diff --git a/.editorconfig b/.editorconfig index a30ae1e1..f61a6a78 100644 --- a/.editorconfig +++ b/.editorconfig @@ -23,11 +23,3 @@ indent_size = unset [/assets/email*] indent_size = unset -# To prevent errors for these test diamond databases -[/assets/test*/*.dmnd] -charset = unset -end_of_line = unset -insert_final_newline = unset -trim_trailing_whitespace = unset -indent_style = unset -indent_size = unset diff --git a/.github/ISSUE_TEMPLATE/bug_report.yml b/.github/ISSUE_TEMPLATE/bug_report.yml index 58919f2a..89aae5cc 100644 --- a/.github/ISSUE_TEMPLATE/bug_report.yml +++ b/.github/ISSUE_TEMPLATE/bug_report.yml @@ -38,7 +38,7 @@ body: id: system attributes: label: System information - description: "* Nextflow version _(eg. 23.04.1)_ + description: "* Nextflow version _(eg. 22.10.1)_ * Hardware _(eg. HPC, Desktop, Cloud)_ diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index 307a3b42..fede1317 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -1,7 +1,12 @@ name: nf-core CI # This workflow runs the pipeline with the minimal test dataset to check that it completes without any syntax errors on: - workflow_dispatch: + push: + branches: + - dev + pull_request: + release: + types: [published] env: NXF_ANSI_LOG: false @@ -19,7 +24,7 @@ jobs: strategy: matrix: NXF_VER: - - "23.04.1" + - "22.10.1" - "latest-everything" steps: - name: Check out pipeline code @@ -30,9 +35,19 @@ jobs: with: version: "${{ matrix.NXF_VER }}" + - name: Download the NCBI taxdump database + run: | + mkdir ncbi_taxdump + curl -L https://ftp.ncbi.nih.gov/pub/taxonomy/new_taxdump/new_taxdump.tar.gz | tar -C ncbi_taxdump -xzf - + + - name: Download the BUSCO lineage database + run: | + mkdir busco_database + curl -L https://tolit.cog.sanger.ac.uk/test-data/resources/busco/blobtoolkit.GCA_922984935.2.2023-08-03.lineages.tar.gz | tar -C busco_database -xzf - + - name: Run pipeline with test data # You can customise CI pipeline run tests as required # For example: adding multiple test runs with different parameters # Remember that you can parallelise this by using strategy.matrix run: | - nextflow run ${GITHUB_WORKSPACE} -profile test,docker --outdir ./results + nextflow run ${GITHUB_WORKSPACE} -profile test,docker --taxdump $PWD/ncbi_taxdump --busco $PWD/busco_database --outdir ./results diff --git a/.github/workflows/fix-linting.yml b/.github/workflows/fix-linting.yml index b7779fad..ff57bf69 100644 --- a/.github/workflows/fix-linting.yml +++ b/.github/workflows/fix-linting.yml @@ -8,21 +8,21 @@ jobs: # Only run if comment is on a PR with the main repo, and if it contains the magic keywords if: > contains(github.event.comment.html_url, '/pull/') && - contains(github.event.comment.body, '@nf-core-bot fix linting') && + contains(github.event.comment.body, '@sanger-tolsoft fix linting') && github.repository == 'sanger-tol/blobtoolkit' runs-on: ubuntu-latest steps: - # Use the @nf-core-bot token to check out so we can push later + # Use the @sanger-tolsoft token to check out so we can push later - uses: actions/checkout@v3 with: - token: ${{ secrets.nf_core_bot_auth_token }} + token: ${{ secrets.sangertolsoft_access_token }} # Action runs on the issue comment, so we don't get the PR by default # Use the gh cli to check out the PR - name: Checkout Pull Request run: gh pr checkout ${{ github.event.issue.number }} env: - GITHUB_TOKEN: ${{ secrets.nf_core_bot_auth_token }} + GITHUB_TOKEN: ${{ secrets.sangertolsoft_access_token }} - uses: actions/setup-node@v3 @@ -46,8 +46,8 @@ jobs: - name: Commit & push changes if: steps.prettier_status.outputs.result == 'fail' run: | - git config user.email "core@nf-co.re" - git config user.name "nf-core-bot" + git config user.email "105875386+sanger-tolsoft@users.noreply.github.com" + git config user.name "sanger-tolsoft" git config push.default upstream git add . git status diff --git a/.github/workflows/sangertest.yml b/.github/workflows/sanger_test.yml similarity index 78% rename from .github/workflows/sangertest.yml rename to .github/workflows/sanger_test.yml index 95479500..406a6280 100644 --- a/.github/workflows/sangertest.yml +++ b/.github/workflows/sanger_test.yml @@ -1,4 +1,4 @@ -name: nf-core Sanger LSF tests +name: sanger-tol LSF tests on: workflow_dispatch: @@ -13,12 +13,11 @@ jobs: if: github.event_name == 'workflow_dispatch' - name: Launch workflow via tower - uses: nf-core/tower-action@v2 + 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 }} - pipeline: ${{ github.repository }} revision: ${{ env.REVISION }} workdir: ${{ secrets.TOWER_WORKDIR_PARENT }}/work/${{ github.repository }}/work-${{ env.REVISION }} parameters: | @@ -26,3 +25,9 @@ jobs: "outdir": "${{ secrets.TOWER_WORKDIR_PARENT }}/results/${{ github.repository }}/results-${{ env.REVISION }}", } profiles: 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/sangerfulltest.yml b/.github/workflows/sanger_test_full.yml similarity index 80% rename from .github/workflows/sangerfulltest.yml rename to .github/workflows/sanger_test_full.yml index addef9bc..e3a25f7b 100644 --- a/.github/workflows/sangerfulltest.yml +++ b/.github/workflows/sanger_test_full.yml @@ -1,4 +1,4 @@ -name: nf-core Sanger LSF full size tests +name: sanger-tol LSF full size tests on: workflow_dispatch: @@ -18,12 +18,11 @@ jobs: if: github.event_name == 'workflow_dispatch' - name: Launch workflow via tower - uses: nf-core/tower-action@v2 + 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 }} - pipeline: ${{ github.repository }} revision: ${{ env.REVISION }} workdir: ${{ secrets.TOWER_WORKDIR_PARENT }}/work/${{ github.repository }}/work-${{ env.REVISION }} parameters: | @@ -31,3 +30,9 @@ jobs: "outdir": "${{ secrets.TOWER_WORKDIR_PARENT }}/results/${{ github.repository }}/results-${{ env.REVISION }}", } profiles: test_full,sanger,singularity,cleanup + - uses: actions/upload-artifact@v3 + with: + name: Tower debug log file + path: | + tower_action_*.log + tower_action_*.json diff --git a/.nf-core.yml b/.nf-core.yml index 5c98553f..6f8fbccc 100644 --- a/.nf-core.yml +++ b/.nf-core.yml @@ -8,6 +8,7 @@ lint: files_unchanged: - LICENSE - .github/ISSUE_TEMPLATE/bug_report.yml + - .github/workflows/linting.yml - assets/sendmail_template.txt - lib/NfcoreTemplate.groovy - .prettierignore diff --git a/README.md b/README.md index 58008e6e..73d24581 100644 --- a/README.md +++ b/README.md @@ -5,7 +5,7 @@ [![GitHub Actions Linting Status](https://github.com/sanger-tol/blobtoolkit/workflows/nf-core%20linting/badge.svg)](https://github.com/sanger-tol/blobtoolkit/actions?query=workflow%3A%22nf-core+linting%22) [![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.7949058-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.7949058) -[![Nextflow](https://img.shields.io/badge/nextflow%20DSL2-%E2%89%A523.04.1-23aa62.svg)](https://www.nextflow.io/) +[![Nextflow](https://img.shields.io/badge/nextflow%20DSL2-%E2%89%A522.10.1-23aa62.svg)](https://www.nextflow.io/) [![run