sanger-tol · DLBPointon · Sep 21, 2023 · Sep 19, 2023 · Sep 19, 2023 · Sep 19, 2023
diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
@@ -48,4 +48,4 @@ jobs:
       - name: Run FULL pipeline with test data
         # Remember that you can parallelise this by using strategy.matrix
         run: |
-          nextflow run ${GITHUB_WORKSPACE} -entry FULL -profile github_test,docker --outdir ./results-full
+          nextflow run ${GITHUB_WORKSPACE} -profile github_test,docker --outdir ./results-full
diff --git a/.github/workflows/sanger_test.yml b/.github/workflows/sanger_test.yml
@@ -0,0 +1,29 @@
+name: sanger-tol LSF tests
+
+on:
+  workflow_dispatch:
+jobs:
+  run-tower:
+    name: Run LSF tests
+    runs-on: ubuntu-latest
+    steps:
+      - name: Launch workflow via tower
+        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 }}
+          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: farm_test,sanger,singularity,cleanup
+
+      - uses: actions/upload-artifact@v3
+        with:
+          name: Tower debug log file
+          path: |
+            tower_action_*.log
+            tower_action_*.json
diff --git a/.github/workflows/sanger_test_full.yml b/.github/workflows/sanger_test_full.yml
@@ -0,0 +1,43 @@
+name: sanger-tol LSF full size tests
+
+on:
+  push:
+    branches:
+      - main
+      - dev
+  workflow_dispatch:
+jobs:
+  run-tower:
+    name: Run LSF full size tests
+    runs-on: ubuntu-latest
+    steps:
+      - name: Sets env vars for push
+        run: |
+          echo "REVISION=${{ github.sha }}" >> $GITHUB_ENV
+        if: github.event_name == 'push'
+
+      - name: Sets env vars for workflow_dispatch
+        run: |
+          echo "REVISION=${{ github.sha }}" >> $GITHUB_ENV
+        if: github.event_name == 'workflow_dispatch'
+
+      - name: Launch workflow via tower
+        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 }}
+          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: farm_test,sanger,singularity,cleanup
+
+      - uses: actions/upload-artifact@v3
+        with:
+          name: Tower debug log file
+          path: |
+            tower_action_*.log
+            tower_action_*.json
diff --git a/README.md b/README.md
@@ -39,7 +39,11 @@ Currently, it is advised to run the pipeline with docker or singularity as a sma
 Now, you can run the pipeline using:
 
 ```bash
-nextflow run main.nf -profile singularity --input treeval.yaml -entry {FULL|RAPID} --outdir {OUTDIR}
+# For the FULL pipeline
+nextflow run main.nf -profile singularity --input treeval.yaml --outdir {OUTDIR}
+
+# For the RAPID subset
+nextflow run main.nf -profile singularity --input treeval.yaml -entry RAPID --outdir {OUTDIR}
 ```
 
 An example treeval.yaml can be found [here](assets/local_testing/nxOscDF5033.yaml).

diff --git a/assets/local_testing/nxOscDF5033.yaml b/assets/local_testing/nxOscDF5033.yaml
@@ -5,11 +5,10 @@ assembly:
   classT: nematode
   asmVersion: 1
   gevalType: DTOL
-reference_file: /lustre/scratch123/tol/resources/treeval/nextflow_test_data/Oscheius_DF5033/assembly/draft/DF5033.hifiasm.noTelos.20211120/DF5033.noTelos.hifiasm.purged.noCont.noMito.fasta
-#/lustre/scratch123/tol/resources/treeval/nextflow_test_data/Oscheius_DF5033/assembly/draft/DF5033.hifiasm.noTelos.20211120/DF5033.noTelos.hifiasm.purged.noCont.noMito.fasta
+reference_file: /lustre/scratch123/tol/resources/nextflow/test-data/TreeValSmallData/Oscheius_DF5033/assembly/draft/DF5033.hifiasm.noTelos.20211120/DF5033.noTelos.hifiasm.purged.noCont.noMito.fasta
 assem_reads:
-  pacbio: /lustre/scratch123/tol/resources/treeval/nextflow_test_data/Oscheius_DF5033/genomic_data/nxOscSpes1/pacbio/fasta/
-  hic: /lustre/scratch123/tol/resources/treeval/nextflow_test_data/Oscheius_DF5033/genomic_data/nxOscSpes1/hic-arima2/full/
+  pacbio: /lustre/scratch123/tol/resources/nextflow/test-data/TreeValSmallData/Oscheius_DF5033/genomic_data/nxOscSpes1/pacbio/fasta/
+  hic: /lustre/scratch123/tol/resources/nextflow/test-data/TreeValSmallData/Oscheius_DF5033/genomic_data/nxOscSpes1/hic-arima2/full/
   supplementary: path
 alignment:
   data_dir: /lustre/scratch123/tol/resources/treeval/gene_alignment_data/

diff --git a/assets/local_testing/nxOscSUBSET.yaml b/assets/local_testing/nxOscSUBSET.yaml
@@ -5,11 +5,11 @@ assembly:
   classT: nematode
   asmVersion: 1
   gevalType: DTOL
-reference_file: /lustre/scratch123/tol/resources/treeval/nextflow_test_data/Oscheius_SUBSET/assembly/draft/SUBSET_genome/Oscheius_SUBSET.fasta
+reference_file: /lustre/scratch123/tol/resources/nextflow/test-data/TreeValSmallData/Oscheius_SUBSET/assembly/draft/SUBSET_genome/Oscheius_SUBSET.fasta
 #/lustre/scratch123/tol/resources/treeval/nextflow_test_data/Oscheius_DF5033/assembly/draft/DF5033.hifiasm.noTelos.20211120/DF5033.noTelos.hifiasm.purged.noCont.noMito.fasta
 assem_reads:
-  pacbio: /lustre/scratch123/tol/resources/treeval/nextflow_test_data/Oscheius_SUBSET/genomic_data/pacbio/
-  hic: /lustre/scratch123/tol/resources/treeval/nextflow_test_data/Oscheius_DF5033/genomic_data/nxOscSpes1/hic-arima2/subset/
+  pacbio: /lustre/scratch123/tol/resources/nextflow/test-data/TreeValSmallData/Oscheius_SUBSET/genomic_data/pacbio/
+  hic: /lustre/scratch123/tol/resources/nextflow/test-data/TreeValSmallData/Oscheius_DF5033/genomic_data/nxOscSpes1/hic-arima2/subset/
   supplementary: path
 alignment:
   data_dir: /lustre/scratch123/tol/resources/treeval/nextflow_test_data/Oscheius_SUBSET/gene_set/

diff --git a/nextflow.config b/nextflow.config
@@ -60,6 +60,7 @@ try {
 
 
 profiles {
+    cleanup { cleanup = true }
     debug {
         dumpHashes             = true
         process.beforeScript   = 'echo $HOSTNAME'