Adding testing

sanger-tol · Sep 19, 2023 · 6ac3177 · 6ac3177
1 parent d802476
commit 6ac3177
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Showing 3 changed files with 30 additions and 13 deletions.
diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
@@ -47,9 +47,9 @@ jobs:
       - name: Run MAPS_ONLY pipeline with test data
         # Remember that you can parallelise this by using strategy.matrix
         run: |
-          nextflow run ${GITHUB_WORKSPACE} --input /home/runner/work/curationpretext/curationpretext/TreeValTinyData/assembly/draft/grTriPseu1.fa --pacbio /home/runner/work/curationpretext/curationpretext/TreeValTinyData/genomic_data/pacbio/ --cram /home/runner/work/curationpretext/curationpretext/TreeValTinyData/genomic_data/hic-arima/ --teloseq TTAGGG -profile test,docker --outdir ./results -entry MAPS_ONLY
+          nextflow run ${GITHUB_WORKSPACE} -profile test,docker --outdir ./results -entry MAPS_ONLY
 
       - name: Run ALL_FILES pipeline with test data
         # Remember that you can parallelise this by using strategy.matrix
         run: |
-          nextflow run ${GITHUB_WORKSPACE} --input /home/runner/work/curationpretext/curationpretext/TreeValTinyData/assembly/draft/grTriPseu1.fa --pacbio /home/runner/work/curationpretext/curationpretext/TreeValTinyData/genomic_data/pacbio/ --cram /home/runner/work/curationpretext/curationpretext/TreeValTinyData/genomic_data/hic-arima/ --teloseq TTAGGG -profile test,docker --outdir ./results -entry ALL_FILES
+          nextflow run ${GITHUB_WORKSPACE} -profile test,docker --outdir ./results -entry ALL_FILES
diff --git a/conf/test.config b/conf/test.config
@@ -11,12 +11,18 @@
 */
 
 params {
-    config_profile_name        = 'Test profile'
+    config_profile_name        = 'GitHub Test profile'
     config_profile_description = 'Minimal test dataset to check pipeline function'
 
     // Limit resources so that this can run on GitHub Actions
-    max_cpus   = 2
-    max_memory = '6.GB'
-    max_time   = '6.h'
+    max_cpus    = 2
+    max_memory  = '6.GB'
+    max_time    = '6.h'
 
+    input       = /home/runner/work/curationpretext/curationpretext/TreeValTinyData/assembly/draft/grTriPseu1.fa
+    outdir      = ./results
+    pacbio      = /home/runner/work/curationpretext/curationpretext/TreeValTinyData/genomic_data/pacbio/
+    cram        = /home/runner/work/curationpretext/curationpretext/TreeValTinyData/genomic_data/hic-arima/
+    sample      = CurationPretextTest
+    teloseq     = TTAGGG
 }
diff --git a/subworkflows/local/generate_maps.nf b/subworkflows/local/generate_maps.nf
@@ -134,13 +134,24 @@ workflow GENERATE_MAPS {
     ch_versions         = ch_versions.mix(PRETEXTMAP_STANDRD.out.versions)
 
     //
-    // MODULE: GENERATE PRETEXT MAP FROM MAPPED BAM FOR HIGH RES
-    //
-    PRETEXTMAP_HIGHRES (
-        pretext_input.input_bam,
-        pretext_input.reference
-    )
-    ch_versions         = ch_versions.mix(PRETEXTMAP_HIGHRES.out.versions)
+    // LOGIC: HIRES IS TOO INTENSIVE FOR RUNNING IN GITHUB CI SO THIS STOPS IT RUNNING
+    //
+    if ( params.config_profile_name ) {
+        config_profile_name = params.config_profile_name
+    } else {
+        config_profile_name = 'Local'
+    }
+
+    if ( !config_profile_name.contains('GitHub') ) {
+        //
+        // MODULE: GENERATE PRETEXT MAP FROM MAPPED BAM FOR HIGH RES
+        //
+        PRETEXTMAP_HIGHRES (
+            pretext_input.input_bam,
+            pretext_input.reference
+        )
+        ch_versions         = ch_versions.mix( PRETEXTMAP_HIGHRES.out.versions )
+    }
 
     //
     // MODULE: GENERATE PNG FROM STANDARD PRETEXT