/raw/master/B.1.1.7.reads.1.fastq.gz > .tests/data/B117.1.fastq.gz
           curl -L https://github.com/thomasbtf/small-kraken-db/raw/master/B.1.1.7.reads.1.fastq.gz > .tests/data/B117.2.fastq.gz
+          curl -L https://github.com/thomasbtf/small-kraken-db/raw/master/ont_reads.fastq.gz > .tests/data/ont_reads.fastq.gz
           curl -L https://github.com/thomasbtf/small-kraken-db/raw/master/ERR5745913.fastq.gz > .tests/data/ion_reads.fastq.gz
           echo sample_name,fq1,fq2,date,is_amplicon_data,technology > .tests/config/pep/samples.csv
           echo illumina-test,data/B117.1.fastq.gz,data/B117.2.fastq.gz,2022-01-01,$AMPLICON,illumina >> .tests/config/pep/samples.csv
+          echo ont-test,data/ont_reads.fastq.gz,,2022-01-01,$AMPLICON,ont >> .tests/config/pep/samples.csv
           echo ion-test,data/ion_reads.fastq.gz,,2022-01-01,$AMPLICON,ion >> .tests/config/pep/samples.csv
       - name: Prepare test data for Illumina
         if: steps.test-data.outputs.cache-hit != true && (startsWith(matrix.rule, 'all') && matrix.technology == 'illumina' || matrix.rule == 'compare_assemblers')
@@ -100,14 +100,14 @@ jobs:
           curl -L https://github.com/thomasbtf/small-kraken-db/raw/master/B.1.1.7.reads.1.fastq.gz > .tests/data/B117.2.fastq.gz
           echo sample_name,fq1,fq2,date,is_amplicon_data,technology > .tests/config/pep/samples.csv
           echo illumina-test,data/B117.1.fastq.gz,data/B117.2.fastq.gz,2022-01-01,$AMPLICON,illumina >> .tests/config/pep/samples.csv
-      # - name: Prepare test data for Oxford Nanopore
-      #   if: steps.test-data.outputs.cache-hit != true && (startsWith(matrix.rule, 'all') && matrix.technology == 'ont' || matrix.rule == 'compare_assemblers')
-      #   run: |
-      #     if [[ "${{ matrix.seq_method }}"  = "shotgun" ]] ; then export AMPLICON=0; else export AMPLICON=1; fi
-      #     mkdir -p .tests/data
-      #     curl -L https://github.com/thomasbtf/small-kraken-db/raw/master/ont_reads.fastq.gz > .tests/data/ont_reads.fastq.gz
-      #     echo sample_name,fq1,date,is_amplicon_data,technology > .tests/config/pep/samples.csv
-      #     echo ont-test,data/ont_reads.fastq.gz,2022-01-01,$AMPLICON,ont >> .tests/config/pep/samples.csv
+      - name: Prepare test data for Oxford Nanopore
+        if: steps.test-data.outputs.cache-hit != true && (startsWith(matrix.rule, 'all') && matrix.technology == 'ont' || matrix.rule == 'compare_assemblers')
+        run: |
+          if [[ "${{ matrix.seq_method }}"  = "shotgun" ]] ; then export AMPLICON=0; else export AMPLICON=1; fi
+          mkdir -p .tests/data
+          curl -L https://github.com/thomasbtf/small-kraken-db/raw/master/ont_reads.fastq.gz > .tests/data/ont_reads.fastq.gz
+          echo sample_name,fq1,date,is_amplicon_data,technology > .tests/config/pep/samples.csv
+          echo ont-test,data/ont_reads.fastq.gz,2022-01-01,$AMPLICON,ont >> .tests/config/pep/samples.csv
       - name: Prepare test data for Ion Torrent
         if: steps.test-data.outputs.cache-hit != true && (startsWith(matrix.rule, 'all') && matrix.technology == 'ion' || matrix.rule == 'compare_assemblers')
         run: |
@@ -176,14 +176,15 @@ jobs:
       - Pre-Commit
     strategy:
       matrix:
-        rule: [
+        rule:
+          [
             benchmark_strain_calling,
             benchmark_assembly,
             benchmark_mixtures,
             benchmark_non_sars_cov_2,
             benchmark_reads,
             compare_assemblers,
-            # generate_test_cases,
+            generate_test_cases,
           ]
     steps:
       - uses: actions/checkout@v2