fix: Enable full pipeline run in CI (#31)

* fix: Change paths in test data

* chore: Change name of nf-test CI

* chore: Change criteria on full pipeline CI

* ci: Update test profile CI template

* refactor: Update test input to be URL

* ci: Only run when pushing to master

.github/workflows/ci.yml

@@ -3,38 +3,36 @@ name: nf-core CI
 on:
   push:
     branches:
-      - dev
+      - master
   pull_request:
   release:
     types: [published]
 
+env:
+  NXF_ANSI_LOG: false
+
 jobs:
   test:
-    name: Run workflow tests
+    name: Run pipeline with test data
     # Only run on push if this is the nf-core dev branch (merged PRs)
-    if: ${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/arete') }}
+    if: "${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'beiko-lab/arete') }}"
     runs-on: ubuntu-latest
-    env:
-      NXF_VER: ${{ matrix.nxf_ver }}
-      NXF_ANSI_LOG: false
     strategy:
       matrix:
-        # Nextflow versions: check pipeline minimum and current latest
-        nxf_ver: [21.03.0-edge]
+        NXF_VER:
+          - "latest-everything"
     steps:
       - name: Check out pipeline code
         uses: actions/checkout@v2
 
       - name: Install Nextflow
-        env:
-          CAPSULE_LOG: none
-        run: |
-          wget -qO- get.nextflow.io | bash
-          sudo mv nextflow /usr/local/bin/
+        uses: nf-core/setup-nextflow@v1
+        with:
+          version: "${{ matrix.NXF_VER }}"
 
       - name: Run pipeline with test data
         # TODO nf-core: You can customise CI pipeline run tests as required
         # For example: adding multiple test runs with different parameters
         # Remember that you can parallelise this by using strategy.matrix
         run: |
-          nextflow run ${GITHUB_WORKSPACE} -profile test,docker
+          nextflow run ${GITHUB_WORKSPACE} -profile test,docker --outdir ./results

.github/workflows/test.yml

@@ -1,4 +1,4 @@
-name: nf-core CI
+name: nf-test CI
 # This workflow runs the nf-test test suite
 on:
   push:

conf/test.config

@@ -20,9 +20,28 @@ params {
     max_time   = 6.h
 
     // Input data
-    input_sample_table = "test/test_dataset.csv"
+    input_sample_table = "https://raw.githubusercontent.com/beiko-lab/arete/master/test/test_dataset.csv"
     use_bakta = false
     db_cache = false
     use_full_alignment = true
     use_fasttree = true
+    skip_kraken = true
+}
+
+process {
+    withLabel:process_low {
+        cpus   =  2
+        memory = 4.GB
+        time   = 4.h
+    }
+    withLabel:process_medium {
+        cpus   =  2
+        memory = 4.GB
+        time   = 4.h
+    }
+    withLabel:process_high {
+        cpus   =  2
+        memory = 4.GB
+        time   = 4.h
+    }
 }

test/test_dataset.csv

@@ -1,5 +1,5 @@
 sample,fastq_1,fastq_2
-test_1,test/NZ_CP013325_1.fq.gz,test/NZ_CP013325_2.fq.gz 
-test_2,test/NZ_CP013325_1.fq.gz,test/NZ_CP013325_2.fq.gz 
-test_3,test/NZ_CP013325_1.fq.gz,test/NZ_CP013325_2.fq.gz 
-test_4,test/NZ_CP013325_1.fq.gz,test/NZ_CP013325_2.fq.gz 
+test_1,https://github.com/beiko-lab/arete/raw/master/test/NZ_CP013325_1.fq.gz,https://github.com/beiko-lab/arete/raw/master/test/NZ_CP013325_2.fq.gz
+test_2,https://github.com/beiko-lab/arete/raw/master/test/NZ_CP013325_1.fq.gz,https://github.com/beiko-lab/arete/raw/master/test/NZ_CP013325_2.fq.gz
+test_3,https://github.com/beiko-lab/arete/raw/master/test/NZ_CP013325_1.fq.gz,https://github.com/beiko-lab/arete/raw/master/test/NZ_CP013325_2.fq.gz
+test_4,https://github.com/beiko-lab/arete/raw/master/test/NZ_CP013325_1.fq.gz,https://github.com/beiko-lab/arete/raw/master/test/NZ_CP013325_2.fq.gz