From 5d1ea048425ad38bf6861b042de3c8fd948a66bf Mon Sep 17 00:00:00 2001 From: nf-core-bot Date: Fri, 30 Jun 2023 16:12:43 +0000 Subject: [PATCH 01/32] Template update for nf-core/tools version 2.9 --- .github/CONTRIBUTING.md | 1 - .github/ISSUE_TEMPLATE/bug_report.yml | 2 +- .github/workflows/awsfulltest.yml | 11 +- .github/workflows/awstest.yml | 10 +- .github/workflows/ci.yml | 2 +- .gitpod.yml | 5 + CHANGELOG.md | 2 +- CITATIONS.md | 6 + README.md | 6 +- assets/methods_description_template.yml | 12 +- assets/multiqc_config.yml | 4 +- assets/nf-core-airrflow_logo_light.png | Bin 10534 -> 70812 bytes assets/slackreport.json | 2 +- conf/test_full.config | 2 - docs/usage.md | 6 +- lib/NfcoreSchema.groovy | 530 ------------------------ lib/NfcoreTemplate.groovy | 2 +- lib/WorkflowAirrflow.groovy | 45 +- lib/WorkflowMain.groovy | 37 -- main.nf | 16 + nextflow.config | 54 ++- nextflow_schema.json | 36 +- workflows/airrflow.nf | 25 +- 23 files changed, 177 insertions(+), 639 deletions(-) delete mode 100755 lib/NfcoreSchema.groovy diff --git a/.github/CONTRIBUTING.md b/.github/CONTRIBUTING.md index efebe9e0..5cb3103c 100644 --- a/.github/CONTRIBUTING.md +++ b/.github/CONTRIBUTING.md @@ -116,4 +116,3 @@ To get started: Devcontainer specs: - [DevContainer config](.devcontainer/devcontainer.json) -- [Dockerfile](.devcontainer/Dockerfile) diff --git a/.github/ISSUE_TEMPLATE/bug_report.yml b/.github/ISSUE_TEMPLATE/bug_report.yml index f2e98962..b0260675 100644 --- a/.github/ISSUE_TEMPLATE/bug_report.yml +++ b/.github/ISSUE_TEMPLATE/bug_report.yml @@ -42,7 +42,7 @@ body: attributes: label: System information description: | - * Nextflow version _(eg. 22.10.1)_ + * Nextflow version _(eg. 23.04.0)_ * Hardware _(eg. HPC, Desktop, Cloud)_ * Executor _(eg. slurm, local, awsbatch)_ * Container engine: _(e.g. Docker, Singularity, Conda, Podman, Shifter, Charliecloud, or Apptainer)_ diff --git a/.github/workflows/awsfulltest.yml b/.github/workflows/awsfulltest.yml index 8f3f758a..4918c9d9 100644 --- a/.github/workflows/awsfulltest.yml +++ b/.github/workflows/awsfulltest.yml @@ -14,7 +14,7 @@ jobs: runs-on: ubuntu-latest steps: - name: Launch workflow via tower - uses: seqeralabs/action-tower-launch@v1 + uses: seqeralabs/action-tower-launch@v2 # TODO nf-core: You can customise AWS full pipeline tests as required # Add full size test data (but still relatively small datasets for few samples) # on the `test_full.config` test runs with only one set of parameters @@ -22,13 +22,18 @@ jobs: workspace_id: ${{ secrets.TOWER_WORKSPACE_ID }} access_token: ${{ secrets.TOWER_ACCESS_TOKEN }} compute_env: ${{ secrets.TOWER_COMPUTE_ENV }} + revision: ${{ github.sha }} workdir: s3://${{ secrets.AWS_S3_BUCKET }}/work/airrflow/work-${{ github.sha }} parameters: | { + "hook_url": "${{ secrets.MEGATESTS_ALERTS_SLACK_HOOK_URL }}", "outdir": "s3://${{ secrets.AWS_S3_BUCKET }}/airrflow/results-${{ github.sha }}" } - profiles: test_full,aws_tower + profiles: test_full + - uses: actions/upload-artifact@v3 with: name: Tower debug log file - path: tower_action_*.log + path: | + tower_action_*.log + tower_action_*.json diff --git a/.github/workflows/awstest.yml b/.github/workflows/awstest.yml index 64fb9141..269c6875 100644 --- a/.github/workflows/awstest.yml +++ b/.github/workflows/awstest.yml @@ -12,18 +12,22 @@ jobs: steps: # Launch workflow using Tower CLI tool action - name: Launch workflow via tower - uses: seqeralabs/action-tower-launch@v1 + 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 }} + revision: ${{ github.sha }} workdir: s3://${{ secrets.AWS_S3_BUCKET }}/work/airrflow/work-${{ github.sha }} parameters: | { "outdir": "s3://${{ secrets.AWS_S3_BUCKET }}/airrflow/results-test-${{ github.sha }}" } - profiles: test,aws_tower + profiles: test + - uses: actions/upload-artifact@v3 with: name: Tower debug log file - path: tower_action_*.log + path: | + tower_action_*.log + tower_action_*.json diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index 6c28fa5b..34dd6616 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -24,7 +24,7 @@ jobs: strategy: matrix: NXF_VER: - - "22.10.1" + - "23.04.0" - "latest-everything" steps: - name: Check out pipeline code diff --git a/.gitpod.yml b/.gitpod.yml index 85d95ecc..25488dcc 100644 --- a/.gitpod.yml +++ b/.gitpod.yml @@ -1,4 +1,9 @@ image: nfcore/gitpod:latest +tasks: + - name: Update Nextflow and setup pre-commit + command: | + pre-commit install --install-hooks + nextflow self-update vscode: extensions: # based on nf-core.nf-core-extensionpack diff --git a/CHANGELOG.md b/CHANGELOG.md index ab3352c4..cd4fd023 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -3,7 +3,7 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/) and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html). -## v3.0 - [date] +## v3.1.0 - [date] Initial release of nf-core/airrflow, created with the [nf-core](https://nf-co.re/) template. diff --git a/CITATIONS.md b/CITATIONS.md index b0f5c3db..7ba186a8 100644 --- a/CITATIONS.md +++ b/CITATIONS.md @@ -12,7 +12,10 @@ - [FastQC](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/) + > Andrews, S. (2010). FastQC: A Quality Control Tool for High Throughput Sequence Data [Online]. Available online https://www.bioinformatics.babraham.ac.uk/projects/fastqc/. + - [MultiQC](https://pubmed.ncbi.nlm.nih.gov/27312411/) + > Ewels P, Magnusson M, Lundin S, Käller M. MultiQC: summarize analysis results for multiple tools and samples in a single report. Bioinformatics. 2016 Oct 1;32(19):3047-8. doi: 10.1093/bioinformatics/btw354. Epub 2016 Jun 16. PubMed PMID: 27312411; PubMed Central PMCID: PMC5039924. ## Software packaging/containerisation tools @@ -31,5 +34,8 @@ - [Docker](https://dl.acm.org/doi/10.5555/2600239.2600241) + > Merkel, D. (2014). Docker: lightweight linux containers for consistent development and deployment. Linux Journal, 2014(239), 2. doi: 10.5555/2600239.2600241. + - [Singularity](https://pubmed.ncbi.nlm.nih.gov/28494014/) + > Kurtzer GM, Sochat V, Bauer MW. Singularity: Scientific containers for mobility of compute. PLoS One. 2017 May 11;12(5):e0177459. doi: 10.1371/journal.pone.0177459. eCollection 2017. PubMed PMID: 28494014; PubMed Central PMCID: PMC5426675. diff --git a/README.md b/README.md index 5ab676d9..6a23f938 100644 --- a/README.md +++ b/README.md @@ -2,7 +2,7 @@ [![AWS CI](https://img.shields.io/badge/CI%20tests-full%20size-FF9900?labelColor=000000&logo=Amazon%20AWS)](https://nf-co.re/airrflow/results)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.XXXXXXX-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.XXXXXXX) -[![Nextflow](https://img.shields.io/badge/nextflow%20DSL2-%E2%89%A522.10.1-23aa62.svg)](https://www.nextflow.io/) +[![Nextflow](https://img.shields.io/badge/nextflow%20DSL2-%E2%89%A523.04.0-23aa62.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/) @@ -66,11 +66,11 @@ nextflow run nf-core/airrflow \ > provided by the `-c` Nextflow option can be used to provide any configuration _**except for parameters**_; > see [docs](https://nf-co.re/usage/configuration#custom-configuration-files). -For more details, please refer to the [usage documentation](https://nf-co.re/airrflow/usage) and the [parameter documentation](https://nf-co.re/airrflow/parameters). +For more details and further functionality, please refer to the [usage documentation](https://nf-co.re/airrflow/usage) and the [parameter documentation](https://nf-co.re/airrflow/parameters). ## Pipeline output -To see the the results of a test run with a full size dataset refer to the [results](https://nf-co.re/airrflow/results) tab on the nf-core website pipeline page. +To see the results of an example test run with a full size dataset refer to the [results](https://nf-co.re/airrflow/results) tab on the nf-core website pipeline page. For more details about the output files and reports, please refer to the [output documentation](https://nf-co.re/airrflow/output). diff --git a/assets/methods_description_template.yml b/assets/methods_description_template.yml index 4b9bedf5..e4acf864 100644 --- a/assets/methods_description_template.yml +++ b/assets/methods_description_template.yml @@ -3,17 +3,21 @@ description: "Suggested text and references to use when describing pipeline usag section_name: "nf-core/airrflow Methods Description" section_href: "https://github.com/nf-core/airrflow" plot_type: "html" -## TODO nf-core: Update the HTML below to your prefered methods description, e.g. add publication citation for this pipeline +## TODO nf-core: Update the HTML below to your preferred methods description, e.g. add publication citation for this pipeline ## You inject any metadata in the Nextflow '${workflow}' object data: |

Methods

-

Data was processed using nf-core/airrflow v${workflow.manifest.version} ${doi_text} of the nf-core collection of workflows (Ewels et al., 2020).

+

Data was processed using nf-core/airrflow v${workflow.manifest.version} ${doi_text} of the nf-core collection of workflows (Ewels et al., 2020), utilising reproducible software environments from the Bioconda (Grüning et al., 2018) and Biocontainers (da Veiga Leprevost et al., 2017) projects.

The pipeline was executed with Nextflow v${workflow.nextflow.version} (Di Tommaso et al., 2017) with the following command:

${workflow.commandLine}
+

${tool_citations}

References

Notes:
diff --git a/assets/multiqc_config.yml b/assets/multiqc_config.yml index c980e3f2..393a88b0 100644 --- a/assets/multiqc_config.yml +++ b/assets/multiqc_config.yml @@ -1,7 +1,7 @@ report_comment: > - This report has been generated by the nf-core/airrflow + This report has been generated by the nf-core/airrflow analysis pipeline. 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"author_icon": "https://www.nextflow.io/docs/latest/_static/favicon.ico", "text": "<% if (success) { %>Pipeline completed successfully!<% } else { %>Pipeline completed with errors<% } %>", "fields": [ diff --git a/conf/test_full.config b/conf/test_full.config index ff79f3e2..9c410f35 100644 --- a/conf/test_full.config +++ b/conf/test_full.config @@ -10,8 +10,6 @@ ---------------------------------------------------------------------------------------- */ -cleanup = true - params { config_profile_name = 'Full test profile' config_profile_description = 'Full test dataset to check pipeline function' diff --git a/docs/usage.md b/docs/usage.md index b947ea51..1f49c7a7 100644 --- a/docs/usage.md +++ b/docs/usage.md @@ -57,7 +57,7 @@ An [example samplesheet](../assets/samplesheet.csv) has been provided with the p The typical command for running the pipeline is as follows: ```bash -nextflow run nf-core/airrflow --input samplesheet.csv --outdir --genome GRCh37 -profile docker +nextflow run nf-core/airrflow --input ./samplesheet.csv --outdir ./results --genome GRCh37 -profile docker ``` This will launch the pipeline with the `docker` configuration profile. See below for more information about profiles. @@ -76,7 +76,8 @@ If you wish to repeatedly use the same parameters for multiple runs, rather than Pipeline settings can be provided in a `yaml` or `json` file via `-params-file `. > ⚠️ Do not use `-c ` to specify parameters as this will result in errors. Custom config files specified with `-c` must only be used for [tuning process resource specifications](https://nf-co.re/docs/usage/configuration#tuning-workflow-resources), other infrastructural tweaks (such as output directories), or module arguments (args). -> The above pipeline run specified with a params file in yaml format: + +The above pipeline run specified with a params file in yaml format: ```bash nextflow run nf-core/airrflow -profile docker -params-file params.yaml @@ -88,7 +89,6 @@ with `params.yaml` containing: input: './samplesheet.csv' outdir: './results/' genome: 'GRCh37' -input: 'data' <...> ``` diff --git a/lib/NfcoreSchema.groovy b/lib/NfcoreSchema.groovy deleted file mode 100755 index 9b34804d..00000000 --- a/lib/NfcoreSchema.groovy +++ /dev/null @@ -1,530 +0,0 @@ -// -// This file holds several functions used to perform JSON parameter validation, help and summary rendering for the nf-core pipeline template. -// - -import nextflow.Nextflow -import org.everit.json.schema.Schema -import org.everit.json.schema.loader.SchemaLoader -import org.everit.json.schema.ValidationException -import org.json.JSONObject -import org.json.JSONTokener -import org.json.JSONArray -import groovy.json.JsonSlurper -import groovy.json.JsonBuilder - -class NfcoreSchema { - - // - // Resolve Schema path relative to main workflow directory - // - public static String getSchemaPath(workflow, schema_filename='nextflow_schema.json') { - return "${workflow.projectDir}/${schema_filename}" - } - - // - // Function to loop over all parameters defined in schema and check - // whether the given parameters adhere to the specifications - // - /* groovylint-disable-next-line UnusedPrivateMethodParameter */ - public static void validateParameters(workflow, params, log, schema_filename='nextflow_schema.json') { - def has_error = false - //~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~// - // Check for nextflow core params and unexpected params - def json = new File(getSchemaPath(workflow, schema_filename=schema_filename)).text - def Map schemaParams = (Map) new JsonSlurper().parseText(json).get('definitions') - def nf_params = [ - // Options for base `nextflow` command - 'bg', - 'c', - 'C', - 'config', - 'd', - 'D', - 'dockerize', - 'h', - 'log', - 'q', - 'quiet', - 'syslog', - 'v', - - // Options for `nextflow run` command - 'ansi', - 'ansi-log', - 'bg', - 'bucket-dir', - 'c', - 'cache', - 'config', - 'dsl2', - 'dump-channels', - 'dump-hashes', - 'E', - 'entry', - 'latest', - 'lib', - 'main-script', - 'N', - 'name', - 'offline', - 'params-file', - 'pi', - 'plugins', - 'poll-interval', - 'pool-size', - 'profile', - 'ps', - 'qs', - 'queue-size', - 'r', - 'resume', - 'revision', - 'stdin', - 'stub', - 'stub-run', - 'test', - 'w', - 'with-apptainer', - 'with-charliecloud', - 'with-conda', - 'with-dag', - 'with-docker', - 'with-mpi', - 'with-notification', - 'with-podman', - 'with-report', - 'with-singularity', - 'with-timeline', - 'with-tower', - 'with-trace', - 'with-weblog', - 'without-docker', - 'without-podman', - 'work-dir' - ] - def unexpectedParams = [] - - // Collect expected parameters from the schema - def expectedParams = [] - def enums = [:] - for (group in schemaParams) { - for (p in group.value['properties']) { - expectedParams.push(p.key) - if (group.value['properties'][p.key].containsKey('enum')) { - enums[p.key] = group.value['properties'][p.key]['enum'] - } - } - } - - for (specifiedParam in params.keySet()) { - // nextflow params - if (nf_params.contains(specifiedParam)) { - log.error "ERROR: You used a core Nextflow option with two hyphens: '--${specifiedParam}'. Please resubmit with '-${specifiedParam}'" - has_error = true - } - // unexpected params - def params_ignore = params.schema_ignore_params.split(',') + 'schema_ignore_params' - def expectedParamsLowerCase = expectedParams.collect{ it.replace("-", "").toLowerCase() } - def specifiedParamLowerCase = specifiedParam.replace("-", "").toLowerCase() - def isCamelCaseBug = (specifiedParam.contains("-") && !expectedParams.contains(specifiedParam) && expectedParamsLowerCase.contains(specifiedParamLowerCase)) - if (!expectedParams.contains(specifiedParam) && !params_ignore.contains(specifiedParam) && !isCamelCaseBug) { - // Temporarily