Fix some template sync errors

.github/workflows/awsfulltest.yml

@@ -16,14 +16,7 @@ jobs:
       matrix:
         aligner: ["bismark", "bismark_hisat", "bwameth"]
     steps:
-      - name: Setup Miniconda
-        uses: conda-incubator/setup-miniconda@v2
-        with:
-          auto-update-conda: true
-          python-version: 3.7
-      - name: Install awscli
-        run: conda install -c conda-forge awscli
-      - name: Start AWS batch job
+      - name: Launch workflow via tower
         uses: nf-core/tower-action@v3
         with:
           workspace_id: ${{ secrets.TOWER_WORKSPACE_ID }}
@@ -32,17 +25,11 @@ jobs:
           workdir: s3://${{ secrets.AWS_S3_BUCKET }}/work/methylseq/work-${{ github.sha }}
           parameters: |
             {
-              "outdir": "s3://${{ secrets.AWS_S3_BUCKET }}/methylseq/results-${{ github.sha }}"
+              "aligner": "${{ matrix.aligner }}",
+              "outdir": "s3://${{ secrets.AWS_S3_BUCKET }}/methylseq/results-${{ github.sha }}/${{matrix.aligner}}"
             }
           profiles: test_full,aws_tower
-          nextflow_config: |
-            process.errorStrategy = 'retry'
-            process.maxRetries = 3
-        # Do a full-scale run with each of the three aligners
-        run: |
-          aws batch submit-job \
-            --region eu-west-1 \
-            --job-name nf-core-methylseq \
-            --job-queue $AWS_JOB_QUEUE \
-            --job-definition $AWS_JOB_DEFINITION \
-            --container-overrides '{"command": ["nf-core/methylseq", "-r '"${GITHUB_SHA}"' -profile test_full --aligner '"${{matrix.aligner}}"' --outdir s3://'"${AWS_S3_BUCKET}"'/methylseq/results-'"${GITHUB_SHA}"'/'"${{matrix.aligner}}"/' -w s3://'"${AWS_S3_BUCKET}"'/methylseq/work-'"${GITHUB_SHA}"'/'"${{matrix.aligner}}" -with-tower"], "environment": [{"name": "TOWER_ACCESS_TOKEN", "value": "'"$TOWER_ACCESS_TOKEN"'"}]}'
+      - uses: actions/upload-artifact@v3
+        with:
+          name: Tower debug log file
+          path: tower_action_*.log

.github/workflows/awstest.yml

@@ -12,39 +12,22 @@ jobs:
     strategy:
       matrix:
         aligner: ["bismark", "bismark_hisat", "bwameth"]
-        include:
-          - aligner: "bismark"
-            ref_index: --bismark_index results/reference_genome/BismarkIndex/
-          - aligner: "bismark_hisat"
-            ref_index: --bismark_index results/reference_genome/BismarkIndex/
-          - aligner: "bwameth"
-            ref_index: --bwa_meth_index results/reference_genome/genome.fa
     steps:
       # Launch workflow using Tower CLI tool action
       - name: Launch workflow via tower
         uses: nf-core/tower-action@v3
         with:
-          auto-update-conda: true
-          python-version: 3.7
           workspace_id: ${{ secrets.TOWER_WORKSPACE_ID }}
           access_token: ${{ secrets.TOWER_ACCESS_TOKEN }}
           compute_env: ${{ secrets.TOWER_COMPUTE_ENV }}
           workdir: s3://${{ secrets.AWS_S3_BUCKET }}/work/methylseq/work-${{ github.sha }}
           parameters: |
             {
-              "outdir": "s3://${{ secrets.AWS_S3_BUCKET }}/methylseq/results-test-${{ github.sha }}"
+              "aligner": "${{ matrix.aligner }}",
+              "outdir": "s3://${{ secrets.AWS_S3_BUCKET }}/methylseq/results-test-${{ github.sha }}/${{matrix.aligner}}"
             }
           profiles: test,aws_tower
-          nextflow_config: |
-            process.errorStrategy = 'retry'
-            process.maxRetries = 3
-      - name: Install awscli
-        run: conda install -c conda-forge awscli
-      - name: Start AWS batch job
-        run: |
-          aws batch submit-job \
-          --region eu-west-1 \
-          --job-name nf-core-methylseq \
-          --job-queue $AWS_JOB_QUEUE \
-          --job-definition $AWS_JOB_DEFINITION \
-          --container-overrides '{"command": ["nf-core/methylseq", "-r '"${GITHUB_SHA}"' -profile test --aligner '"${{matrix.aligner}}"' --outdir s3://'"${AWS_S3_BUCKET}"'/methylseq/results-'"${GITHUB_SHA}"'/'"${{matrix.aligner}}"/' -w s3://'"${AWS_S3_BUCKET}"'/methylseq/work-'"${GITHUB_SHA}"'/'"${{matrix.aligner}}" -with-tower"], "environment": [{"name": "TOWER_ACCESS_TOKEN", "value": "'"$TOWER_ACCESS_TOKEN"'"}]}'
+      - uses: actions/upload-artifact@v3
+        with:
+          name: Tower debug log file
+          path: tower_action_*.log

.github/workflows/ci.yml

@@ -37,13 +37,13 @@ jobs:
           version: "${{ matrix.NXF_VER }}"
 
       - name: Test - Single End
-        run: nextflow run ${GITHUB_WORKSPACE} -profile test,docker --aligner ${{matrix.aligner}} --save_reference
+        run: nextflow run ${GITHUB_WORKSPACE} -profile test,docker --aligner ${{matrix.aligner}} --save_reference --outdir ./results
 
       - name: Test - Single End with index
-        run: nextflow run ${GITHUB_WORKSPACE} -profile test,docker --aligner ${{matrix.aligner}} ${{matrix.ref_index}}
+        run: nextflow run ${GITHUB_WORKSPACE} -profile test,docker --aligner ${{matrix.aligner}} ${{matrix.ref_index}} --outdir ./results
 
       - name: Test - Single End RRBS
-        run: nextflow run ${GITHUB_WORKSPACE} -profile test,docker --aligner ${{matrix.aligner}} --skip_trimming --rrbs
+        run: nextflow run ${GITHUB_WORKSPACE} -profile test,docker --aligner ${{matrix.aligner}} --skip_trimming --rrbs --outdir ./results
 
       - name: Test - Paired End with index
-        run: nextflow run ${GITHUB_WORKSPACE} -profile test_paired,docker --aligner ${{matrix.aligner}} ${{matrix.ref_index}}
+        run: nextflow run ${GITHUB_WORKSPACE} -profile test_paired,docker --aligner ${{matrix.aligner}} ${{matrix.ref_index}} --outdir ./results

.gitignore

@@ -6,3 +6,4 @@ results/
 testing/
 testing*
 *.pyc
+.vscode