Make --outdir mandatory

.github/PULL_REQUEST_TEMPLATE.md

@@ -19,7 +19,7 @@ Learn more about contributing: [CONTRIBUTING.md](https://github.com/nf-core/chip
     - [ ] If you've added a new tool - have you followed the pipeline conventions in the [contribution docs](https://github.com/nf-core/chipseq/tree/master/.github/CONTRIBUTING.md)
     - [ ] If necessary, also make a PR on the nf-core/chipseq _branch_ on the [nf-core/test-datasets](https://github.com/nf-core/test-datasets) repository.
 - [ ] Make sure your code lints (`nf-core lint`).
-- [ ] Ensure the test suite passes (`nextflow run . -profile test,docker`).
+- [ ] Ensure the test suite passes (`nextflow run . -profile test,docker --outdir <OUTDIR>`).
 - [ ] Usage Documentation in `docs/usage.md` is updated.
 - [ ] Output Documentation in `docs/output.md` is updated.
 - [ ] `CHANGELOG.md` is updated.

.github/workflows/awsfulltest.yml

@@ -12,17 +12,24 @@ jobs:
     name: Run AWS full tests
     if: github.repository == 'nf-core/chipseq'
     runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        # aligner: ["bwa", "bowtie2", "chromap", "star"] //TODO uncomment when chromap implemented
+        aligner: ["bwa", "bowtie2", "star"]
     steps:
       - name: Launch workflow via tower
         uses: nf-core/tower-action@v3
         with:
           workspace_id: ${{ secrets.TOWER_WORKSPACE_ID }}
           access_token: ${{ secrets.TOWER_ACCESS_TOKEN }}
           compute_env: ${{ secrets.TOWER_COMPUTE_ENV }}
+          pipeline: ${{ github.repository }}
+          revision: ${{ github.sha }}
           workdir: s3://${{ secrets.AWS_S3_BUCKET }}/work/chipseq/work-${{ github.sha }}
           parameters: |
             {
               "outdir": "s3://${{ secrets.AWS_S3_BUCKET }}/chipseq/results-${{ github.sha }}"
+              "aligner": "${{ matrix.aligner }}"
             }
           profiles: test_full,aws_tower
           nextflow_config: |

.github/workflows/ci.yml

@@ -14,7 +14,7 @@ env:
 
 jobs:
   test:
-    name: Run workflow tests
+    name: Run pipeline with test data
     # Only run on push if this is the nf-core dev branch (merged PRs)
     if: ${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/chipseq') }}
     runs-on: ubuntu-latest
@@ -44,7 +44,8 @@ jobs:
 
       - name: Run pipeline with test data
         run: |
-          nextflow run ${GITHUB_WORKSPACE} -profile test,docker
+          nextflow run ${GITHUB_WORKSPACE} -profile test,docker --outdir ./results
+
 
   parameters:
     name: Test workflow parameters
@@ -66,7 +67,7 @@ jobs:
 
       - name: Run pipeline with various parameters
         run: |
-          nextflow run ${GITHUB_WORKSPACE} -profile test,docker ${{ matrix.parameters }}
+          nextflow run ${GITHUB_WORKSPACE} -profile test,docker ${{ matrix.parameters }} --outdir ./results
 
   aligners:
     name: Test available aligners
@@ -76,6 +77,7 @@ jobs:
       matrix:
         aligner:
           - "bowtie2"
+          # - "chromap" #TODO uncomment when implemented
           - "star"
     steps:
       - name: Check out pipeline code
@@ -88,4 +90,4 @@ jobs:
 
       - name: Run pipeline with the different aligners available
         run: |
-          nextflow run ${GITHUB_WORKSPACE} -profile test,docker --aligner ${{ matrix.aligner }}
+          nextflow run ${GITHUB_WORKSPACE} -profile test,docker --aligner ${{ matrix.aligner }} --outdir ./results

.nf-core.yml

@@ -10,5 +10,6 @@ lint:
     - .github/workflows/branch.yml
     - .github/workflows/linting_comment.yml
     - .github/workflows/linting.yml
+    - .github/PULL_REQUEST_TEMPLATE.md
 
 repository_type: pipeline

CHANGELOG.md

@@ -5,21 +5,19 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ## [Unpublished Version / DEV]
 
-### Major enhancements
+### Enhancements & fixes
 
 * Port pipeline to the updated Nextflow DSL2 syntax adopted on nf-core/modules
     * Removed `--publish_dir_mode` as it is no longer required for the new syntax
 * Bump minimum Nextflow version from `21.04.0` -> `21.10.3`
 * Updated pipeline template to [nf-core/tools 2.2](https://github.com/nf-core/tools/releases/tag/2.2)
 * Added `python3` shebang to appropriate scripts in `bin/` directory
 * [[#160](https://github.com/nf-core/chipseq/issues/160)] - Add `bowtie2` and `star` as available aligners, via the `--aligner` parameter
-
-### Other enhancements & fixes
-
 * Update pipeline template to nf-core/tools `2.1`
 * Add `--save_unaligned` parameter (only available for `bowtie2` and `star`)
 * Update `igenomes.config` to fetch whole `BWAIndex/version0.6.0/` folder
 * [[228](https://github.com/nf-core/chipseq/issues/228)] - Update blacklist bed files.
+* [nf-core/tools#1415](https://github.com/nf-core/tools/issues/1415) - Make `--outdir` a mandatory parameter
 
 ### Parameters
 

README.md

@@ -63,7 +63,7 @@ The pipeline is built using [Nextflow](https://www.nextflow.io), a workflow tool
 3. Download the pipeline and test it on a minimal dataset with a single command:
 
     ```console
-    nextflow run nf-core/chipseq -profile test,YOURPROFILE
+    nextflow run nf-core/chipseq -profile test,YOURPROFILE --outdir <OUTDIR>
     ```
 
     Note that some form of configuration will be needed so that Nextflow knows how to fetch the required software. This is usually done in the form of a config profile (`YOURPROFILE` in the example command above). You can chain multiple config profiles in a comma-separated string.
@@ -78,6 +78,7 @@ The pipeline is built using [Nextflow](https://www.nextflow.io), a workflow tool
     ```bash
     nextflow run nf-core/chipseq \
         --input samplesheet.csv \
+        --outdir <OUTDIR> \
         --genome GRCh37 \
         -profile <docker/singularity/podman/conda/institute>
     ```