remove camelCase/camel-case params #1035 - def unexpectedParamsLowerCase = unexpectedParams.collect{ it.replace("-", "").toLowerCase()} - if (!unexpectedParamsLowerCase.contains(specifiedParamLowerCase)){ - unexpectedParams.push(specifiedParam) - } - } - } - - //~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~// - // Validate parameters against the schema - InputStream input_stream = new File(getSchemaPath(workflow, schema_filename=schema_filename)).newInputStream() - JSONObject raw_schema = new JSONObject(new JSONTokener(input_stream)) - - // Remove anything that's in params.schema_ignore_params - raw_schema = removeIgnoredParams(raw_schema, params) - - Schema schema = SchemaLoader.load(raw_schema) - - // Clean the parameters - def cleanedParams = cleanParameters(params) - - // Convert to JSONObject - def jsonParams = new JsonBuilder(cleanedParams) - JSONObject params_json = new JSONObject(jsonParams.toString()) - - // Validate - try { - schema.validate(params_json) - } catch (ValidationException e) { - println '' - log.error 'ERROR: Validation of pipeline parameters failed!' - JSONObject exceptionJSON = e.toJSON() - printExceptions(exceptionJSON, params_json, log, enums) - println '' - has_error = true - } - - // Check for unexpected parameters - if (unexpectedParams.size() > 0) { - Map colors = NfcoreTemplate.logColours(params.monochrome_logs) - println '' - def warn_msg = 'Found unexpected parameters:' - for (unexpectedParam in unexpectedParams) { - warn_msg = warn_msg + "\n* --${unexpectedParam}: ${params[unexpectedParam].toString()}" - } - log.warn warn_msg - log.info "- ${colors.dim}Ignore this warning: params.schema_ignore_params = \"${unexpectedParams.join(',')}\" ${colors.reset}" - println '' - } - - if (has_error) { - Nextflow.error('Exiting!') - } - } - - // - // Beautify parameters for --help - // - public static String paramsHelp(workflow, params, command, schema_filename='nextflow_schema.json') { - Map colors = NfcoreTemplate.logColours(params.monochrome_logs) - Integer num_hidden = 0 - String output = '' - output += 'Typical pipeline command:\n\n' - output += " ${colors.cyan}${command}${colors.reset}\n\n" - Map params_map = paramsLoad(getSchemaPath(workflow, schema_filename=schema_filename)) - Integer max_chars = paramsMaxChars(params_map) + 1 - Integer desc_indent = max_chars + 14 - Integer dec_linewidth = 160 - desc_indent - for (group in params_map.keySet()) { - Integer num_params = 0 - String group_output = colors.underlined + colors.bold + group + colors.reset + '\n' - def group_params = params_map.get(group) // This gets the parameters of that particular group - for (param in group_params.keySet()) { - if (group_params.get(param).hidden && !params.show_hidden_params) { - num_hidden += 1 - continue; - } - def type = '[' + group_params.get(param).type + ']' - def description = group_params.get(param).description - def defaultValue = group_params.get(param).default != null ? " [default: " + group_params.get(param).default.toString() + "]" : '' - def description_default = description + colors.dim + defaultValue + colors.reset - // Wrap long description texts - // Loosely based on https://dzone.com/articles/groovy-plain-text-word-wrap - if (description_default.length() > dec_linewidth){ - List olines = [] - String oline = "" // " " * indent - description_default.split(" ").each() { wrd -> - if ((oline.size() + wrd.size()) <= dec_linewidth) { - oline += wrd + " " - } else { - olines += oline - oline = wrd + " " - } - } - olines += oline - description_default = olines.join("\n" + " " * desc_indent) - } - group_output += " --" + param.padRight(max_chars) + colors.dim + type.padRight(10) + colors.reset + description_default + '\n' - num_params += 1 - } - group_output += '\n' - if (num_params > 0){ - output += group_output - } - } - if (num_hidden > 0){ - output += colors.dim + "!! Hiding $num_hidden params, use --show_hidden_params to show them !!\n" + colors.reset - } - output += NfcoreTemplate.dashedLine(params.monochrome_logs) - return output - } - - // - // Groovy Map summarising parameters/workflow options used by the pipeline - // - public static LinkedHashMap paramsSummaryMap(workflow, params, schema_filename='nextflow_schema.json') { - // Get a selection of core Nextflow workflow options - def Map workflow_summary = [:] - if (workflow.revision) { - workflow_summary['revision'] = workflow.revision - } - workflow_summary['runName'] = workflow.runName - if (workflow.containerEngine) { - workflow_summary['containerEngine'] = workflow.containerEngine - } - if (workflow.container) { - workflow_summary['container'] = workflow.container - } - workflow_summary['launchDir'] = workflow.launchDir - workflow_summary['workDir'] = workflow.workDir - workflow_summary['projectDir'] = workflow.projectDir - workflow_summary['userName'] = workflow.userName - workflow_summary['profile'] = workflow.profile - workflow_summary['configFiles'] = workflow.configFiles.join(', ') - - // Get pipeline parameters defined in JSON Schema - def Map params_summary = [:] - def params_map = paramsLoad(getSchemaPath(workflow, schema_filename=schema_filename)) - for (group in params_map.keySet()) { - def sub_params = new LinkedHashMap() - def group_params = params_map.get(group) // This gets the parameters of that particular group - for (param in group_params.keySet()) { - if (params.containsKey(param)) { - def params_value = params.get(param) - def schema_value = group_params.get(param).default - def param_type = group_params.get(param).type - if (schema_value != null) { - if (param_type == 'string') { - if (schema_value.contains('$projectDir') || schema_value.contains('${projectDir}')) { - def sub_string = schema_value.replace('\$projectDir', '') - sub_string = sub_string.replace('\${projectDir}', '') - if (params_value.contains(sub_string)) { - schema_value = params_value - } - } - if (schema_value.contains('$params.outdir') || schema_value.contains('${params.outdir}')) { - def sub_string = schema_value.replace('\$params.outdir', '') - sub_string = sub_string.replace('\${params.outdir}', '') - if ("${params.outdir}${sub_string}" == params_value) { - schema_value = params_value - } - } - } - } - - // We have a default in the schema, and this isn't it - if (schema_value != null && params_value != schema_value) { - sub_params.put(param, params_value) - } - // No default in the schema, and this isn't empty - else if (schema_value == null && params_value != "" && params_value != null && params_value != false) { - sub_params.put(param, params_value) - } - } - } - params_summary.put(group, sub_params) - } - return [ 'Core Nextflow options' : workflow_summary ] << params_summary - } - - // - // Beautify parameters for summary and return as string - // - public static String paramsSummaryLog(workflow, params) { - Map colors = NfcoreTemplate.logColours(params.monochrome_logs) - String output = '' - def params_map = paramsSummaryMap(workflow, params) - def max_chars = paramsMaxChars(params_map) - for (group in params_map.keySet()) { - def group_params = params_map.get(group) // This gets the parameters of that particular group - if (group_params) { - output += colors.bold + group + colors.reset + '\n' - for (param in group_params.keySet()) { - output += " " + colors.blue + param.padRight(max_chars) + ": " + colors.green + group_params.get(param) + colors.reset + '\n' - } - output += '\n' - } - } - output += "!! Only displaying parameters that differ from the pipeline defaults !!\n" - output += NfcoreTemplate.dashedLine(params.monochrome_logs) - return output - } - - // - // Loop over nested exceptions and print the causingException - // - private static void printExceptions(ex_json, params_json, log, enums, limit=5) { - def causingExceptions = ex_json['causingExceptions'] - if (causingExceptions.length() == 0) { - def m = ex_json['message'] =~ /required key \[([^\]]+)\] not found/ - // Missing required param - if (m.matches()) { - log.error "* Missing required parameter: --${m[0][1]}" - } - // Other base-level error - else if (ex_json['pointerToViolation'] == '#') { - log.error "* ${ex_json['message']}" - } - // Error with specific param - else { - def param = ex_json['pointerToViolation'] - ~/^#\// - def param_val = params_json[param].toString() - if (enums.containsKey(param)) { - def error_msg = "* --${param}: '${param_val}' is not a valid choice (Available choices" - if (enums[param].size() > limit) { - log.error "${error_msg} (${limit} of ${enums[param].size()}): ${enums[param][0..limit-1].join(', ')}, ... )" - } else { - log.error "${error_msg}: ${enums[param].join(', ')})" - } - } else { - log.error "* --${param}: ${ex_json['message']} (${param_val})" - } - } - } - for (ex in causingExceptions) { - printExceptions(ex, params_json, log, enums) - } - } - - // - // Remove an element from a JSONArray - // - private static JSONArray removeElement(json_array, element) { - def list = [] - int len = json_array.length() - for (int i=0;i - if(raw_schema.keySet().contains('definitions')){ - raw_schema.definitions.each { definition -> - for (key in definition.keySet()){ - if (definition[key].get("properties").keySet().contains(ignore_param)){ - // Remove the param to ignore - definition[key].get("properties").remove(ignore_param) - // If the param was required, change this - if (definition[key].has("required")) { - def cleaned_required = removeElement(definition[key].required, ignore_param) - definition[key].put("required", cleaned_required) - } - } - } - } - } - if(raw_schema.keySet().contains('properties') && raw_schema.get('properties').keySet().contains(ignore_param)) { - raw_schema.get("properties").remove(ignore_param) - } - if(raw_schema.keySet().contains('required') && raw_schema.required.contains(ignore_param)) { - def cleaned_required = removeElement(raw_schema.required, ignore_param) - raw_schema.put("required", cleaned_required) - } - } - return raw_schema - } - - // - // Clean and check parameters relative to Nextflow native classes - // - private static Map cleanParameters(params) { - def new_params = params.getClass().newInstance(params) - for (p in params) { - // remove anything evaluating to false - if (!p['value']) { - new_params.remove(p.key) - } - // Cast MemoryUnit to String - if (p['value'].getClass() == nextflow.util.MemoryUnit) { - new_params.replace(p.key, p['value'].toString()) - } - // Cast Duration to String - if (p['value'].getClass() == nextflow.util.Duration) { - new_params.replace(p.key, p['value'].toString().replaceFirst(/d(?!\S)/, "day")) - } - // Cast LinkedHashMap to String - if (p['value'].getClass() == LinkedHashMap) { - new_params.replace(p.key, p['value'].toString()) - } - } - return new_params - } - - // - // This function tries to read a JSON params file - // - private static LinkedHashMap paramsLoad(String json_schema) { - def params_map = new LinkedHashMap() - try { - params_map = paramsRead(json_schema) - } catch (Exception e) { - println "Could not read parameters settings from JSON. $e" - params_map = new LinkedHashMap() - } - return params_map - } - - // - // Method to actually read in JSON file using Groovy. - // Group (as Key), values are all parameters - // - Parameter1 as Key, Description as Value - // - Parameter2 as Key, Description as Value - // .... - // Group - // - - private static LinkedHashMap paramsRead(String json_schema) throws Exception { - def json = new File(json_schema).text - def Map schema_definitions = (Map) new JsonSlurper().parseText(json).get('definitions') - def Map schema_properties = (Map) new JsonSlurper().parseText(json).get('properties') - /* Tree looks like this in nf-core schema - * definitions <- this is what the first get('definitions') gets us - group 1 - title - description - properties - parameter 1 - type - description - parameter 2 - type - description - group 2 - title - description - properties - parameter 1 - type - description - * properties <- parameters can also be ungrouped, outside of definitions - parameter 1 - type - description - */ - - // Grouped params - def params_map = new LinkedHashMap() - schema_definitions.each { key, val -> - def Map group = schema_definitions."$key".properties // Gets the property object of the group - def title = schema_definitions."$key".title - def sub_params = new LinkedHashMap() - group.each { innerkey, value -> - sub_params.put(innerkey, value) - } - params_map.put(title, sub_params) - } - - // Ungrouped params - def ungrouped_params = new LinkedHashMap() - schema_properties.each { innerkey, value -> - ungrouped_params.put(innerkey, value) - } - params_map.put("Other parameters", ungrouped_params) - - return params_map - } - - // - // Get maximum number of characters across all parameter names - // - private static Integer paramsMaxChars(params_map) { - Integer max_chars = 0 - for (group in params_map.keySet()) { - def group_params = params_map.get(group) // This gets the parameters of that particular group - for (param in group_params.keySet()) { - if (param.size() > max_chars) { - max_chars = param.size() - } - } - } - return max_chars - } -} diff --git a/lib/NfcoreTemplate.groovy b/lib/NfcoreTemplate.groovy index 25a0a74a..408951ae 100755 --- a/lib/NfcoreTemplate.groovy +++ b/lib/NfcoreTemplate.groovy @@ -128,7 +128,7 @@ class NfcoreTemplate { def email_html = html_template.toString() // Render the sendmail template - def max_multiqc_email_size = params.max_multiqc_email_size as nextflow.util.MemoryUnit + def max_multiqc_email_size = (params.containsKey('max_multiqc_email_size') ? params.max_multiqc_email_size : 0) as nextflow.util.MemoryUnit def smail_fields = [ email: email_address, subject: subject, email_txt: email_txt, email_html: email_html, projectDir: "$projectDir", mqcFile: mqc_report, mqcMaxSize: max_multiqc_email_size.toBytes() ] def sf = new File("$projectDir/assets/sendmail_template.txt") def sendmail_template = engine.createTemplate(sf).make(smail_fields) diff --git a/lib/WorkflowAirrflow.groovy b/lib/WorkflowAirrflow.groovy index ac4d4892..1a4ed820 100755 --- a/lib/WorkflowAirrflow.groovy +++ b/lib/WorkflowAirrflow.groovy @@ -11,6 +11,7 @@ class WorkflowAirrflow { // Check and validate parameters // public static void initialise(params, log) { + genomeExistsError(params, log) @@ -46,15 +47,57 @@ class WorkflowAirrflow { return yaml_file_text } - public static String methodsDescriptionText(run_workflow, mqc_methods_yaml) { + // + // Generate methods description for MultiQC + // + + public static String toolCitationText(params) { + + // TODO Optionally add in-text citation tools to this list. + // Can use ternary operators to dynamically construct based conditions, e.g. params["run_xyz"] ? "Tool (Foo et al. 2023)" : "", + // Uncomment function in methodsDescriptionText to render in MultiQC report + def citation_text = [ + "Tools used in the workflow included:", + "FastQC (Andrews 2010),", + "MultiQC (Ewels et al. 2016)", + "." + ].join(' ').trim() + + return citation_text + } + + public static String toolBibliographyText(params) { + + // TODO Optionally add bibliographic entries to this list. + // Can use ternary operators to dynamically construct based conditions, e.g. params["run_xyz"] ? "

  • Author (2023) Pub name, Journal, DOI
    • " : "", + // Uncomment function in methodsDescriptionText to render in MultiQC report + def reference_text = [ + "
  • Andrews S, (2010) FastQC, URL: https://www.bioinformatics.babraham.ac.uk/projects/fastqc/).
