Added the cleanup profile and use it for our Tower Sanger tests

.github/workflows/sangertest.yml → .github/workflows/sanger_test.yml

@@ -8,16 +8,22 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Launch workflow via tower
-        uses: nf-core/tower-action@v2
+        uses: seqeralabs/action-tower-launch@v2
         with:
           workspace_id: ${{ secrets.TOWER_WORKSPACE_ID }}
           access_token: ${{ secrets.TOWER_ACCESS_TOKEN }}
           compute_env: ${{ secrets.TOWER_COMPUTE_ENV }}
-          pipeline: ${{ github.repository }}
           revision: ${{ github.sha }}
           workdir: ${{ secrets.TOWER_WORKDIR_PARENT }}/work/${{ github.repository }}/work-${{ github.sha }}
           parameters: |
             {
               "outdir": "${{ secrets.TOWER_WORKDIR_PARENT }}/results/${{ github.repository }}/results-${{ github.sha }}",
             }
-          profiles: test,sanger,singularity
+          profiles: test,sanger,singularity,cleanup
+
+      - uses: actions/upload-artifact@v3
+        with:
+          name: Tower debug log file
+          path: |
+            tower_action_*.log
+            tower_action_*.json

.github/workflows/sangerfulltest.yml → .github/workflows/sanger_test_full.yml

@@ -22,16 +22,22 @@ jobs:
         if: github.event_name == 'workflow_dispatch'
 
       - name: Launch workflow via tower
-        uses: nf-core/tower-action@v2
+        uses: seqeralabs/action-tower-launch@v2
         with:
           workspace_id: ${{ secrets.TOWER_WORKSPACE_ID }}
           access_token: ${{ secrets.TOWER_ACCESS_TOKEN }}
           compute_env: ${{ secrets.TOWER_COMPUTE_ENV }}
-          pipeline: ${{ github.repository }}
           revision: ${{ env.REVISION }}
           workdir: ${{ secrets.TOWER_WORKDIR_PARENT }}/work/${{ github.repository }}/work-${{ env.REVISION }}
           parameters: |
             {
               "outdir": "${{ secrets.TOWER_WORKDIR_PARENT }}/results/${{ github.repository }}/results-${{ env.REVISION }}",
             }
-          profiles: test_full,sanger,singularity
+          profiles: test_full,sanger,singularity,cleanup
+
+      - uses: actions/upload-artifact@v3
+        with:
+          name: Tower debug log file
+          path: |
+            tower_action_*.log
+            tower_action_*.json

conf/modules.config

@@ -83,7 +83,7 @@ process {
 
     withName: SAMPLESHEET_CHECK {
         publishDir = [
-            path: { "${params.outdir}/readmapping_info" },
+            path: { "${params.outdir}/pipeline_info/readmapping" },
             mode: params.publish_dir_mode,
             saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
         ]
@@ -131,7 +131,7 @@ process {
 
     withName: CUSTOM_DUMPSOFTWAREVERSIONS {
         publishDir = [
-            path: { "${params.outdir}/readmapping_info" },
+            path: { "${params.outdir}/pipeline_info/readmapping" },
             mode: params.publish_dir_mode,
             pattern: '*_versions.yml'
         ]

docs/output.md

@@ -113,7 +113,7 @@ A number of genome-specific files are generated by the pipeline because they are
 <details markdown="1">
 <summary>Output files</summary>
 
-- `readmapping_info/`
+- `pipeline_info/readmapping/`
   - Reports generated by Nextflow: `execution_report.html`, `execution_timeline.html`, `execution_trace.txt` and `pipeline_dag.dot`/`pipeline_dag.svg`.
   - Reports generated by the pipeline: `pipeline_report.html`, `pipeline_report.txt` and `software_versions.yml`. The `pipeline_report*` files will only be present if the `--email` / `--email_on_fail` parameter's are used when running the pipeline.
   - Reformatted samplesheet files used as input to the pipeline: `samplesheet.valid.csv`.

lib/NfcoreTemplate.groovy

@@ -132,7 +132,7 @@ class NfcoreTemplate {
         }
 
         // Write summary e-mail HTML to a file
-        def output_d = new File("${params.outdir}/readmapping_info/")
+        def output_d = new File("${params.outdir}/pipeline_info/readmapping/")
         if (!output_d.exists()) {
             output_d.mkdirs()
         }

nextflow.config

@@ -18,7 +18,7 @@ params {
 
     // Boilerplate options
     outdir                     = "./results"
-    tracedir                   = "${params.outdir}/readmapping_info"
+    tracedir                   = "${params.outdir}/pipeline_info/readmapping"
     publish_dir_mode           = 'copy'
     email                      = null
     email_on_fail              = null
@@ -69,6 +69,7 @@ try {
 
 
 profiles {
+    cleanup { cleanup = true }
     debug { process.beforeScript = 'echo $HOSTNAME' }
     conda {
         conda.enabled          = true

nextflow_schema.json

@@ -208,7 +208,7 @@
                 "tracedir": {
                     "type": "string",
                     "description": "Directory to keep pipeline Nextflow logs and reports.",
-                    "default": "${params.outdir}/readmapping_info",
+                    "default": "${params.outdir}/pipeline_info/readmapping",
                     "fa_icon": "fas fa-cogs",
                     "hidden": true
                 },