From e912404d3dfbcb1f20b45e79f650ccd06b5e2af9 Mon Sep 17 00:00:00 2001 From: JoseEspinosa Date: Mon, 7 Mar 2022 16:34:20 +0100 Subject: [PATCH 1/3] Make --outdir mandatory --- .github/PULL_REQUEST_TEMPLATE.md | 2 +- .github/workflows/awsfulltest.yml | 7 +++++++ .github/workflows/ci.yml | 10 ++++++---- CHANGELOG.md | 6 ++---- README.md | 3 ++- conf/modules.config | 8 ++++---- conf/test.config | 2 +- conf/test_full.config | 2 +- docs/usage.md | 2 +- lib/WorkflowMain.groovy | 2 +- nextflow.config | 2 +- nextflow_schema.json | 4 ++-- 12 files changed, 29 insertions(+), 21 deletions(-) diff --git a/.github/PULL_REQUEST_TEMPLATE.md b/.github/PULL_REQUEST_TEMPLATE.md index 2f5f6925..f0a3ff06 100644 --- a/.github/PULL_REQUEST_TEMPLATE.md +++ b/.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 `). - [ ] Usage Documentation in `docs/usage.md` is updated. - [ ] Output Documentation in `docs/output.md` is updated. - [ ] `CHANGELOG.md` is updated. diff --git a/.github/workflows/awsfulltest.yml b/.github/workflows/awsfulltest.yml index 3015ffe7..6d200a5e 100644 --- a/.github/workflows/awsfulltest.yml +++ b/.github/workflows/awsfulltest.yml @@ -12,6 +12,10 @@ 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 @@ -19,10 +23,13 @@ jobs: 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: | diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index a47a74e6..25c505b0 100755 --- a/.github/workflows/ci.yml +++ b/.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 diff --git a/CHANGELOG.md b/CHANGELOG.md index 8e496fce..6573b686 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -5,7 +5,7 @@ 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 @@ -13,13 +13,11 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 * 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 diff --git a/README.md b/README.md index e31aa418..fc1bf270 100644 --- a/README.md +++ b/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 ``` 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 \ --genome GRCh37 \ -profile ``` diff --git a/conf/modules.config b/conf/modules.config index bd17ccf3..a20c6b09 100644 --- a/conf/modules.config +++ b/conf/modules.config @@ -3,10 +3,10 @@ Config file for defining DSL2 per module options and publishing paths ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Available keys to override module options: - ext.args = Additional arguments appended to command in module. - ext.args2 = Second set of arguments appended to command in module (multi-tool modules). - ext.args3 = Third set of arguments appended to command in module (multi-tool modules). - ext.prefix = File name prefix for output files. + ext.args = Additional arguments appended to command in module. + ext.args2 = Second set of arguments appended to command in module (multi-tool modules). + ext.args3 = Third set of arguments appended to command in module (multi-tool modules). + ext.prefix = File name prefix for output files. --------------------------------------------------------------------------------------------------------- */ diff --git a/conf/test.config b/conf/test.config index 2afa57f6..d9c938a0 100644 --- a/conf/test.config +++ b/conf/test.config @@ -5,7 +5,7 @@ Defines input files and everything required to run a fast and simple pipeline test. Use as follows: - nextflow run nf-core/chipseq -profile test, + nextflow run nf-core/chipseq -profile test, --outdir ---------------------------------------------------------------------------------------- */ diff --git a/conf/test_full.config b/conf/test_full.config index 66bac305..de612053 100644 --- a/conf/test_full.config +++ b/conf/test_full.config @@ -5,7 +5,7 @@ Defines input files and everything required to run a full size pipeline test. Use as follows: - nextflow run nf-core/chipseq -profile test_full, + nextflow run nf-core/chipseq -profile test_full, --outdir ---------------------------------------------------------------------------------------- */ diff --git a/docs/usage.md b/docs/usage.md index 89423dc3..425066f3 100644 --- a/docs/usage.md +++ b/docs/usage.md @@ -117,7 +117,7 @@ wget -L https://www.encodeproject.org/files/ENCFF356LFX/@@download/ENCFF356LFX.b The typical command for running the pipeline is as follows: ```console -nextflow run nf-core/chipseq --input samplesheet.csv --genome GRCh37 -profile docker +nextflow run nf-core/chipseq --input samplesheet.csv --outdir --genome GRCh37 -profile docker ``` This will launch the pipeline with the `docker` configuration profile. See below for more information about profiles. diff --git a/lib/WorkflowMain.groovy b/lib/WorkflowMain.groovy index 3ebf7521..e17aadd9 100755 --- a/lib/WorkflowMain.groovy +++ b/lib/WorkflowMain.groovy @@ -21,7 +21,7 @@ class WorkflowMain { // Print help to screen if required // public static String help(workflow, params, log) { - def command = "nextflow run ${workflow.manifest.name} --input samplesheet.csv --genome GRCh37 -profile docker" + def command = "nextflow run ${workflow.manifest.name} --input samplesheet.csv --outdir --genome GRCh37 -profile docker" def help_string = '' help_string += NfcoreTemplate.logo(workflow, params.monochrome_logs) help_string += NfcoreSchema.paramsHelp(workflow, params, command) diff --git a/nextflow.config b/nextflow.config index f11ad56a..f68ef6f6 100644 --- a/nextflow.config +++ b/nextflow.config @@ -74,7 +74,7 @@ params { max_multiqc_email_size = '25.MB' // Boilerplate options - outdir = './results' + outdir = null tracedir = "${params.outdir}/pipeline_info" publish_dir_mode = 'copy' email = null diff --git a/nextflow_schema.json b/nextflow_schema.json index cf98ed2d..34825a35 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -37,8 +37,8 @@ }, "outdir": { "type": "string", - "description": "Path to the output directory where the results will be saved.", - "default": "./results", + "format": "directory-path", + "description": "The output directory where the results will be saved. You have to use absolute paths to storage on Cloud infrastructure.", "fa_icon": "fas fa-folder-open" }, "email": { From 3cab81d689110a7b9f0b7e48212430e8a7e8e385 Mon Sep 17 00:00:00 2001 From: JoseEspinosa Date: Mon, 7 Mar 2022 17:14:15 +0100 Subject: [PATCH 2/3] Delete deprecated blacklist files --- assets/blacklists/old/GRCm38-blacklist.bed | 164 --------------------- assets/blacklists/old/hg38-blacklist.bed | 38 ----- assets/blacklists/old/mm10-blacklist.bed | 164 --------------------- mm10-blacklist.bed | 164 --------------------- 4 files changed, 530 deletions(-) delete mode 100755 assets/blacklists/old/GRCm38-blacklist.bed delete mode 100644 assets/blacklists/old/hg38-blacklist.bed delete mode 100755 assets/blacklists/old/mm10-blacklist.bed delete mode 100755 mm10-blacklist.bed diff --git a/assets/blacklists/old/GRCm38-blacklist.bed b/assets/blacklists/old/GRCm38-blacklist.bed deleted file mode 100755 index 3699d020..00000000 --- a/assets/blacklists/old/GRCm38-blacklist.bed +++ 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JoseEspinosa Date: Mon, 7 Mar 2022 17:14:26 +0100 Subject: [PATCH 3/3] Make nf-core lint happy --- .nf-core.yml | 1 + 1 file changed, 1 insertion(+) diff --git a/.nf-core.yml b/.nf-core.yml index aca9e11f..1e3aafb1 100644 --- a/.nf-core.yml +++ b/.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