    • ", + "
  • Ewels, P., Magnusson, M., Lundin, S., & Käller, M. (2016). MultiQC: summarize analysis results for multiple tools and samples in a single report. Bioinformatics , 32(19), 3047–3048. doi: /10.1093/bioinformatics/btw354
    • " + ].join(' ').trim() + + return reference_text + } + + public static String methodsDescriptionText(run_workflow, mqc_methods_yaml, params) { // Convert to a named map so can be used as with familar NXF ${workflow} variable syntax in the MultiQC YML file def meta = [:] meta.workflow = run_workflow.toMap() meta["manifest_map"] = run_workflow.manifest.toMap() + // Pipeline DOI meta["doi_text"] = meta.manifest_map.doi ? "(doi: ${meta.manifest_map.doi})" : "" meta["nodoi_text"] = meta.manifest_map.doi ? "": "
  • If available, make sure to update the text to include the Zenodo DOI of version of the pipeline used.
    • " + // Tool references + meta["tool_citations"] = "" + meta["tool_bibliography"] = "" + + // TODO Only uncomment below if logic in toolCitationText/toolBibliographyText has been filled! + //meta["tool_citations"] = toolCitationText(params).replaceAll(", \\.", ".").replaceAll("\\. \\.", ".").replaceAll(", \\.", ".") + //meta["tool_bibliography"] = toolBibliographyText(params) + + def methods_text = mqc_methods_yaml.text def engine = new SimpleTemplateEngine() diff --git a/lib/WorkflowMain.groovy b/lib/WorkflowMain.groovy index 93af2d9e..66a2c83c 100755 --- a/lib/WorkflowMain.groovy +++ b/lib/WorkflowMain.groovy @@ -20,40 +20,11 @@ class WorkflowMain { " https://github.com/${workflow.manifest.name}/blob/master/CITATIONS.md" } - // - // Generate help string - // - public static String help(workflow, params) { - def command = "nextflow run ${workflow.manifest.name} --input samplesheet.csv --genome GRCh37 -profile docker" - def help_string = '' - help_string += NfcoreTemplate.logo(workflow, params.monochrome_logs) - help_string += NfcoreSchema.paramsHelp(workflow, params, command) - help_string += '\n' + citation(workflow) + '\n' - help_string += NfcoreTemplate.dashedLine(params.monochrome_logs) - return help_string - } - - // - // Generate parameter summary log string - // - public static String paramsSummaryLog(workflow, params) { - def summary_log = '' - summary_log += NfcoreTemplate.logo(workflow, params.monochrome_logs) - summary_log += NfcoreSchema.paramsSummaryLog(workflow, params) - summary_log += '\n' + citation(workflow) + '\n' - summary_log += NfcoreTemplate.dashedLine(params.monochrome_logs) - return summary_log - } // // Validate parameters and print summary to screen // public static void initialise(workflow, params, log) { - // Print help to screen if required - if (params.help) { - log.info help(workflow, params) - System.exit(0) - } // Print workflow version and exit on --version if (params.version) { @@ -62,14 +33,6 @@ class WorkflowMain { System.exit(0) } - // Print parameter summary log to screen - log.info paramsSummaryLog(workflow, params) - - // Validate workflow parameters via the JSON schema - if (params.validate_params) { - NfcoreSchema.validateParameters(workflow, params, log) - } - // Check that a -profile or Nextflow config has been provided to run the pipeline NfcoreTemplate.checkConfigProvided(workflow, log) diff --git a/main.nf b/main.nf index f64d452c..a999695c 100644 --- a/main.nf +++ b/main.nf @@ -25,6 +25,22 @@ params.fasta = WorkflowMain.getGenomeAttribute(params, 'fasta') ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ */ +include { validateParameters; paramsHelp } from 'plugin/nf-validation' + +// Print help message if needed +if (params.help) { + def logo = NfcoreTemplate.logo(workflow, params.monochrome_logs) + def citation = '\n' + WorkflowMain.citation(workflow) + '\n' + def String command = "nextflow run ${workflow.manifest.name} --input samplesheet.csv --genome GRCh37 -profile docker" + log.info logo + paramsHelp(command) + citation + NfcoreTemplate.dashedLine(params.monochrome_logs) + System.exit(0) +} + +// Validate input parameters +if (params.validate_params) { + validateParameters() +} + WorkflowMain.initialise(workflow, params, log) /* diff --git a/nextflow.config b/nextflow.config index f2b13c12..6332ca41 100644 --- a/nextflow.config +++ b/nextflow.config @@ -12,12 +12,12 @@ params { // TODO nf-core: Specify your pipeline's command line flags // Input options input = null - - // References genome = null igenomes_base = 's3://ngi-igenomes/igenomes' igenomes_ignore = false + + // MultiQC options multiqc_config = null multiqc_title = null @@ -27,7 +27,6 @@ params { // Boilerplate options outdir = null - tracedir = "${params.outdir}/pipeline_info" publish_dir_mode = 'copy' email = null email_on_fail = null @@ -36,19 +35,15 @@ params { hook_url = null help = false version = false - validate_params = true - show_hidden_params = false - schema_ignore_params = 'genomes' - // Config options + config_profile_name = null + config_profile_description = null custom_config_version = 'master' custom_config_base = "https://raw.githubusercontent.com/nf-core/configs/${params.custom_config_version}" - config_profile_description = null config_profile_contact = null config_profile_url = null - config_profile_name = null - + // Max resource options // Defaults only, expecting to be overwritten @@ -56,6 +51,13 @@ params { max_cpus = 16 max_time = '240.h' + // Schema validation default options + validationFailUnrecognisedParams = false + validationLenientMode = false + validationSchemaIgnoreParams = 'genomes' + validationShowHiddenParams = false + validate_params = true + } // Load base.config by default for all pipelines @@ -75,13 +77,11 @@ try { // } catch (Exception e) { // System.err.println("WARNING: Could not load nf-core/config/airrflow profiles: ${params.custom_config_base}/pipeline/airrflow.config") // } - - profiles { debug { dumpHashes = true process.beforeScript = 'echo $HOSTNAME' - cleanup = false + cleanup = false } conda { conda.enabled = true @@ -104,7 +104,6 @@ profiles { } docker { docker.enabled = true - docker.registry = 'quay.io' docker.userEmulation = true conda.enabled = false singularity.enabled = false @@ -128,7 +127,6 @@ profiles { } podman { podman.enabled = true - podman.registry = 'quay.io' conda.enabled = false docker.enabled = false singularity.enabled = false @@ -172,6 +170,18 @@ profiles { test_full { includeConfig 'conf/test_full.config' } } +// Set default registry for Apptainer, Docker, Podman and Singularity independent of -profile +// Will not be used unless Apptainer / Docker / Podman / Singularity are enabled +// Set to your registry if you have a mirror of containers +apptainer.registry = 'quay.io' +docker.registry = 'quay.io' +podman.registry = 'quay.io' +singularity.registry = 'quay.io' + +// Nextflow plugins +plugins { + id 'nf-validation' // Validation of pipeline parameters and creation of an input channel from a sample sheet +} // Load igenomes.config if required if (!params.igenomes_ignore) { @@ -179,8 +189,6 @@ if (!params.igenomes_ignore) { } else { params.genomes = [:] } - - // Export these variables to prevent local Python/R libraries from conflicting with those in the container // The JULIA depot path has been adjusted to a fixed path `/usr/local/share/julia` that needs to be used for packages in the container. // See https://apeltzer.github.io/post/03-julia-lang-nextflow/ for details on that. Once we have a common agreement on where to keep Julia packages, this is adjustable. @@ -198,19 +206,19 @@ process.shell = ['/bin/bash', '-euo', 'pipefail'] def trace_timestamp = new java.util.Date().format( 'yyyy-MM-dd_HH-mm-ss') timeline { enabled = true - file = "${params.tracedir}/execution_timeline_${trace_timestamp}.html" + file = "${params.outdir}/pipeline_info/execution_timeline_${trace_timestamp}.html" } report { enabled = true - file = "${params.tracedir}/execution_report_${trace_timestamp}.html" + file = "${params.outdir}/pipeline_info/execution_report_${trace_timestamp}.html" } trace { enabled = true - file = "${params.tracedir}/execution_trace_${trace_timestamp}.txt" + file = "${params.outdir}/pipeline_info/execution_trace_${trace_timestamp}.txt" } dag { enabled = true - file = "${params.tracedir}/pipeline_dag_${trace_timestamp}.html" + file = "${params.outdir}/pipeline_info/pipeline_dag_${trace_timestamp}.html" } manifest { @@ -219,8 +227,8 @@ manifest { homePage = 'https://github.com/nf-core/airrflow' description = """B and T cell repertoire analysis pipeline with the Immcantation framework.""" mainScript = 'main.nf' - nextflowVersion = '!>=22.10.1' - version = '3.0' + nextflowVersion = '!>=23.04.0' + version = '3.1.0' doi = '' } diff --git a/nextflow_schema.json b/nextflow_schema.json index 9e272c13..1225d229 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -15,9 +15,9 @@ "input": { "type": "string", "format": "file-path", + "exists": true, "mimetype": "text/csv", "pattern": "^\\S+\\.csv$", - "schema": "assets/schema_input.json", "description": "Path to comma-separated file containing information about the samples in the experiment.", "help_text": "You will need to create a design file with information about the samples in your experiment before running the pipeline. Use this parameter to specify its location. It has to be a comma-separated file with 3 columns, and a header row. See [usage docs](https://nf-co.re/airrflow/usage#samplesheet-input).", "fa_icon": "fas fa-file-csv" @@ -57,6 +57,7 @@ "fasta": { "type": "string", "format": "file-path", + "exists": true, "mimetype": "text/plain", "pattern": "^\\S+\\.fn?a(sta)?(\\.gz)?$", "description": "Path to FASTA genome file.", @@ -157,7 +158,7 @@ "description": "Maximum amount of time that can be requested for any single job.", "default": "240.h", "fa_icon": "far fa-clock", - "pattern": "^(\\d+\\.?\\s*(s|m|h|day)\\s*)+$", + "pattern": "^(\\d+\\.?\\s*(s|m|h|d|day)\\s*)+$", "hidden": true, "help_text": "Use to set an upper-limit for the time requirement for each process. Should be a string in the format integer-unit e.g. `--max_time '2.h'`" } @@ -174,12 +175,14 @@ "type": "boolean", "description": "Display help text.", "fa_icon": "fas fa-question-circle", + "default": false, "hidden": true }, "version": { "type": "boolean", "description": "Display version and exit.", "fa_icon": "fas fa-question-circle", + "default": false, "hidden": true }, "publish_dir_mode": { @@ -203,6 +206,7 @@ "type": "boolean", "description": "Send plain-text email instead of HTML.", "fa_icon": "fas fa-remove-format", + "default": false, "hidden": true }, "max_multiqc_email_size": { @@ -217,6 +221,7 @@ "type": "boolean", "description": "Do not use coloured log outputs.", "fa_icon": "fas fa-palette", + "default": false, "hidden": true }, "hook_url": { @@ -228,6 +233,7 @@ }, "multiqc_config": { "type": "string", + "format": "file-path", "description": "Custom config file to supply to MultiQC.", "fa_icon": "fas fa-cog", "hidden": true @@ -243,13 +249,6 @@ "description": "Custom MultiQC yaml file containing HTML including a methods description.", "fa_icon": "fas fa-cog" }, - "tracedir": { - "type": "string", - "description": "Directory to keep pipeline Nextflow logs and reports.", - "default": "${params.outdir}/pipeline_info", - "fa_icon": "fas fa-cogs", - "hidden": true - }, "validate_params": { "type": "boolean", "description": "Boolean whether to validate parameters against the schema at runtime", @@ -257,12 +256,29 @@ "fa_icon": "fas fa-check-square", "hidden": true }, - "show_hidden_params": { + "validationShowHiddenParams": { "type": "boolean", "fa_icon": "far fa-eye-slash", "description": "Show all params when using `--help`", + "default": false, "hidden": true, "help_text": "By default, parameters set as _hidden_ in the schema are not shown on the command line when a user runs with `--help`. Specifying this option will tell the pipeline to show all parameters." + }, + "validationFailUnrecognisedParams": { + "type": "boolean", + "fa_icon": "far fa-check-circle", + "description": "Validation of parameters fails when an unrecognised parameter is found.", + "default": false, + "hidden": true, + "help_text": "By default, when an unrecognised parameter is found, it returns a warinig." + }, + "validationLenientMode": { + "type": "boolean", + "fa_icon": "far fa-check-circle", + "description": "Validation of parameters in lenient more.", + "default": false, + "hidden": true, + "help_text": "Allows string values that are parseable as numbers or booleans. For further information see [JSONSchema docs](https://github.com/everit-org/json-schema#lenient-mode)." } } } diff --git a/workflows/airrflow.nf b/workflows/airrflow.nf index b1ed19c4..b71b315e 100644 --- a/workflows/airrflow.nf +++ b/workflows/airrflow.nf @@ -1,21 +1,19 @@ /* ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - VALIDATE INPUTS + PRINT PARAMS SUMMARY ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ */ -def summary_params = NfcoreSchema.paramsSummaryMap(workflow, params) +include { paramsSummaryLog; paramsSummaryMap } from 'plugin/nf-validation' -// Validate input parameters -WorkflowAirrflow.initialise(params, log) +def logo = NfcoreTemplate.logo(workflow, params.monochrome_logs) +def citation = '\n' + WorkflowMain.citation(workflow) + '\n' +def summary_params = paramsSummaryMap(workflow) -// TODO nf-core: Add all file path parameters for the pipeline to the list below -// Check input path parameters to see if they exist -def checkPathParamList = [ params.input, params.multiqc_config, params.fasta ] -for (param in checkPathParamList) { if (param) { file(param, checkIfExists: true) } } +// Print parameter summary log to screen +log.info logo + paramsSummaryLog(workflow) + citation -// Check mandatory parameters -if (params.input) { ch_input = file(params.input) } else { exit 1, 'Input samplesheet not specified!' } +WorkflowAirrflow.initialise(params, log) /* ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -69,9 +67,12 @@ workflow AIRRFLOW { // SUBWORKFLOW: Read in samplesheet, validate and stage input files // INPUT_CHECK ( - ch_input + file(params.input) ) ch_versions = ch_versions.mix(INPUT_CHECK.out.versions) + // TODO: OPTIONAL, you can use nf-validation plugin to create an input channel from the samplesheet with Channel.fromSamplesheet("input") + // See the documentation https://nextflow-io.github.io/nf-validation/samplesheets/fromSamplesheet/ + // ! There is currently no tooling to help you write a sample sheet schema // // MODULE: Run FastQC @@ -91,7 +92,7 @@ workflow AIRRFLOW { workflow_summary = WorkflowAirrflow.paramsSummaryMultiqc(workflow, summary_params) ch_workflow_summary = Channel.value(workflow_summary) - methods_description = WorkflowAirrflow.methodsDescriptionText(workflow, ch_multiqc_custom_methods_description) + methods_description = WorkflowAirrflow.methodsDescriptionText(workflow, ch_multiqc_custom_methods_description, params) ch_methods_description = Channel.value(methods_description) ch_multiqc_files = Channel.empty() From 623d60ec2211cec458a95b316a2c001a4080773f Mon Sep 17 00:00:00 2001 From: Gisela Gabernet Date: Sun, 23 Jul 2023 17:47:02 -0400 Subject: [PATCH 02/32] allow passing custom fields buildconsensus --- conf/modules.config | 5 ++++- modules/local/presto/presto_buildconsensus.nf | 11 +++++++---- 2 files changed, 11 insertions(+), 5 deletions(-) diff --git a/conf/modules.config b/conf/modules.config index 029b68af..54c24a04 100644 --- a/conf/modules.config +++ b/conf/modules.config @@ -178,12 +178,15 @@ process { ] } - withName: PRESTO_BUILDCONSENSUS { + withName: PRESTO_BUILDCONSENSUS_UMI { publishDir = [ path: { "${params.outdir}/presto/06-build-consensus/${meta.id}" }, mode: params.publish_dir_mode, saveAs: { filename -> filename.equals('versions.yml') ? null : filename } ] + ext.args = '' + ext.args2 = '' + ext.args3 = 'ID BARCODE SEQCOUNT PRIMER PRCOUNT PRCONS PRFREQ CONSCOUNT' } withName: PRESTO_POSTCONSENSUS_PAIRSEQ { diff --git a/modules/local/presto/presto_buildconsensus.nf b/modules/local/presto/presto_buildconsensus.nf index d5e92621..6f5d9b20 100644 --- a/modules/local/presto/presto_buildconsensus.nf +++ b/modules/local/presto/presto_buildconsensus.nf @@ -20,11 +20,14 @@ process PRESTO_BUILDCONSENSUS { path "versions.yml" , emit: versions script: - def barcode_field = params.cluster_sets ? "CLUSTER" : "BARCODE" + def barcode_field = params.cluster_sets ? 'CLUSTER' : 'BARCODE' + def args = task.ext.args ?: '' + def args2 = task.ext.args2 ?: '' + def args3 = task.ext.args3 ?: '' """ - BuildConsensus.py -s $R1 --bf ${barcode_field} --nproc ${task.cpus} --pf PRIMER --prcons $params.primer_consensus --maxerror $params.buildconsensus_maxerror --maxgap $params.buildconsensus_maxgap --outname ${meta.id}_R1 --log ${meta.id}_R1.log > ${meta.id}_command_log.txt - BuildConsensus.py -s $R2 --bf ${barcode_field} --nproc ${task.cpus} --pf PRIMER --prcons $params.primer_consensus --maxerror $params.buildconsensus_maxerror --maxgap $params.buildconsensus_maxgap --outname ${meta.id}_R2 --log ${meta.id}_R2.log >> ${meta.id}_command_log.txt - ParseLog.py -l ${meta.id}_R1.log ${meta.id}_R2.log -f ID BARCODE SEQCOUNT PRIMER PRCOUNT PRCONS PRFREQ CONSCOUNT + BuildConsensus.py -s $R1 --bf ${barcode_field} --nproc ${task.cpus} --pf PRIMER --prcons ${params.primer_consensus} --maxerror ${params.buildconsensus_maxerror} --maxgap ${params.buildconsensus_maxgap} ${args} --outname ${meta.id}_R1 --log ${meta.id}_R1.log > ${meta.id}_command_log.txt + BuildConsensus.py -s $R2 --bf ${barcode_field} --nproc ${task.cpus} --pf PRIMER --prcons ${params.primer_consensus} --maxerror ${params.buildconsensus_maxerror} --maxgap ${params.buildconsensus_maxgap} ${args2} --outname ${meta.id}_R2 --log ${meta.id}_R2.log >> ${meta.id}_command_log.txt + ParseLog.py -l ${meta.id}_R1.log ${meta.id}_R2.log -f ${args3} cat <<-END_VERSIONS > versions.yml "${task.process}": From e2deaa1fbbe9dc32c208151a5489dc250c4b67dd Mon Sep 17 00:00:00 2001 From: ssnn-airr <20683719+ssnn-airr@users.noreply.github.com> Date: Wed, 26 Jul 2023 12:59:37 +0200 Subject: [PATCH 03/32] updated config for threshold report with subsample --- conf/modules.config | 6 ++++++ 1 file changed, 6 insertions(+) diff --git a/conf/modules.config b/conf/modules.config index 029b68af..0c5a3724 100644 --- a/conf/modules.config +++ b/conf/modules.config @@ -434,6 +434,12 @@ process { mode: params.publish_dir_mode, saveAs: { filename -> filename.equals('versions.yml') ? null : filename } ] + ext.args = ['findthreshold_method':'gmm', + 'findthreshold_model':'gamma-norm', + 'findthreshold_edge':0.9, + 'findthreshold_cutoff':'user', + 'findthreshold_spc':0.995, + 'subsample':10000] } withName: DEFINE_CLONES_COMPUTE { From e9b59c64eb3d96964c076cabaf0c095157697972 Mon Sep 17 00:00:00 2001 From: Gisela Gabernet Date: Wed, 26 Jul 2023 22:05:17 -0400 Subject: [PATCH 04/32] add default params to report threshold --- conf/modules.config | 6 ++++++ 1 file changed, 6 insertions(+) diff --git a/conf/modules.config b/conf/modules.config index 54c24a04..72a4e4ae 100644 --- a/conf/modules.config +++ b/conf/modules.config @@ -437,6 +437,12 @@ process { mode: params.publish_dir_mode, saveAs: { filename -> filename.equals('versions.yml') ? null : filename } ] + ext.args = ['findthreshold_method':'gmm', + 'findthreshold_model':'gamma-norm', + 'findthreshold_edge':0.9, + 'findthreshold_cutoff':'user', + 'findthreshold_spc':0.995, + 'subsample':8000] } withName: DEFINE_CLONES_COMPUTE { From 5b53226512b0c48a37feb0de02d5df3b77c4dfe7 Mon Sep 17 00:00:00 2001 From: Gisela Gabernet Date: Wed, 26 Jul 2023 23:03:42 -0400 Subject: [PATCH 05/32] fix igphyml param docs --- nextflow_schema.json | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/nextflow_schema.json b/nextflow_schema.json index e6a3365e..b05ac808 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -350,7 +350,7 @@ }, "igphyml": { "type": "string", - "default": "/usr/local/share/igphyml/src/igphyml", + "default": "/usr/local/bin/igphyml", "description": "Path to IgPhyml executable.", "fa_icon": "fas fa-file" }, From 9a05343e8ec52f02e58f1cb860b61f7899dbf579 Mon Sep 17 00:00:00 2001 From: Gisela Gabernet Date: Thu, 27 Jul 2023 21:21:39 -0400 Subject: [PATCH 06/32] partial fix for docker container --- conf/modules.config | 1 + 1 file changed, 1 insertion(+) diff --git a/conf/modules.config b/conf/modules.config index 72a4e4ae..0fa05b80 100644 --- a/conf/modules.config +++ b/conf/modules.config @@ -479,6 +479,7 @@ process { 'minseq':5, 'traits':'c_call', 'tips':'c_call'] + ext.singularity_pull_docker_container = true } // ------------------------------- From 6f44bbd6f0566300d83688b53d3dc108d66741fa Mon Sep 17 00:00:00 2001 From: Gisela Gabernet Date: Thu, 27 Jul 2023 21:28:36 -0400 Subject: [PATCH 07/32] update changelog --- CHANGELOG.md | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 9f9dd337..5cee8f39 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -12,13 +12,14 @@ and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0. - [#259](https://github.com/nf-core/airrflow/pull/259) Update to `EnchantR v0.1.3`. - [#266](https://github.com/nf-core/airrflow/pull/266) Added clonal reports tables to final report folder. - [#266](https://github.com/nf-core/airrflow/pull/266) Added processes to include sampleID to filename in assembled workflow to keep it unique. - +- [#276](https://github.com/nf-core/airrflow/pull/276) Parametrize FindThreshold Report and Presto Buildconsensus UMI. ### `Fixed` - [#268](https://github.com/nf-core/airrflow/pull/268) Allows for uppercase and lowercase locus in samplesheet `pcr_target_locus`. - [#259](https://github.com/nf-core/airrflow/pull/259) Samplesheet only allows data from one species. - [#259](https://github.com/nf-core/airrflow/pull/259) Introduced fix for a too long command with hundreds of datasets. - [#266](https://github.com/nf-core/airrflow/pull/266) Convert samplesheet required columns to strings when needed. +- [#276](https://github.com/nf-core/airrflow/pull/266) Temporary fix for Dowser with singularity ### `Dependencies` From 85d533aaabba61a97ea42d9ff68ee88b4aa98f18 Mon Sep 17 00:00:00 2001 From: Gisela Gabernet Date: Fri, 28 Jul 2023 13:39:27 -0400 Subject: [PATCH 08/32] update nextflow config --- CHANGELOG.md | 1 + nextflow.config | 6 ++++-- 2 files changed, 5 insertions(+), 2 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 5cee8f39..785ff83a 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -13,6 +13,7 @@ and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0. - [#266](https://github.com/nf-core/airrflow/pull/266) Added clonal reports tables to final report folder. - [#266](https://github.com/nf-core/airrflow/pull/266) Added processes to include sampleID to filename in assembled workflow to keep it unique. - [#276](https://github.com/nf-core/airrflow/pull/276) Parametrize FindThreshold Report and Presto Buildconsensus UMI. + ### `Fixed` - [#268](https://github.com/nf-core/airrflow/pull/268) Allows for uppercase and lowercase locus in samplesheet `pcr_target_locus`. diff --git a/nextflow.config b/nextflow.config index 77d8ef57..21647655 100644 --- a/nextflow.config +++ b/nextflow.config @@ -157,8 +157,10 @@ try { // } catch (Exception e) { // System.err.println("WARNING: Could not load nf-core/config/airrflow profiles: ${params.custom_config_base}/pipeline/airrflow.config") // } -docker.registry = 'quay.io' -podman.registry = 'quay.io' +apptainer.registry = 'quay.io' +docker.registry = 'quay.io' +podman.registry = 'quay.io' +singularity.registry = 'quay.io' profiles { debug { From 9828750854bbec7c60a042843577d1ed668707ff Mon Sep 17 00:00:00 2001 From: Gisela Gabernet Date: Fri, 28 Jul 2023 13:43:56 -0400 Subject: [PATCH 09/32] try fix docker singularity issue --- conf/modules.config | 1 - 1 file changed, 1 deletion(-) diff --git a/conf/modules.config b/conf/modules.config index 0fa05b80..72a4e4ae 100644 --- a/conf/modules.config +++ b/conf/modules.config @@ -479,7 +479,6 @@ process { 'minseq':5, 'traits':'c_call', 'tips':'c_call'] - ext.singularity_pull_docker_container = true } // ------------------------------- From f738e5b9adef750e4ea3a224f987d1b9c75a9b56 Mon Sep 17 00:00:00 2001 From: Gisela Gabernet Garriga Date: Sat, 29 Jul 2023 11:14:12 -0400 Subject: [PATCH 10/32] add skip report threshold --- nextflow.config | 1 + nextflow_schema.json | 5 +++++ subworkflows/local/clonal_analysis.nf | 15 ++++++++------- 3 files changed, 14 insertions(+), 7 deletions(-) diff --git a/nextflow.config b/nextflow.config index 21647655..2b226b99 100644 --- a/nextflow.config +++ b/nextflow.config @@ -79,6 +79,7 @@ params { singlecell = 'single_cell' clonal_threshold = 'auto' skip_all_clones_report = false + skip_report_threshold = false // tree lineage options igphyml="/usr/local/bin/igphyml" diff --git a/nextflow_schema.json b/nextflow_schema.json index b05ac808..541fb42d 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -364,6 +364,11 @@ "type": "boolean", "description": "Skip report of EnchantR DefineClones for all samples together.", "fa_icon": "fas fa-angle-double-right" + }, + "skip_report_threshold": { + "type": "boolean", + "description": "Skip report of EnchantR FindThreshold for all samples together.", + "fa_icon": "fas fa-angle-double-right" } }, "help_text": "By default, the pipeline will define clones for each of the samples, as two sequences having the same V-gene assignment, C-gene assignment, J-gene assignment, and junction length. Additionally, the similarity of the CDR3 sequences will be assessed by Hamming distances. \n\nA distance threshold for determining if two sequences come from the same clone or not is automatically determined by the process find threshold. Alternatively, a hamming distance threshold can be manually set by setting the `--clonal_threshold` parameter.", diff --git a/subworkflows/local/clonal_analysis.nf b/subworkflows/local/clonal_analysis.nf index ff4afacf..2907fa2a 100644 --- a/subworkflows/local/clonal_analysis.nf +++ b/subworkflows/local/clonal_analysis.nf @@ -51,13 +51,14 @@ workflow CLONAL_ANALYSIS { .dump(tag: 'ch_find_threshold_samplesheet') .collectFile(name: 'find_threshold_samplesheet.txt', newLine: true) - REPORT_THRESHOLD ( - ch_find_threshold, - ch_logo, - ch_find_threshold_samplesheet - ) - ch_versions = ch_versions.mix(REPORT_THRESHOLD.out.versions) - + if !(params.skip_report_threshold){ + REPORT_THRESHOLD ( + ch_find_threshold, + ch_logo, + ch_find_threshold_samplesheet + ) + ch_versions = ch_versions.mix(REPORT_THRESHOLD.out.versions) + } } // prepare ch for define clones From a05bcfff08eb22f4ee28ce038fa26788753d7b97 Mon Sep 17 00:00:00 2001 From: Gisela Gabernet Garriga Date: Sat, 29 Jul 2023 11:20:57 -0400 Subject: [PATCH 11/32] fix param skip threshold --- subworkflows/local/clonal_analysis.nf | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/subworkflows/local/clonal_analysis.nf b/subworkflows/local/clonal_analysis.nf index 2907fa2a..b4c413f6 100644 --- a/subworkflows/local/clonal_analysis.nf +++ b/subworkflows/local/clonal_analysis.nf @@ -51,7 +51,7 @@ workflow CLONAL_ANALYSIS { .dump(tag: 'ch_find_threshold_samplesheet') .collectFile(name: 'find_threshold_samplesheet.txt', newLine: true) - if !