diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index 4b48abfb..73d68b15 100755 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -59,6 +59,9 @@ jobs: runs-on: ubuntu-latest strategy: matrix: + NXF_VER: + - "24.04.2" + - "latest-everything" parameters: - "--skip_trimming" - "--skip_consensus_peaks" @@ -88,5 +91,5 @@ jobs: - name: Run pipeline with various parameters (conda) run: | - nextflow run ${GITHUB_WORKSPACE} -profile test,conda --outdir ./results ${{ matrix.parameters }} + nextflow run ${GITHUB_WORKSPACE} -profile test,conda --outdir ./results ${{ matrix.parameters }} if: "${{ github.base_ref == 'master' }}" diff --git a/CHANGELOG.md b/CHANGELOG.md index d25be267..61789e4f 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -9,9 +9,9 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 ### Parameters -| Old parameter | New parameter | -| ------------- | -------------------------------- | -| | | +| Old parameter | New parameter | +| ------------- | ------------- | +| | | > **NB:** Parameter has been **updated** if both old and new parameter information is present. > **NB:** Parameter has been **added** if just the new parameter information is present. diff --git a/main.nf b/main.nf index 0511159d..bee79135 100755 --- a/main.nf +++ b/main.nf @@ -112,7 +112,7 @@ workflow { args, params.outdir ) - + // // WORKFLOW: Run main workflow // diff --git a/nextflow.config b/nextflow.config index 9a9a07c2..39359f71 100644 --- a/nextflow.config +++ b/nextflow.config @@ -304,10 +304,10 @@ validation { """ afterText = """${manifest.doi ? "* The pipeline\n" : ""}${manifest.doi.tokenize(",").collect { " https://doi.org/${it.trim().replace('https://doi.org/','')}"}.join("\n")}${manifest.doi ? "\n" : ""} * The nf-core framework - https://doi.org/10.1038/s41587-020-0439-x + https://doi.org/10.1038/s41587-020-0439-x * Software dependencies - https://github.com/${manifest.name}/blob/master/CITATIONS.md + https://github.com/${manifest.name}/blob/master/CITATIONS.md """ } summary { diff --git a/subworkflows/local/utils_nfcore_chipseq_pipeline/main.nf b/subworkflows/local/utils_nfcore_chipseq_pipeline/main.nf index fc6a824b..4255b5e8 100644 --- a/subworkflows/local/utils_nfcore_chipseq_pipeline/main.nf +++ b/subworkflows/local/utils_nfcore_chipseq_pipeline/main.nf @@ -46,7 +46,6 @@ workflow PIPELINE_INITIALISATION { workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1 ) - // // Validate parameters and generate parameter summary to stdout // @@ -55,7 +54,7 @@ workflow PIPELINE_INITIALISATION { validate_params, null ) - + // // Check config provided to the pipeline // @@ -91,7 +90,6 @@ workflow PIPELINE_COMPLETION { email // string: email address email_on_fail // string: email address sent on pipeline failure plaintext_email // boolean: Send plain-text email instead of HTML - outdir // path: Path to output directory where results will be published monochrome_logs // boolean: Disable ANSI colour codes in log output hook_url // string: hook URL for notifications