Added stub test to ci

Plant-Food-Research-Open · Feb 21, 2024 · ec4c33d · ec4c33d
1 parent 94b6761
commit ec4c33d
Show file tree

Hide file tree

Showing 5 changed files with 28 additions and 10 deletions.
diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
@@ -26,18 +26,18 @@ jobs:
         NXF_VER:
           - "23.04.0"
           - "latest-everything"
+        RUN_CONFIG:
+          - "-profile test,docker"
+          - "-profile docker -c ./tests/stub/stub.config -stub"
     steps:
       - name: Check out pipeline code
         uses: actions/checkout@v4
 
       - name: Install Nextflow
         uses: nf-core/setup-nextflow@v1
         with:
-          version: "${{ matrix.NXF_VER }}"
+          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 --outdir ./results
+          nextflow run ${GITHUB_WORKSPACE} --outdir ./results ${{ matrix.RUN_CONFIG }}
diff --git a/assets/schema_input.json b/assets/schema_input.json
@@ -57,11 +57,7 @@
                 "anyOf": [
                     {
                         "type": "string",
-                        "pattern": "^SR\\w+$"
-                    },
-                    {
-                        "type": "string",
-                        "pattern": "^\\S+_R\\{1,2\\}\\.f(ast)?q\\.gz$"
+                        "pattern": "^\\S+\\.tsv$"
                     },
                     {
                         "type": "string",

diff --git a/lib/WorkflowMain.groovy b/lib/WorkflowMain.groovy
@@ -47,6 +47,11 @@ class WorkflowMain {
         if (!params.ncbi_fcs_gx_skip && !params.ncbi_fcs_gx_tax_id) {
             Nextflow.error('ncbi_fcs_gx_tax_id must be provided when executing NCBI FCS GX')
         }
+
+        // Check for ncbi_fcs_gx_db_path
+        if (!params.ncbi_fcs_gx_skip && !params.ncbi_fcs_gx_db_path) {
+            Nextflow.error('ncbi_fcs_gx_db_path must be provided when executing NCBI FCS GX')
+        }
     }
     //
     // Get attribute from genome config file e.g. fasta

diff --git a/tests/stub/gxdb/test/test-only.gxi b/tests/stub/gxdb/test/test-only.gxi
diff --git a/tests/stub/stub.config b/tests/stub/stub.config
@@ -0,0 +1,17 @@
+params {
+    config_profile_name        = 'Full stub test'
+    config_profile_description = 'Full test of the pipeline in stub mode'
+
+    input                       = 'https://raw.githubusercontent.com/Plant-Food-Research-Open/assemblyqc/dev/tests/stub/assemblysheet.csv'
+
+    ncbi_fcs_adaptor_skip       = false
+
+    ncbi_fcs_gx_skip            = false
+    ncbi_fcs_gx_tax_id          = 12
+    ncbi_fcs_gx_db_path         = 'https://raw.githubusercontent.com/Plant-Food-Research-Open/assemblyqc/dev/tests/stub/gxdb/test'
+
+    // Limit resources so that this can run on GitHub Actions
+    max_cpus                    = 2
+    max_memory                  = '6.GB'
+    max_time                    = '6.h'
+}