(params.skip_report_threshold){ + if (!params.skip_report_threshold){ REPORT_THRESHOLD ( ch_find_threshold, ch_logo, From 9a00f038d213d3a03c7a178fc51fd2904dfdb622 Mon Sep 17 00:00:00 2001 From: Gisela Gabernet Date: Sat, 29 Jul 2023 12:55:34 -0400 Subject: [PATCH 12/32] add immcantation container for dowser --- modules/local/enchantr/dowser_lineages.nf | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/modules/local/enchantr/dowser_lineages.nf b/modules/local/enchantr/dowser_lineages.nf index 2e398f58..1e0ca243 100644 --- a/modules/local/enchantr/dowser_lineages.nf +++ b/modules/local/enchantr/dowser_lineages.nf @@ -24,7 +24,7 @@ process DOWSER_LINEAGES { conda "bioconda::r-enchantr=0.1.3" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/r-enchantr:0.1.3--r42hdfd78af_0': - 'biocontainers/r-enchantr:0.1.3--r42hdfd78af_0' }" + 'docker.io/immcantation/suite:devel' }" input: tuple val(meta), path(tabs) From feedb3f52bad2f51c00ef2ec579eda517c7dbcba Mon Sep 17 00:00:00 2001 From: ssnn-airr <20683719+ssnn-airr@users.noreply.github.com> Date: Tue, 1 Aug 2023 09:05:29 +0200 Subject: [PATCH 13/32] updated path for enchantr 0.1.4 --- docs/output.md | 6 +++--- modules/local/enchantr/find_threshold.nf | 4 ++-- 2 files changed, 5 insertions(+), 5 deletions(-) diff --git a/docs/output.md b/docs/output.md index e2477c8d..e6632c57 100644 --- a/docs/output.md +++ b/docs/output.md @@ -388,10 +388,10 @@ This folder is genereated when `detect_contamination` is set to `true`. - `clonal_analysis/find_threshold/` - `*log`: Log of the process that will be parsed to generate a report. - - `all_reps_threshold-mean.tsv`: Mean of all hamming distance thresholds of the - Junction regions as determined by Shazam. - - `all_reps_threshold-summary.tsv`: Thresholds for each group of `--cloneby` samples. - `all_reps_dist_report`: Report + - `tables/all_reps_threshold-mean.tsv`: Mean of all hamming distance thresholds of the + Junction regions as determined by Shazam. + - `tables/all_reps_threshold-summary.tsv`: Thresholds for each group of `--cloneby` samples. diff --git a/modules/local/enchantr/find_threshold.nf b/modules/local/enchantr/find_threshold.nf index 32ff652e..a87759b1 100644 --- a/modules/local/enchantr/find_threshold.nf +++ b/modules/local/enchantr/find_threshold.nf @@ -36,8 +36,8 @@ process FIND_THRESHOLD { // tuple val(meta), path("*threshold-pass.tsv"), emit: tab // sequence tsv in AIRR format path("*_command_log.txt"), emit: logs //process logs path "*_report" - path "*_threshold-summary.tsv", emit: threshold_summary - path "*_threshold-mean.tsv", emit: mean_threshold + path "all_reps_dist_report/tables/*_threshold-summary.tsv", emit: threshold_summary + path "all_reps_dist_report/tables/*_threshold-mean.tsv", emit: mean_threshold path "versions.yml", emit: versions script: From 33da6e5bbe6e9b3dd3d32e5cb5fd20c2b1546287 Mon Sep 17 00:00:00 2001 From: Gisela Gabernet Garriga Date: Mon, 18 Sep 2023 18:00:35 -0400 Subject: [PATCH 14/32] test immcantation suite prerelease --- modules/local/airrflow_report/airrflow_report.nf | 4 ++-- modules/local/enchantr/collapse_duplicates.nf | 4 ++-- modules/local/enchantr/define_clones.nf | 4 ++-- modules/local/enchantr/detect_contamination.nf | 4 ++-- modules/local/enchantr/dowser_lineages.nf | 2 +- modules/local/enchantr/find_threshold.nf | 4 ++-- modules/local/enchantr/remove_chimeric.nf | 4 ++-- modules/local/enchantr/report_file_size.nf | 4 ++-- modules/local/enchantr/single_cell_qc.nf | 4 ++-- modules/local/enchantr/validate_input.nf | 4 ++-- modules/local/reveal/add_meta_to_tab.nf | 4 ++-- modules/local/reveal/filter_junction_mod3.nf | 4 ++-- modules/local/reveal/filter_quality.nf | 4 ++-- 13 files changed, 25 insertions(+), 25 deletions(-) diff --git a/modules/local/airrflow_report/airrflow_report.nf b/modules/local/airrflow_report/airrflow_report.nf index 9621d685..856b33ab 100644 --- a/modules/local/airrflow_report/airrflow_report.nf +++ b/modules/local/airrflow_report/airrflow_report.nf @@ -4,8 +4,8 @@ process AIRRFLOW_REPORT { conda "bioconda::r-enchantr=0.1.3" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/r-enchantr:0.1.3--r42hdfd78af_0': - 'biocontainers/r-enchantr:0.1.3--r42hdfd78af_0' }" + 'docker.io/ssnn/suite:prerelease': + 'docker.io/ssnn/suite:prerelease' }" input: tuple val(meta), path(tab) // sequence tsv table in AIRR format diff --git a/modules/local/enchantr/collapse_duplicates.nf b/modules/local/enchantr/collapse_duplicates.nf index 2257913f..7308c092 100644 --- a/modules/local/enchantr/collapse_duplicates.nf +++ b/modules/local/enchantr/collapse_duplicates.nf @@ -6,8 +6,8 @@ process COLLAPSE_DUPLICATES { conda "bioconda::r-enchantr=0.1.3" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/r-enchantr:0.1.3--r42hdfd78af_0': - 'biocontainers/r-enchantr:0.1.3--r42hdfd78af_0' }" + 'docker.io/ssnn/suite:prerelease': + 'docker.io/ssnn/suite:prerelease' }" input: tuple val(meta), path(tabs) // tuple [val(meta), sequence tsv in AIRR format ] diff --git a/modules/local/enchantr/define_clones.nf b/modules/local/enchantr/define_clones.nf index 7321603a..839b2463 100644 --- a/modules/local/enchantr/define_clones.nf +++ b/modules/local/enchantr/define_clones.nf @@ -23,8 +23,8 @@ process DEFINE_CLONES { conda "bioconda::r-enchantr=0.1.3" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/r-enchantr:0.1.3--r42hdfd78af_0': - 'biocontainers/r-enchantr:0.1.3--r42hdfd78af_0' }" + 'docker.io/ssnn/suite:prerelease': + 'docker.io/ssnn/suite:prerelease' }" input: tuple val(meta), path(tabs) // meta, sequence tsv in AIRR format diff --git a/modules/local/enchantr/detect_contamination.nf b/modules/local/enchantr/detect_contamination.nf index 003c2126..161865dd 100644 --- a/modules/local/enchantr/detect_contamination.nf +++ b/modules/local/enchantr/detect_contamination.nf @@ -7,8 +7,8 @@ process DETECT_CONTAMINATION { conda "bioconda::r-enchantr=0.1.3" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/r-enchantr:0.1.3--r42hdfd78af_0': - 'biocontainers/r-enchantr:0.1.3--r42hdfd78af_0' }" + 'docker.io/ssnn/suite:prerelease': + 'docker.io/ssnn/suite:prerelease' }" input: path(tabs) diff --git a/modules/local/enchantr/dowser_lineages.nf b/modules/local/enchantr/dowser_lineages.nf index 1e0ca243..7db286d0 100644 --- a/modules/local/enchantr/dowser_lineages.nf +++ b/modules/local/enchantr/dowser_lineages.nf @@ -23,7 +23,7 @@ process DOWSER_LINEAGES { conda "bioconda::r-enchantr=0.1.3" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/r-enchantr:0.1.3--r42hdfd78af_0': + 'docker.io/ssnn/suite:prerelease': 'docker.io/immcantation/suite:devel' }" input: diff --git a/modules/local/enchantr/find_threshold.nf b/modules/local/enchantr/find_threshold.nf index a87759b1..67f792d2 100644 --- a/modules/local/enchantr/find_threshold.nf +++ b/modules/local/enchantr/find_threshold.nf @@ -23,8 +23,8 @@ process FIND_THRESHOLD { conda "bioconda::r-enchantr=0.1.3" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/r-enchantr:0.1.3--r42hdfd78af_0': - 'biocontainers/r-enchantr:0.1.3--r42hdfd78af_0' }" + 'docker.io/ssnn/suite:prerelease': + 'docker.io/ssnn/suite:prerelease' }" input: diff --git a/modules/local/enchantr/remove_chimeric.nf b/modules/local/enchantr/remove_chimeric.nf index 41467ecb..5095a43f 100644 --- a/modules/local/enchantr/remove_chimeric.nf +++ b/modules/local/enchantr/remove_chimeric.nf @@ -7,8 +7,8 @@ process REMOVE_CHIMERIC { conda "bioconda::r-enchantr=0.1.3" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/r-enchantr:0.1.3--r42hdfd78af_0': - 'biocontainers/r-enchantr:0.1.3--r42hdfd78af_0' }" + 'docker.io/ssnn/suite:prerelease': + 'docker.io/ssnn/suite:prerelease' }" input: diff --git a/modules/local/enchantr/report_file_size.nf b/modules/local/enchantr/report_file_size.nf index c9a2052c..6ff1558c 100644 --- a/modules/local/enchantr/report_file_size.nf +++ b/modules/local/enchantr/report_file_size.nf @@ -8,8 +8,8 @@ process REPORT_FILE_SIZE { conda "bioconda::r-enchantr=0.1.3" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/r-enchantr:0.1.3--r42hdfd78af_0': - 'biocontainers/r-enchantr:0.1.3--r42hdfd78af_0' }" + 'docker.io/ssnn/suite:prerelease': + 'docker.io/ssnn/suite:prerelease' }" input: path logs diff --git a/modules/local/enchantr/single_cell_qc.nf b/modules/local/enchantr/single_cell_qc.nf index 3275c523..e8cf8830 100644 --- a/modules/local/enchantr/single_cell_qc.nf +++ b/modules/local/enchantr/single_cell_qc.nf @@ -22,8 +22,8 @@ process SINGLE_CELL_QC { conda "bioconda::r-enchantr=0.1.3" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/r-enchantr:0.1.3--r42hdfd78af_0': - 'biocontainers/r-enchantr:0.1.3--r42hdfd78af_0' }" + 'docker.io/ssnn/suite:prerelease': + 'docker.io/ssnn/suite:prerelease' }" input: path(tabs) diff --git a/modules/local/enchantr/validate_input.nf b/modules/local/enchantr/validate_input.nf index fd6bd345..e503ddf7 100644 --- a/modules/local/enchantr/validate_input.nf +++ b/modules/local/enchantr/validate_input.nf @@ -8,8 +8,8 @@ process VALIDATE_INPUT { conda "bioconda::r-enchantr=0.1.3" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/r-enchantr:0.1.3--r42hdfd78af_0': - 'biocontainers/r-enchantr:0.1.3--r42hdfd78af_0' }" + 'docker.io/ssnn/suite:prerelease': + 'docker.io/ssnn/suite:prerelease' }" input: file samplesheet diff --git a/modules/local/reveal/add_meta_to_tab.nf b/modules/local/reveal/add_meta_to_tab.nf index f24433e2..71a2de00 100644 --- a/modules/local/reveal/add_meta_to_tab.nf +++ b/modules/local/reveal/add_meta_to_tab.nf @@ -5,8 +5,8 @@ process ADD_META_TO_TAB { conda "bioconda::r-enchantr=0.1.3" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/r-enchantr:0.1.3--r42hdfd78af_0': - 'biocontainers/r-enchantr:0.1.3--r42hdfd78af_0' }" + 'docker.io/ssnn/suite:prerelease': + 'docker.io/ssnn/suite:prerelease' }" cache 'deep' // Without 'deep' this process would run when using -resume diff --git a/modules/local/reveal/filter_junction_mod3.nf b/modules/local/reveal/filter_junction_mod3.nf index 841fbba9..246d3b25 100644 --- a/modules/local/reveal/filter_junction_mod3.nf +++ b/modules/local/reveal/filter_junction_mod3.nf @@ -5,8 +5,8 @@ process FILTER_JUNCTION_MOD3 { conda "bioconda::r-enchantr=0.1.3" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/r-enchantr:0.1.3--r42hdfd78af_0': - 'biocontainers/r-enchantr:0.1.3--r42hdfd78af_0' }" + 'docker.io/ssnn/suite:prerelease': + 'docker.io/ssnn/suite:prerelease' }" input: tuple val(meta), path(tab) // sequence tsv in AIRR format diff --git a/modules/local/reveal/filter_quality.nf b/modules/local/reveal/filter_quality.nf index a649caef..4287c562 100644 --- a/modules/local/reveal/filter_quality.nf +++ b/modules/local/reveal/filter_quality.nf @@ -5,8 +5,8 @@ process FILTER_QUALITY { conda "bioconda::r-enchantr=0.1.3" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/r-enchantr:0.1.3--r42hdfd78af_0': - 'biocontainers/r-enchantr:0.1.3--r42hdfd78af_0' }" + 'docker.io/ssnn/suite:prerelease': + 'docker.io/ssnn/suite:prerelease' }" input: tuple val(meta), path(tab) // sequence tsv in AIRR format From 216706e3034e4739b0b8a330a6e736d421734107 Mon Sep 17 00:00:00 2001 From: Gisela Gabernet Garriga Date: Mon, 18 Sep 2023 18:37:48 -0400 Subject: [PATCH 15/32] update path igphyml --- nextflow.config | 2 +- nextflow_schema.json | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/nextflow.config b/nextflow.config index 2b226b99..b929a34d 100644 --- a/nextflow.config +++ b/nextflow.config @@ -82,7 +82,7 @@ params { skip_report_threshold = false // tree lineage options - igphyml="/usr/local/bin/igphyml" + igphyml="/usr/local/share/igphyml/src/igphyml" skip_lineage = false // ----------------------- diff --git a/nextflow_schema.json b/nextflow_schema.json index 541fb42d..511deb29 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -350,7 +350,7 @@ }, "igphyml": { "type": "string", - "default": "/usr/local/bin/igphyml", + "default": "/usr/local/share/igphyml/src/igphyml", "description": "Path to IgPhyml executable.", "fa_icon": "fas fa-file" }, From 0b44403f5820a5d9b009e13822468f7a262d75b0 Mon Sep 17 00:00:00 2001 From: Gisela Gabernet Date: Tue, 19 Sep 2023 10:25:08 -0400 Subject: [PATCH 16/32] change dowser lineages container --- conf/test_full.config | 9 +++++++++ modules/local/enchantr/dowser_lineages.nf | 2 +- 2 files changed, 10 insertions(+), 1 deletion(-) diff --git a/conf/test_full.config b/conf/test_full.config index 52781925..0b028c4c 100644 --- a/conf/test_full.config +++ b/conf/test_full.config @@ -28,3 +28,12 @@ params { umi_start = 0 umi_position = 'R1' } + +process { + withName:DOWSER_LINEAGES{ + ext.args = ['build':'igphyml', + 'minseq':5, + 'traits':'c_primer', + 'tips':'c_primer'] + } +} diff --git a/modules/local/enchantr/dowser_lineages.nf b/modules/local/enchantr/dowser_lineages.nf index 7db286d0..7f173c37 100644 --- a/modules/local/enchantr/dowser_lineages.nf +++ b/modules/local/enchantr/dowser_lineages.nf @@ -24,7 +24,7 @@ process DOWSER_LINEAGES { conda "bioconda::r-enchantr=0.1.3" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'docker.io/ssnn/suite:prerelease': - 'docker.io/immcantation/suite:devel' }" + 'docker.io/ssnn/suite:prerelease' }" input: tuple val(meta), path(tabs) From 58792cef13f0f6eced74b7f4819968191d6bcee2 Mon Sep 17 00:00:00 2001 From: nf-core-bot Date: Mon, 25 Sep 2023 14:10:31 +0000 Subject: [PATCH 17/32] [automated] Fix linting with Prettier --- docs/output.