with conda](http://img.shields.io/badge/run%20with-conda-3EB049?labelColor=000000&logo=anaconda)](https://docs.conda.io/en/latest/) [![run with docker](https://img.shields.io/badge/run%20with-docker-0db7ed?labelColor=000000&logo=docker)](https://www.docker.com/) [![run with singularity](https://img.shields.io/badge/run%20with-singularity-1d355c.svg?labelColor=000000)](https://sylabs.io/docs/) diff --git a/assets/test/mCerEla1.1.buscogenes.dmnd b/assets/test/mCerEla1.1.buscogenes.dmnd deleted file mode 100644 index bccca41d..00000000 Binary files a/assets/test/mCerEla1.1.buscogenes.dmnd and /dev/null differ diff --git a/assets/test_full/full_samplesheet.csv b/assets/test_full/full_samplesheet.csv index 88fc7462..6a3ba69d 100644 --- a/assets/test_full/full_samplesheet.csv +++ b/assets/test_full/full_samplesheet.csv @@ -1,3 +1,3 @@ sample,datatype,datafile -gfLaeSulp1,hic,/lustre/scratch123/tol/projects/.sandbox/data/fungi/Laetiporus_sulphureus/analysis/gfLaeSulp1.1/read_mapping/hic/GCA_927399515.1.unmasked.hic.gfLaeSulp1.cram -gfLaeSulp1,pacbio,/lustre/scratch123/tol/projects/.sandbox/data/fungi/Laetiporus_sulphureus/analysis/gfLaeSulp1.1/read_mapping/pacbio/GCA_927399515.1.unmasked.pacbio.gfLaeSulp1.cram +gfLaeSulp1,hic,/lustre/scratch123/tol/resources/nextflow/test-data/Laetiporus_sulphureus/analysis/gfLaeSulp1.1/read_mapping/hic/GCA_927399515.1.unmasked.hic.gfLaeSulp1.cram +gfLaeSulp1,pacbio,/lustre/scratch123/tol/resources/nextflow/test-data/Laetiporus_sulphureus/analysis/gfLaeSulp1.1/read_mapping/pacbio/GCA_927399515.1.unmasked.pacbio.gfLaeSulp1.cram diff --git a/assets/test_full/gfLaeSulp1.1.buscogenes.dmnd b/assets/test_full/gfLaeSulp1.1.buscogenes.dmnd deleted file mode 100644 index a0d0e1d2..00000000 Binary files a/assets/test_full/gfLaeSulp1.1.buscogenes.dmnd and /dev/null differ diff --git a/conf/modules.config b/conf/modules.config index ebf62694..1cf58859 100644 --- a/conf/modules.config +++ b/conf/modules.config @@ -14,7 +14,7 @@ process { withName: "SAMPLESHEET_CHECK" { publishDir = [ - path: { "${params.outdir}/blobtoolkit_info" }, + path: { "${params.outdir}/pipeline_info/blobtoolkit" }, mode: params.publish_dir_mode, saveAs: { filename -> filename.equals("versions.yml") ? null : filename } ] @@ -30,6 +30,7 @@ process { withName: "BUSCO" { scratch = true + // Overridden in the test profile, see at the end of this file ext.args = "--mode genome --force" } @@ -68,7 +69,7 @@ process { withName: "CUSTOM_DUMPSOFTWAREVERSIONS" { publishDir = [ - path: { "${params.outdir}/blobtoolkit_info" }, + path: { "${params.outdir}/pipeline_info/blobtoolkit" }, mode: params.publish_dir_mode, pattern: "*_versions.yml" ] @@ -84,3 +85,22 @@ process { } } + + +/* +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + Additional configuration to speed processes up during testing. + +---------------------------------------------------------------------------------------- +*/ + +profiles { + test { + process { + withName: BUSCO { + // Note: BUSCO *must* see the double-quotes around the parameters + ext.args = '--mode genome --force --metaeuk_parameters \'"-s=2"\' --metaeuk_rerun_parameters \'"-s=2"\'' + } + } + } +} diff --git a/conf/test.config b/conf/test.config index 165bfff6..e064008b 100644 --- a/conf/test.config +++ b/conf/test.config @@ -22,15 +22,15 @@ params { // Input test data // Specify the paths to your test data // Give any required params for the test so that command line flags are not needed - input = "${projectDir}/assets/test/samplesheet.csv" + input = "${projectDir}/assets/test/samplesheet_s3.csv" // Fasta references - fasta = "/lustre/scratch123/tol/resources/nextflow/test-data/Meles_meles/assembly/release/mMelMel3.1_paternal_haplotype/GCA_922984935.2.subset.fasta.gz" + fasta = "https://tolit.cog.sanger.ac.uk/test-data/Meles_meles/assembly/release/mMelMel3.1_paternal_haplotype/GCA_922984935.2.subset.fasta.gz" accession = "GCA_922984935.2" taxon = "Meles meles" // Databases taxdump = "/lustre/scratch123/tol/teams/grit/geval_pipeline/btk_databases/taxdump" - busco = "/lustre/scratch123/tol/resources/nextflow/busco_2021_06_reduced/" - uniprot = "${projectDir}/assets/test/mCerEla1.1.buscogenes.dmnd" + busco = "/lustre/scratch123/tol/resources/nextflow/busco/blobtoolkit.GCA_922984935.2.2023-08-03" + uniprot = "https://tolit.cog.sanger.ac.uk/test-data/resources/diamond/mCerEla1.1.buscogenes.dmnd" } diff --git a/conf/test_full.config b/conf/test_full.config index ee22dba2..47fe81d7 100644 --- a/conf/test_full.config +++ b/conf/test_full.config @@ -22,12 +22,12 @@ params { input = "${projectDir}/assets/test_full/full_samplesheet.csv" // Fasta references - fasta = "/lustre/scratch124/tol/projects/darwin/data/fungi/Laetiporus_sulphureus/assembly/release/gfLaeSulp1.1/insdc/GCA_927399515.1.fasta.gz" + fasta = "/lustre/scratch123/tol/resources/nextflow/test-data/Laetiporus_sulphureus/assembly/release/gfLaeSulp1.1/insdc/GCA_927399515.1.fasta.gz" accession = "GCA_927399515.1" taxon = "Laetiporus sulphureus" // Databases taxdump = "/lustre/scratch123/tol/teams/grit/geval_pipeline/btk_databases/taxdump" busco = "/lustre/scratch123/tol/resources/busco/v5/" - uniprot = "${projectDir}/assets/test_full/gfLaeSulp1.1.buscogenes.dmnd" + uniprot = "https://tolit.cog.sanger.ac.uk/test-data/resources/diamond/gfLaeSulp1.1.buscogenes.dmnd" } diff --git a/docs/output.md b/docs/output.md index 437c6df7..33040ea0 100644 --- a/docs/output.md +++ b/docs/output.md @@ -52,7 +52,7 @@ Results generated by MultiQC collate pipeline QC from supported tools. The pipel
Output files -- `blobtoolkit_info/` +- `pipeline_info/blobtoolkit/` - Reports generated by Nextflow: `execution_report.html`, `execution_timeline.html`, `execution_trace.txt` and `pipeline_dag.dot`/`pipeline_dag.svg`. - Reports generated by the pipeline: `pipeline_report.html`, `pipeline_report.txt` and `software_versions.yml`. The `pipeline_report*` files will only be present if the `--email` / `--email_on_fail` parameter's are used when running the pipeline. - Reformatted samplesheet files used as input to the pipeline: `samplesheet.valid.csv`. diff --git a/lib/NfcoreTemplate.groovy b/lib/NfcoreTemplate.groovy index 2777ae2b..e463d9ed 100755 --- a/lib/NfcoreTemplate.groovy +++ b/lib/NfcoreTemplate.groovy @@ -154,7 +154,7 @@ class NfcoreTemplate { } // Write summary e-mail HTML to a file - def output_d = new File("${params.outdir}/blobtoolkit_info/") + def output_d = new File("${params.outdir}/pipeline_info/blobtoolkit/") if (!output_d.exists()) { output_d.mkdirs() } diff --git a/modules/local/blobtoolkit/blobdir.nf b/modules/local/blobtoolkit/blobdir.nf index 3f064bce..baf46df1 100644 --- a/modules/local/blobtoolkit/blobdir.nf +++ b/modules/local/blobtoolkit/blobdir.nf @@ -5,7 +5,7 @@ process BLOBTOOLKIT_BLOBDIR { if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) { exit 1, "BLOBTOOLKIT_BLOBDIR module does not support Conda. Please use Docker / Singularity / Podman instead." } - container "genomehubs/blobtoolkit:4.1.5" + container "docker.io/genomehubs/blobtoolkit:4.1.5" input: tuple val(meta), path(window, stageAs: 'windowstats/*') diff --git a/modules/local/blobtoolkit/config.nf b/modules/local/blobtoolkit/config.nf index ce1e3adc..ed7bba45 100644 --- a/modules/local/blobtoolkit/config.nf +++ b/modules/local/blobtoolkit/config.nf @@ -5,7 +5,7 @@ process BLOBTOOLKIT_CONFIG { if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) { exit 1, "GENERATE_CONFIG module does not support Conda. Please use Docker / Singularity / Podman instead." } - container "genomehubs/blobtoolkit:4.1.5" + container "docker.io/genomehubs/blobtoolkit:4.1.5" input: tuple val(meta), path(fasta) diff --git a/modules/local/blobtoolkit/countbuscos.nf b/modules/local/blobtoolkit/countbuscos.nf index 1379cbac..b118f702 100644 --- a/modules/local/blobtoolkit/countbuscos.nf +++ b/modules/local/blobtoolkit/countbuscos.nf @@ -5,7 +5,7 @@ process BLOBTOOLKIT_COUNTBUSCOS { if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) { exit 1, "BLOBTOOLKIT_COUNTBUSCOS module does not support Conda. Please use Docker / Singularity / Podman instead." } - container "genomehubs/blobtoolkit:4.1.5" + container "docker.io/genomehubs/blobtoolkit:4.1.5" input: tuple val(meta), path(table, stageAs: 'dir??/*') diff --git a/modules/local/blobtoolkit/extractbuscos.nf b/modules/local/blobtoolkit/extractbuscos.nf index 23c73247..cd9441b6 100644 --- a/modules/local/blobtoolkit/extractbuscos.nf +++ b/modules/local/blobtoolkit/extractbuscos.nf @@ -5,7 +5,7 @@ process BLOBTOOLKIT_EXTRACTBUSCOS { if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) { exit 1, "BLOBTOOLKIT_EXTRACTBUSCOS module does not support Conda. Please use Docker / Singularity / Podman instead." } - container "genomehubs/blobtoolkit:4.1.5" + container "docker.io/genomehubs/blobtoolkit:4.1.5" input: tuple val(meta), path(fasta) diff --git a/modules/local/blobtoolkit/images.nf b/modules/local/blobtoolkit/images.nf index 11bdd485..8cfbae22 100644 --- a/modules/local/blobtoolkit/images.nf +++ b/modules/local/blobtoolkit/images.nf @@ -5,7 +5,7 @@ process BLOBTOOLKIT_IMAGES { if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) { exit 1, "BLOBTOOLKIT_IMAGES module does not support Conda. Please use Docker / Singularity / Podman instead." } - container "genomehubs/blobtk:0.3.3" + container "docker.io/genomehubs/blobtk:0.3.3" input: tuple val(meta), path(blobdir) diff --git a/modules/local/blobtoolkit/metadata.nf b/modules/local/blobtoolkit/metadata.nf index 32339c48..30f47538 100644 --- a/modules/local/blobtoolkit/metadata.nf +++ b/modules/local/blobtoolkit/metadata.nf @@ -5,7 +5,7 @@ process BLOBTOOLKIT_METADATA { if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) { exit 1, "BLOBTOOLKIT_METADATA module does not support Conda. Please use Docker / Singularity / Podman instead." } - container "genomehubs/blobtoolkit:4.1.5" + container "docker.io/genomehubs/blobtoolkit:4.1.5" input: tuple val(meta), path(yaml) diff --git a/modules/local/blobtoolkit/summary.nf b/modules/local/blobtoolkit/summary.nf index d1059d8a..36e4ad25 100644 --- a/modules/local/blobtoolkit/summary.nf +++ b/modules/local/blobtoolkit/summary.nf @@ -5,7 +5,7 @@ process BLOBTOOLKIT_SUMMARY { if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) { exit 1, "BLOBTOOLKIT_SUMMARY module does not support Conda. Please use Docker / Singularity / Podman instead." } - container "genomehubs/blobtoolkit:4.1.5" + container "docker.io/genomehubs/blobtoolkit:4.1.5" input: tuple val(meta), path(blobdir) diff --git a/modules/local/blobtoolkit/windowstats.nf b/modules/local/blobtoolkit/windowstats.nf index 0517535f..06dd3c42 100644 --- a/modules/local/blobtoolkit/windowstats.nf +++ b/modules/local/blobtoolkit/windowstats.nf @@ -5,7 +5,7 @@ process BLOBTOOLKIT_WINDOWSTATS { if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) { exit 1, "GET_WINDOW_STATS module does not support Conda. Please use Docker / Singularity / Podman instead." } - container "genomehubs/blobtoolkit:4.1.5" + container "docker.io/genomehubs/blobtoolkit:4.1.5" input: tuple val(meta), path(tsv) diff --git a/modules/local/create_bed.nf b/modules/local/create_bed.nf index 034ab1e6..3158a732 100644 --- a/modules/local/create_bed.nf +++ b/modules/local/create_bed.nf @@ -5,7 +5,7 @@ process CREATE_BED { conda "conda-forge::gawk=5.1.0" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/gawk:5.1.0' : - 'quay.io/biocontainers/gawk:5.1.0' }" + 'biocontainers/gawk:5.1.0' }" input: tuple val(meta), path(tsv) //path to tsv output from fasta windows diff --git a/modules/local/samplesheet_check.nf b/modules/local/samplesheet_check.nf index 5798da0e..760f3e44 100644 --- a/modules/local/samplesheet_check.nf +++ b/modules/local/samplesheet_check.nf @@ -5,7 +5,7 @@ process SAMPLESHEET_CHECK { conda "conda-forge::python=3.9.1" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/python:3.9--1' : - 'quay.io/biocontainers/python:3.9--1' }" + 'biocontainers/python:3.9--1' }" input: path samplesheet diff --git a/modules/local/windowstats_input.nf b/modules/local/windowstats_input.nf index f366025d..1c660442 100644 --- a/modules/local/windowstats_input.nf +++ b/modules/local/windowstats_input.nf @@ -5,7 +5,7 @@ process WINDOWSTATS_INPUT { conda "conda-forge::pandas=1.5.2" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/pandas:1.5.2': - 'quay.io/biocontainers/pandas:1.5.2' }" + 'biocontainers/pandas:1.5.2' }" input: tuple val(meta), path(freq) diff --git a/nextflow.config b/nextflow.config index 988b2a1c..098c0365 100644 --- a/nextflow.config +++ b/nextflow.config @@ -36,7 +36,7 @@ params { // Boilerplate options outdir = 'results' - tracedir = "${params.outdir}/blobtoolkit_info" + tracedir = "${params.outdir}/pipeline_info/blobtoolkit" publish_dir_mode = 'copy' email = null email_on_fail = null @@ -220,7 +220,7 @@ manifest { homePage = 'https://github.com/sanger-tol/blobtoolkit' description = """Quality assessment of genome assemblies""" mainScript = 'main.nf' - nextflowVersion = '!>=23.04.1' + nextflowVersion = '!>=22.10.1' version = '0.2.0' doi = '10.5281/zenodo.7949058' } diff --git a/nextflow_schema.json b/nextflow_schema.json index a960bee2..21c2c2e0 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -287,7 +287,7 @@ "tracedir": { "type": "string", "description": "Directory to keep pipeline Nextflow logs and reports.", - "default": "${params.outdir}/blobtoolkit_info", + "default": "${params.outdir}/pipeline_info/blobtoolkit", "fa_icon": "fas fa-cogs", "hidden": true },