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/output.md b/docs/output.md index e6632c57..cf269b42 100644 --- a/docs/output.md +++ b/docs/output.md @@ -390,7 +390,7 @@ This folder is genereated when `detect_contamination` is set to `true`. - `*log`: Log of the process that will be parsed to generate a report. - `all_reps_dist_report`: Report - `tables/all_reps_threshold-mean.tsv`: Mean of all hamming distance thresholds of the - Junction regions as determined by Shazam. + Junction regions as determined by Shazam. - `tables/all_reps_threshold-summary.tsv`: Thresholds for each group of `--cloneby` samples. From db93f270cfc61d0bf39e4cfb869d709c3a6be88a Mon Sep 17 00:00:00 2001 From: Gisela Gabernet Date: Mon, 25 Sep 2023 10:13:25 -0400 Subject: [PATCH 18/32] fix editorconfig linting --- conf/test_full.config | 12 ++++++------ 1 file changed, 6 insertions(+), 6 deletions(-) diff --git a/conf/test_full.config b/conf/test_full.config index 0b028c4c..8196a9d3 100644 --- a/conf/test_full.config +++ b/conf/test_full.config @@ -30,10 +30,10 @@ params { } process { - withName:DOWSER_LINEAGES{ - ext.args = ['build':'igphyml', - 'minseq':5, - 'traits':'c_primer', - 'tips':'c_primer'] - } + withName:DOWSER_LINEAGES{ + ext.args = ['build':'igphyml', + 'minseq':5, + 'traits':'c_primer', + 'tips':'c_primer'] + } } From 710acccf8ff7143c202cdd9b6006429a715a69b4 Mon Sep 17 00:00:00 2001 From: Gisela Gabernet Date: Mon, 25 Sep 2023 12:04:34 -0400 Subject: [PATCH 19/32] add input schema --- assets/schema_input.json | 57 ++++++++++++++++++++++++++++++++++++++++ nextflow_schema.json | 2 +- 2 files changed, 58 insertions(+), 1 deletion(-) create mode 100644 assets/schema_input.json diff --git a/assets/schema_input.json b/assets/schema_input.json new file mode 100644 index 00000000..cdddf739 --- /dev/null +++ b/assets/schema_input.json @@ -0,0 +1,57 @@ +{ + "$schema": "http://json-schema.org/draft-07/schema", + "$id": "https://raw.githubusercontent.com/nf-core/airrflow/master/assets/schema_input.json", + "title": "nf-core/airrflow pipeline - params.input schema", + "description": "Schema for the file provided with params.input", + "type": "array", + "items": { + "type": "object", + "properties": { + "sample_id": { + "type": "string", + "pattern": "^\\S+$", + "errorMessage": "Sample name must be provided and cannot contain spaces" + }, + "subject_id": { + "type": "string", + "pattern": "^\\S+$", + "errorMessage": "Subject name must be provided and cannot contain spaces" + }, + "species": { + "type": "string", + "enum": ["mouse", "human"], + "errorMessage": "Species name must be provided and must be one of: mouse, human" + }, + "pcr_target_locus": { + "type": "string", + "enum": ["TR", "IG"], + "errorMessage": "PCR target locus must be provided and must be one of: TR, IG" + }, + "tissue": { + "type": "string", + "pattern": "^\\S+$", + "errorMessage": "Tissue name must be provided and cannot contain spaces" + }, + "sex": { + "type": "string", + "pattern": "^\\S+$", + "errorMessage": "Sex must be provided, specify NA if unknown." + }, + "age": { + "type": "string", + "errorMessage": "Age must be provided, specify NA if unknown." + }, + "biomaterial_provider": { + "type": "string", + "pattern": "^\\S+$", + "errorMessage": "Biomaterial provider must be provided and cannot contain spaces" + }, + "single_cell": { + "type": "boolean", + "pattern": "^\\S+$", + "errorMessage": "Single cell must be provided as a TRUE/FALSE value" + } + }, + "required": ["sample_id", "subject_id", "species", "pcr_target_locus", "tissue", "sex", "age", "biomaterial_provider" ] + } +} \ No newline at end of file diff --git a/nextflow_schema.json b/nextflow_schema.json index d0261195..e1e77e77 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -17,7 +17,7 @@ "format": "file-path", "exists": true, "mimetype": "text/csv", - "pattern": "^\\S+\\.csv$", + "pattern": "^\\S+\\.tsv$", "schema": "assets/schema_input.json", "description": "Path to comma-separated file containing information about the samples in the experiment.", "help_text": "You will need to create a design file with information about the samples in your experiment before running the pipeline. Use this parameter to specify its location. It has to be a comma-separated file with 3 columns, and a header row. See [usage docs](https://nf-co.re/airrflow/usage#samplesheet-input).", From 78072bd92bb2bb467147db2e58d35ef03ad2ec1c Mon Sep 17 00:00:00 2001 From: Gisela Gabernet Date: Mon, 25 Sep 2023 15:12:34 -0400 Subject: [PATCH 20/32] fix samplesheet validation --- assets/schema_input.json | 17 ++++++++--------- nextflow.config | 2 ++ 2 files changed, 10 insertions(+), 9 deletions(-) diff --git a/assets/schema_input.json b/assets/schema_input.json index cdddf739..eb1c54eb 100644 --- a/assets/schema_input.json +++ b/assets/schema_input.json @@ -10,27 +10,27 @@ "sample_id": { "type": "string", "pattern": "^\\S+$", - "errorMessage": "Sample name must be provided and cannot contain spaces" + "errorMessage": "Sample name must be provided and cannot contain spaces." }, "subject_id": { "type": "string", "pattern": "^\\S+$", - "errorMessage": "Subject name must be provided and cannot contain spaces" + "errorMessage": "Subject name must be provided and cannot contain spaces." }, "species": { "type": "string", "enum": ["mouse", "human"], - "errorMessage": "Species name must be provided and must be one of: mouse, human" + "errorMessage": "Species name must be provided and must be one of: mouse, human." }, "pcr_target_locus": { "type": "string", - "enum": ["TR", "IG"], - "errorMessage": "PCR target locus must be provided and must be one of: TR, IG" + "enum": ["TR", "IG", "ig", "tr", "Ig", "Tr"], + "errorMessage": "PCR target locus must be provided and must be one of: TR, IG." }, "tissue": { "type": "string", "pattern": "^\\S+$", - "errorMessage": "Tissue name must be provided and cannot contain spaces" + "errorMessage": "Tissue name must be provided and cannot contain spaces." }, "sex": { "type": "string", @@ -43,13 +43,12 @@ }, "biomaterial_provider": { "type": "string", - "pattern": "^\\S+$", - "errorMessage": "Biomaterial provider must be provided and cannot contain spaces" + "errorMessage": "Biomaterial provider must be provided." }, "single_cell": { "type": "boolean", "pattern": "^\\S+$", - "errorMessage": "Single cell must be provided as a TRUE/FALSE value" + "errorMessage": "Single cell must be provided as a TRUE/FALSE value." } }, "required": ["sample_id", "subject_id", "species", "pcr_target_locus", "tissue", "sex", "age", "biomaterial_provider" ] diff --git a/nextflow.config b/nextflow.config index d67b5933..c4d958c6 100644 --- a/nextflow.config +++ b/nextflow.config @@ -294,6 +294,8 @@ env { PYTHONNOUSERSITE = 1 R_PROFILE_USER = "/.Rprofile" R_ENVIRON_USER = "/.Renviron" + R_LIBS_SITE = "NULL" + R_LIBS_USER = "NULL" JULIA_DEPOT_PATH = "/usr/local/share/julia" } From 6db55b0a178008e04e8f16077093bf12a739174a Mon Sep 17 00:00:00 2001 From: Gisela Gabernet Date: Mon, 25 Sep 2023 15:14:05 -0400 Subject: [PATCH 21/32] update nextflow ver --- .github/workflows/ci_immcantation.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/ci_immcantation.yml b/.github/workflows/ci_immcantation.yml index 8669923d..b2b1dff9 100644 --- a/.github/workflows/ci_immcantation.yml +++ b/.github/workflows/ci_immcantation.yml @@ -23,7 +23,7 @@ jobs: strategy: matrix: NXF_VER: - - "22.10.1" + - "23.04.0" - "latest-everything" profile: [ From 56756a269759dab02b1417cd519022e50b0cf57b Mon Sep 17 00:00:00 2001 From: Gisela Gabernet Date: Mon, 25 Sep 2023 15:28:02 -0400 Subject: [PATCH 22/32] fix nextflow badge --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index 4150fa26..7fb75a1c 100644 --- a/README.md +++ b/README.md @@ -4,7 +4,7 @@ [![GitHub Actions Linting Status](https://github.com/nf-core/airrflow/workflows/nf-core%20linting/badge.svg)](https://github.com/nf-core/airrflow/actions?query=workflow%3A%22nf-core+linting%22) [![AWS CI](https://img.shields.io/badge/CI%20tests-full%20size-FF9900?labelColor=000000&logo=Amazon%20AWS)](https://nf-co.re/airrflow/results) [![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.2642009-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.2642009) -[![Nextflow](https://img.shields.io/badge/nextflow%20DSL2-%E2%89%A522.10.1-23aa62.svg)](https://www.nextflow.io/) +[![Nextflow](https://img.shields.io/badge/nextflow%20DSL2-%E2%89%A523.04.0-23aa62.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/) From 61b34035b0c85fdd24f266f952f9036d31b818e5 Mon Sep 17 00:00:00 2001 From: Gisela Gabernet Date: Mon, 25 Sep 2023 15:41:08 -0400 Subject: [PATCH 23/32] fix lint errors --- .nf-core.yml | 2 ++ assets/multiqc_config.yml | 2 +- assets/schema_input.json | 13 +++++++++++-- 3 files changed, 14 insertions(+), 3 deletions(-) diff --git a/.nf-core.yml b/.nf-core.yml index 2c0141ff..4ae6f7f0 100644 --- a/.nf-core.yml +++ b/.nf-core.yml @@ -1,4 +1,6 @@ lint: files_exist: - conf/igenomes.config + multiqc_config: + - report_comment repository_type: pipeline diff --git a/assets/multiqc_config.yml b/assets/multiqc_config.yml index 1bd4a16b..889351d6 100644 --- a/assets/multiqc_config.yml +++ b/assets/multiqc_config.yml @@ -1,4 +1,4 @@ -report_comment: > +report_comment: This report has been generated by the nf-core/airrflow analysis pipeline. For information about how to interpret these results, please see the documentation. diff --git a/assets/schema_input.json b/assets/schema_input.json index eb1c54eb..327564f0 100644 --- a/assets/schema_input.json +++ b/assets/schema_input.json @@ -51,6 +51,15 @@ "errorMessage": "Single cell must be provided as a TRUE/FALSE value." } }, - "required": ["sample_id", "subject_id", "species", "pcr_target_locus", "tissue", "sex", "age", "biomaterial_provider" ] + "required": [ + "sample_id", + "subject_id", + "species", + "pcr_target_locus", + "tissue", + "sex", + "age", + "biomaterial_provider" + ] } -} \ No newline at end of file +} From c9321eef03a05b25f8c8dcd35d2ea4a40cd8c331 Mon Sep 17 00:00:00 2001 From: Gisela Gabernet Date: Mon, 25 Sep 2023 16:25:15 -0400 Subject: [PATCH 24/32] update to immcantation/airrflow container --- modules/local/airrflow_report/airrflow_report.nf | 8 +++++--- modules/local/enchantr/collapse_duplicates.nf | 8 +++++--- modules/local/enchantr/define_clones.nf | 8 +++++--- modules/local/enchantr/detect_contamination.nf | 8 +++++--- modules/local/enchantr/dowser_lineages.nf | 8 +++++--- modules/local/enchantr/find_threshold.nf | 8 +++++--- modules/local/enchantr/remove_chimeric.nf | 8 +++++--- modules/local/enchantr/report_file_size.nf | 8 +++++--- modules/local/enchantr/single_cell_qc.nf | 8 +++++--- modules/local/enchantr/validate_input.nf | 8 +++++--- modules/local/reveal/add_meta_to_tab.nf | 8 +++++--- modules/local/reveal/filter_junction_mod3.nf | 8 +++++--- modules/local/reveal/filter_quality.nf | 8 +++++--- 13 files changed, 65 insertions(+), 39 deletions(-) diff --git a/modules/local/airrflow_report/airrflow_report.nf b/modules/local/airrflow_report/airrflow_report.nf index 856b33ab..0ba78193 100644 --- a/modules/local/airrflow_report/airrflow_report.nf +++ b/modules/local/airrflow_report/airrflow_report.nf @@ -2,10 +2,12 @@ process AIRRFLOW_REPORT { tag "${meta.id}" label 'process_high' - conda "bioconda::r-enchantr=0.1.3" + if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) { + error "nf-core/airrflow currently does not support Conda. Please use a container profile instead." + } container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'docker.io/ssnn/suite:prerelease': - 'docker.io/ssnn/suite:prerelease' }" + 'docker.io/immcantation/airrflow:devel': + 'docker.io/immcantation/airrflow:devel' }" input: tuple val(meta), path(tab) // sequence tsv table in AIRR format diff --git a/modules/local/enchantr/collapse_duplicates.nf b/modules/local/enchantr/collapse_duplicates.nf index 7308c092..6880de53 100644 --- a/modules/local/enchantr/collapse_duplicates.nf +++ b/modules/local/enchantr/collapse_duplicates.nf @@ -4,10 +4,12 @@ process COLLAPSE_DUPLICATES { label 'process_long_parallelized' label 'immcantation' - conda "bioconda::r-enchantr=0.1.3" + if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) { + error "nf-core/airrflow currently does not support Conda. Please use a container profile instead." + } container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'docker.io/ssnn/suite:prerelease': - 'docker.io/ssnn/suite:prerelease' }" + 'docker.io/immcantation/airrflow:devel': + 'docker.io/immcantation/airrflow:devel' }" input: tuple val(meta), path(tabs) // tuple [val(meta), sequence tsv in AIRR format ] diff --git a/modules/local/enchantr/define_clones.nf b/modules/local/enchantr/define_clones.nf index 839b2463..8f843516 100644 --- a/modules/local/enchantr/define_clones.nf +++ b/modules/local/enchantr/define_clones.nf @@ -21,10 +21,12 @@ process DEFINE_CLONES { label 'process_long_parallelized' label 'immcantation' - conda "bioconda::r-enchantr=0.1.3" + if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) { + error "nf-core/airrflow currently does not support Conda. Please use a container profile instead." + } container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'docker.io/ssnn/suite:prerelease': - 'docker.io/ssnn/suite:prerelease' }" + 'docker.io/immcantation/airrflow:devel': + 'docker.io/immcantation/airrflow:devel' }" input: tuple val(meta), path(tabs) // meta, sequence tsv in AIRR format diff --git a/modules/local/enchantr/detect_contamination.nf b/modules/local/enchantr/detect_contamination.nf index 161865dd..6cdc2fa5 100644 --- a/modules/local/enchantr/detect_contamination.nf +++ b/modules/local/enchantr/detect_contamination.nf @@ -5,10 +5,12 @@ process DETECT_CONTAMINATION { label 'immcantation' - conda "bioconda::r-enchantr=0.1.3" + if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) { + error "nf-core/airrflow currently does not support Conda. Please use a container profile instead." + } container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'docker.io/ssnn/suite:prerelease': - 'docker.io/ssnn/suite:prerelease' }" + 'docker.io/immcantation/airrflow:devel': + 'docker.io/immcantation/airrflow:devel' }" input: path(tabs) diff --git a/modules/local/enchantr/dowser_lineages.nf b/modules/local/enchantr/dowser_lineages.nf index 7f173c37..51930bb9 100644 --- a/modules/local/enchantr/dowser_lineages.nf +++ b/modules/local/enchantr/dowser_lineages.nf @@ -21,10 +21,12 @@ process DOWSER_LINEAGES { label 'process_long_parallelized' label 'immcantation' - conda "bioconda::r-enchantr=0.1.3" + if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) { + error "nf-core/airrflow currently does not support Conda. Please use a container profile instead." + } container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'docker.io/ssnn/suite:prerelease': - 'docker.io/ssnn/suite:prerelease' }" + 'docker.io/immcantation/airrflow:devel': + 'docker.io/immcantation/airrflow:devel' }" input: tuple val(meta), path(tabs) diff --git a/modules/local/enchantr/find_threshold.nf b/modules/local/enchantr/find_threshold.nf index 67f792d2..8f3a533b 100644 --- a/modules/local/enchantr/find_threshold.nf +++ b/modules/local/enchantr/find_threshold.nf @@ -21,10 +21,12 @@ process FIND_THRESHOLD { label 'process_long_parallelized' label 'immcantation' - conda "bioconda::r-enchantr=0.1.3" + if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) { + error "nf-core/airrflow currently does not support Conda. Please use a container profile instead." + } container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'docker.io/ssnn/suite:prerelease': - 'docker.io/ssnn/suite:prerelease' }" + 'docker.io/immcantation/airrflow:devel': + 'docker.io/immcantation/airrflow:devel' }" input: diff --git a/modules/local/enchantr/remove_chimeric.nf b/modules/local/enchantr/remove_chimeric.nf index 5095a43f..2489362e 100644 --- a/modules/local/enchantr/remove_chimeric.nf +++ b/modules/local/enchantr/remove_chimeric.nf @@ -5,10 +5,12 @@ process REMOVE_CHIMERIC { label 'immcantation' - conda "bioconda::r-enchantr=0.1.3" + if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) { + error "nf-core/airrflow currently does not support Conda. Please use a container profile instead." + } container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'docker.io/ssnn/suite:prerelease': - 'docker.io/ssnn/suite:prerelease' }" + 'docker.io/immcantation/airrflow:devel': + 'docker.io/immcantation/airrflow:devel' }" input: diff --git a/modules/local/enchantr/report_file_size.nf b/modules/local/enchantr/report_file_size.nf index 6ff1558c..b43e1c35 100644 --- a/modules/local/enchantr/report_file_size.nf +++ b/modules/local/enchantr/report_file_size.nf @@ -6,10 +6,12 @@ process REPORT_FILE_SIZE { label 'immcantation' label 'process_single' - conda "bioconda::r-enchantr=0.1.3" + if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) { + error "nf-core/airrflow currently does not support Conda. Please use a container profile instead." + } container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'docker.io/ssnn/suite:prerelease': - 'docker.io/ssnn/suite:prerelease' }" + 'docker.io/immcantation/airrflow:devel': + 'docker.io/immcantation/airrflow:devel' }" input: path logs diff --git a/modules/local/enchantr/single_cell_qc.nf b/modules/local/enchantr/single_cell_qc.nf index e8cf8830..5f1190e1 100644 --- a/modules/local/enchantr/single_cell_qc.nf +++ b/modules/local/enchantr/single_cell_qc.nf @@ -20,10 +20,12 @@ process SINGLE_CELL_QC { label 'immcantation' label 'process_medium' - conda "bioconda::r-enchantr=0.1.3" + if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) { + error "nf-core/airrflow currently does not support Conda. Please use a container profile instead." + } container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'docker.io/ssnn/suite:prerelease': - 'docker.io/ssnn/suite:prerelease' }" + 'docker.io/immcantation/airrflow:devel': + 'docker.io/immcantation/airrflow:devel' }" input: path(tabs) diff --git a/modules/local/enchantr/validate_input.nf b/modules/local/enchantr/validate_input.nf index e503ddf7..d87b27b2 100644 --- a/modules/local/enchantr/validate_input.nf +++ b/modules/local/enchantr/validate_input.nf @@ -6,10 +6,12 @@ process VALIDATE_INPUT { label 'immcantation' label 'process_single' - conda "bioconda::r-enchantr=0.1.3" + if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) { + error "nf-core/airrflow currently does not support Conda. Please use a container profile instead." + } container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'docker.io/ssnn/suite:prerelease': - 'docker.io/ssnn/suite:prerelease' }" + 'docker.io/immcantation/airrflow:devel': + 'docker.io/immcantation/airrflow:devel' }" input: file samplesheet diff --git a/modules/local/reveal/add_meta_to_tab.nf b/modules/local/reveal/add_meta_to_tab.nf index 71a2de00..b6c817a1 100644 --- a/modules/local/reveal/add_meta_to_tab.nf +++ b/modules/local/reveal/add_meta_to_tab.nf @@ -3,10 +3,12 @@ process ADD_META_TO_TAB { label 'immcantation' label 'process_single' - conda "bioconda::r-enchantr=0.1.3" + if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) { + error "nf-core/airrflow currently does not support Conda. Please use a container profile instead." + } container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'docker.io/ssnn/suite:prerelease': - 'docker.io/ssnn/suite:prerelease' }" + 'docker.io/immcantation/airrflow:devel': + 'docker.io/immcantation/airrflow:devel' }" cache 'deep' // Without 'deep' this process would run when using -resume diff --git a/modules/local/reveal/filter_junction_mod3.nf b/modules/local/reveal/filter_junction_mod3.nf index 246d3b25..fa312ece 100644 --- a/modules/local/reveal/filter_junction_mod3.nf +++ b/modules/local/reveal/filter_junction_mod3.nf @@ -3,10 +3,12 @@ process FILTER_JUNCTION_MOD3 { label 'immcantation' label 'process_single' - conda "bioconda::r-enchantr=0.1.3" + if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) { + error "nf-core/airrflow currently does not support Conda. Please use a container profile instead." + } container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'docker.io/ssnn/suite:prerelease': - 'docker.io/ssnn/suite:prerelease' }" + 'docker.io/immcantation/airrflow:devel': + 'docker.io/immcantation/airrflow:devel' }" input: tuple val(meta), path(tab) // sequence tsv in AIRR format diff --git a/modules/local/reveal/filter_quality.nf b/modules/local/reveal/filter_quality.nf index 4287c562..202840a4 100644 --- a/modules/local/reveal/filter_quality.nf +++ b/modules/local/reveal/filter_quality.nf @@ -3,10 +3,12 @@ process FILTER_QUALITY { label 'immcantation' label 'process_single' - conda "bioconda::r-enchantr=0.1.3" + if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) { + error "nf-core/airrflow currently does not support Conda. Please use a container profile instead." + } container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'docker.io/ssnn/suite:prerelease': - 'docker.io/ssnn/suite:prerelease' }" + 'docker.io/immcantation/airrflow:devel': + 'docker.io/immcantation/airrflow:devel' }" input: tuple val(meta), path(tab) // sequence tsv in AIRR format From 41f5e123d3c5ccd3709af812aae7881ce4e6cc5b Mon Sep 17 00:00:00 2001 From: Gisela Gabernet Date: Mon, 25 Sep 2023 16:36:44 -0400 Subject: [PATCH 25/32] update changelog --- CHANGELOG.md | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 785ff83a..5d02bbeb 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -13,6 +13,7 @@ and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0. - [#266](https://github.com/nf-core/airrflow/pull/266) Added clonal reports tables to final report folder. - [#266](https://github.com/nf-core/airrflow/pull/266) Added processes to include sampleID to filename in assembled workflow to keep it unique. - [#276](https://github.com/nf-core/airrflow/pull/276) Parametrize FindThreshold Report and Presto Buildconsensus UMI. +- [#279](https://github.com/nf-core/airrflow/pull/279) Update to nf-core tools v2.10. ### `Fixed` @@ -26,7 +27,7 @@ and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0. | Dependency | Old version | New version | | ---------- | ----------- | ----------- | -| r-enchantr | 0.1.2 | 0.1.3 | +| r-enchantr | 0.1.2 | 0.1.5 | ## [3.1.0] - 2023-06-05 "Protego" From 5a2f42d93b1ba13d536e0aa7a8569fd5c778576b Mon Sep 17 00:00:00 2001 From: Gisela Gabernet Date: Mon, 25 Sep 2023 16:45:57 -0400 Subject: [PATCH 26/32] fix linting errors nf-core v2.10 --- .github/CONTRIBUTING.md | 4 +- .github/workflows/linting.yml | 2 +- CODE_OF_CONDUCT.md | 133 ++++++++++++++++++++++++++-------- lib/NfcoreTemplate.groovy | 16 ++++ 4 files changed, 122 insertions(+), 33 deletions(-) diff --git a/.github/CONTRIBUTING.md b/.github/CONTRIBUTING.md index 5cb3103c..902a3782 100644 --- a/.github/CONTRIBUTING.md +++ b/.github/CONTRIBUTING.md @@ -9,7 +9,9 @@ Please use the pre-filled template to save time. However, don't be put off by this template - other more general issues and suggestions are welcome! Contributions to the code are even more welcome ;) -> If you need help using or modifying nf-core/airrflow then the best place to ask is on the nf-core Slack [#airrflow](https://nfcore.slack.com/channels/airrflow) channel ([join our Slack here](https://nf-co.re/join/slack)). +:::info +If you need help using or modifying nf-core/airrflow then the best place to ask is on the nf-core Slack [#airrflow](https://nfcore.slack.com/channels/airrflow) channel ([join our Slack here](https://nf-co.re/join/slack)). +::: ## Contribution workflow diff --git a/.github/workflows/linting.yml b/.github/workflows/linting.yml index 888cb4bc..b8bdd214 100644 --- a/.github/workflows/linting.yml +++ b/.github/workflows/linting.yml @@ -78,7 +78,7 @@ jobs: - uses: actions/setup-python@v4 with: - python-version: "3.8" + python-version: "3.11" architecture: "x64" - name: Install dependencies diff --git a/CODE_OF_CONDUCT.md b/CODE_OF_CONDUCT.md index f4fd052f..c089ec78 100644 --- a/CODE_OF_CONDUCT.md +++ b/CODE_OF_CONDUCT.md @@ -1,18 +1,20 @@ -# Code of Conduct at nf-core (v1.0) +# Code of Conduct at nf-core (v1.4) ## Our Pledge -In the interest of fostering an open, collaborative, and welcoming environment, we as contributors and maintainers of nf-core, pledge to making participation in our projects and community a harassment-free experience for everyone, regardless of: +In the interest of fostering an open, collaborative, and welcoming environment, we as contributors and maintainers of nf-core pledge to making participation in our projects and community a harassment-free experience for everyone, regardless of: - Age +- Ability - Body size +- Caste - Familial status - Gender identity and expression - Geographical location - Level of experience - Nationality and national origins - Native language -- Physical and neurological ability +- Neurodiversity - Race or ethnicity - Religion - Sexual identity and orientation @@ -22,80 +24,133 @@ Please note that the list above is alphabetised and is therefore not ranked in a ## Preamble -> Note: This Code of Conduct (CoC) has been drafted by the nf-core Safety Officer and been edited after input from members of the nf-core team and others. "We", in this document, refers to the Safety Officer and members of the nf-core core team, both of whom are deemed to be members of the nf-core community and are therefore required to abide by this Code of Conduct. This document will amended periodically to keep it up-to-date, and in case of any dispute, the most current version will apply. +:::note +This Code of Conduct (CoC) has been drafted by Renuka Kudva, Cris Tuñí, and Michael Heuer, with input from the nf-core Core Team and Susanna Marquez from the nf-core community. "We", in this document, refers to the Safety Officers and members of the nf-core Core Team, both of whom are deemed to be members of the nf-core community and are therefore required to abide by this Code of Conduct. This document will be amended periodically to keep it up-to-date. In case of any dispute, the most current version will apply. +::: -An up-to-date list of members of the nf-core core team can be found [here](https://nf-co.re/about). Our current safety officer is Renuka Kudva. +An up-to-date list of members of the nf-core core team can be found [here](https://nf-co.re/about). + +Our Safety Officers are Saba Nafees, Cris Tuñí, and Michael Heuer. nf-core is a young and growing community that welcomes contributions from anyone with a shared vision for [Open Science Policies](https://www.fosteropenscience.eu/taxonomy/term/8). Open science policies encompass inclusive behaviours and we strive to build and maintain a safe and inclusive environment for all individuals. -We have therefore adopted this code of conduct (CoC), which we require all members of our community and attendees in nf-core events to adhere to in all our workspaces at all times. Workspaces include but are not limited to Slack, meetings on Zoom, Jitsi, YouTube live etc. +We have therefore adopted this CoC, which we require all members of our community and attendees of nf-core events to adhere to in all our workspaces at all times. Workspaces include, but are not limited to, Slack, meetings on Zoom, gather.town, YouTube live etc. -Our CoC will be strictly enforced and the nf-core team reserve the right to exclude participants who do not comply with our guidelines from our workspaces and future nf-core activities. +Our CoC will be strictly enforced and the nf-core team reserves the right to exclude participants who do not comply with our guidelines from our workspaces and future nf-core activities. -We ask all members of our community to help maintain a supportive and productive workspace and to avoid behaviours that can make individuals feel unsafe or unwelcome. Please help us maintain and uphold this CoC. +We ask all members of our community to help maintain supportive and productive workspaces and to avoid behaviours that can make individuals feel unsafe or unwelcome. Please help us maintain and uphold this CoC. -Questions, concerns or ideas on what we can include? Contact safety [at] nf-co [dot] re +Questions, concerns, or ideas on what we can include? Contact members of the Safety Team on Slack or email safety [at] nf-co [dot] re. ## Our Responsibilities -The safety officer is responsible for clarifying the standards of acceptable behavior and are expected to take appropriate and fair corrective action in response to any instances of unacceptable behaviour. +Members of the Safety Team (the Safety Officers) are responsible for clarifying the standards of acceptable behavior and are expected to take appropriate and fair corrective action in response to any instances of unacceptable behaviour. -The safety officer in consultation with the nf-core core team have the right and responsibility to remove, edit, or reject comments, commits, code, wiki edits, issues, and other contributions that are not aligned to this Code of Conduct, or to ban temporarily or permanently any contributor for other behaviors that they deem inappropriate, threatening, offensive, or harmful. +The Safety Team, in consultation with the nf-core core team, have the right and responsibility to remove, edit, or reject comments, commits, code, wiki edits, issues, and other contributions that are not aligned to this CoC, or to ban temporarily or permanently any contributor for other behaviors that they deem inappropriate, threatening, offensive, or harmful. -Members of the core team or the safety officer who violate the CoC will be required to recuse themselves pending investigation. They will not have access to any reports of the violations and be subject to the same actions as others in violation of the CoC. +Members of the core team or the Safety Team who violate the CoC will be required to recuse themselves pending investigation. They will not have access to any reports of the violations and will be subject to the same actions as others in violation of the CoC. -## When are where does this Code of Conduct apply? +## When and where does this Code of Conduct apply? -Participation in the nf-core community is contingent on following these guidelines in all our workspaces and events. This includes but is not limited to the following listed alphabetically and therefore in no order of preference: +Participation in the nf-core community is contingent on following these guidelines in all our workspaces and events, such as hackathons, workshops, bytesize, and collaborative workspaces on gather.town. These guidelines include, but are not limited to, the following (listed alphabetically and therefore in no order of preference): - Communicating with an official project email address. - Communicating with community members within the nf-core Slack channel. - Participating in hackathons organised by nf-core (both online and in-person events). -- Participating in collaborative work on GitHub, Google Suite, community calls, mentorship meetings, email correspondence. -- Participating in workshops, training, and seminar series organised by nf-core (both online and in-person events). This applies to events hosted on web-based platforms such as Zoom, Jitsi, YouTube live etc. +- Participating in collaborative work on GitHub, Google Suite, community calls, mentorship meetings, email correspondence, and on the nf-core gather.town workspace. +- Participating in workshops, training, and seminar series organised by nf-core (both online and in-person events). This applies to events hosted on web-based platforms such as Zoom, gather.town, Jitsi, YouTube live etc. - Representing nf-core on social media. This includes both official and personal accounts. ## nf-core cares 😊 -nf-core's CoC and expectations of respectful behaviours for all participants (including organisers and the nf-core team) include but are not limited to the following (listed in alphabetical order): +nf-core's CoC and expectations of respectful behaviours for all participants (including organisers and the nf-core team) include, but are not limited to, the following (listed in alphabetical order): - Ask for consent before sharing another community member’s personal information (including photographs) on social media. - Be respectful of differing viewpoints and experiences. We are all here to learn from one another and a difference in opinion can present a good learning opportunity. -- Celebrate your accomplishments at events! (Get creative with your use of emojis 🎉 🥳 💯 🙌 !) +- Celebrate your accomplishments! (Get creative with your use of emojis 🎉 🥳 💯 🙌 !) - Demonstrate empathy towards other community members. (We don’t all have the same amount of time to dedicate to nf-core. If tasks are pending, don’t hesitate to gently remind members of your team. If you are leading a task, ask for help if you feel overwhelmed.) - Engage with and enquire after others. (This is especially important given the geographically remote nature of the nf-core community, so let’s do this the best we can) - Focus on what is best for the team and the community. (When in doubt, ask) -- Graciously accept constructive criticism, yet be unafraid to question, deliberate, and learn. +- Accept feedback, yet be unafraid to question, deliberate, and learn. - Introduce yourself to members of the community. (We’ve all been outsiders and we know that talking to strangers can be hard for some, but remember we’re interested in getting to know you and your visions for open science!) -- Show appreciation and **provide clear feedback**. (This is especially important because we don’t see each other in person and it can be harder to interpret subtleties. Also remember that not everyone understands a certain language to the same extent as you do, so **be clear in your communications to be kind.**) +- Show appreciation and **provide clear feedback**. (This is especially important because we don’t see each other in person and it can be harder to interpret subtleties. Also remember that not everyone understands a certain language to the same extent as you do, so **be clear in your communication to be kind.**) - Take breaks when you feel like you need them. -- Using welcoming and inclusive language. (Participants are encouraged to display their chosen pronouns on Zoom or in communication on Slack.) +- Use welcoming and inclusive language. (Participants are encouraged to display their chosen pronouns on Zoom or in communication on Slack) ## nf-core frowns on 😕 -The following behaviours from any participants within the nf-core community (including the organisers) will be considered unacceptable under this code of conduct. Engaging or advocating for any of the following could result in expulsion from nf-core workspaces. +The following behaviours from any participants within the nf-core community (including the organisers) will be considered unacceptable under this CoC. Engaging or advocating for any of the following could result in expulsion from nf-core workspaces: - Deliberate intimidation, stalking or following and sustained disruption of communication among participants of the community. This includes hijacking shared screens through actions such as using the annotate tool in conferencing software such as Zoom. - “Doxing” i.e. posting (or threatening to post) another person’s personal identifying information online. - Spamming or trolling of individuals on social media. -- Use of sexual or discriminatory imagery, comments, or jokes and unwelcome sexual attention. -- Verbal and text comments that reinforce social structures of domination related to gender, gender identity and expression, sexual orientation, ability, physical appearance, body size, race, age, religion or work experience. +- Use of sexual or discriminatory imagery, comments, jokes, or unwelcome sexual attention. +- Verbal and text comments that reinforce social structures of domination related to gender, gender identity and expression, sexual orientation, ability, physical appearance, body size, race, age, religion, or work experience. ### Online Trolling -The majority of nf-core interactions and events are held online. Unfortunately, holding events online comes with the added issue of online trolling. This is unacceptable, reports of such behaviour will be taken very seriously, and perpetrators will be excluded from activities immediately. +The majority of nf-core interactions and events are held online. Unfortunately, holding events online comes with the risk of online trolling. This is unacceptable — reports of such behaviour will be taken very seriously and perpetrators will be excluded from activities immediately. -All community members are required to ask members of the group they are working within for explicit consent prior to taking screenshots of individuals during video calls. +All community members are **required** to ask members of the group they are working with for explicit consent prior to taking screenshots of individuals during video calls. -## Procedures for Reporting CoC violations +## Procedures for reporting CoC violations If someone makes you feel uncomfortable through their behaviours or actions, report it as soon as possible. -You can reach out to members of the [nf-core core team](https://nf-co.re/about) and they will forward your concerns to the safety officer(s). +You can reach out to members of the Safety Team (Saba Nafees, Cris Tuñí, and Michael Heuer) on Slack. Alternatively, contact a member of the nf-core core team [nf-core core team](https://nf-co.re/about), and they will forward your concerns to the Safety Team. + +Issues directly concerning members of the Core Team or the Safety Team will be dealt with by other members of the core team and the safety manager — possible conflicts of interest will be taken into account. nf-core is also in discussions about having an ombudsperson and details will be shared in due course. + +All reports will be handled with the utmost discretion and confidentiality. + +You can also report any CoC violations to safety [at] nf-co [dot] re. In your email report, please do your best to include: + +- Your contact information. +- Identifying information (e.g. names, nicknames, pseudonyms) of the participant who has violated the Code of Conduct. +- The behaviour that was in violation and the circumstances surrounding the incident. +- The approximate time of the behaviour (if different than the time the report was made). +- Other people involved in the incident, if applicable. +- If you believe the incident is ongoing. +- If there is a publicly available record (e.g. mailing list record, a screenshot). +- Any additional information. + +After you file a report, one or more members of our Safety Team will contact you to follow up on your report. + +## Who will read and handle reports + +All reports will be read and handled by the members of the Safety Team at nf-core. + +If members of the Safety Team are deemed to have a conflict of interest with a report, they will be required to recuse themselves as per our Code of Conduct and will not have access to any follow-ups. + +To keep this first report confidential from any of the Safety Team members, please submit your first report by direct messaging on Slack/direct email to any of the nf-core members you are comfortable disclosing the information to, and be explicit about which member(s) you do not consent to sharing the information with. + +## Reviewing reports + +After receiving the report, members of the Safety Team will review the incident report to determine whether immediate action is required, for example, whether there is immediate threat to participants’ safety. + +The Safety Team, in consultation with members of the nf-core core team, will assess the information to determine whether the report constitutes a Code of Conduct violation, for them to decide on a course of action. + +In the case of insufficient information, one or more members of the Safety Team may contact the reporter, the reportee, or any other attendees to obtain more information. -Issues directly concerning members of the core team will be dealt with by other members of the core team and the safety manager, and possible conflicts of interest will be taken into account. nf-core is also in discussions about having an ombudsperson, and details will be shared in due course. +Once additional information is gathered, the Safety Team will collectively review and decide on the best course of action to take, if any. The Safety Team reserves the right to not act on a report. -All reports will be handled with utmost discretion and confidentially. +## Confidentiality + +All reports, and any additional information included, are only shared with the team of safety officers (and possibly members of the core team, in case the safety officer is in violation of the CoC). We will respect confidentiality requests for the purpose of protecting victims of abuse. + +We will not name harassment victims, beyond discussions between the safety officer and members of the nf-core team, without the explicit consent of the individuals involved. + +## Enforcement + +Actions taken by the nf-core’s Safety Team may include, but are not limited to: + +- Asking anyone to stop a behaviour. +- Asking anyone to leave the event and online spaces either temporarily, for the remainder of the event, or permanently. +- Removing access to the gather.town and Slack, either temporarily or permanently. +- Communicating to all participants to reinforce our expectations for conduct and remind what is unacceptable behaviour; this may be public for practical reasons. +- Communicating to all participants that an incident has taken place and how we will act or have acted — this may be for the purpose of letting event participants know we are aware of and dealing with the incident. +- Banning anyone from participating in nf-core-managed spaces, future events, and activities, either temporarily or permanently. +- No action. ## Attribution and Acknowledgements @@ -106,6 +161,22 @@ All reports will be handled with utmost discretion and confidentially. ## Changelog -### v1.0 - March 12th, 2021 +### v1.4 - February 8th, 2022 + +- Included a new member of the Safety Team. Corrected a typographical error in the text. + +### v1.3 - December 10th, 2021 + +- Added a statement that the CoC applies to nf-core gather.town workspaces. Corrected typographical errors in the text. + +### v1.2 - November 12th, 2021 + +- Removed information specific to reporting CoC violations at the Hackathon in October 2021. + +### v1.1 - October 14th, 2021 + +- Updated with names of new Safety Officers and specific information for the hackathon in October 2021. + +### v1.0 - March 15th, 2021 - Complete rewrite from original [Contributor Covenant](http://contributor-covenant.org/) CoC. diff --git a/lib/NfcoreTemplate.groovy b/lib/NfcoreTemplate.groovy index 408951ae..01b8653d 100755 --- a/lib/NfcoreTemplate.groovy +++ b/lib/NfcoreTemplate.groovy @@ -3,6 +3,7 @@ // import org.yaml.snakeyaml.Yaml +import groovy.json.JsonOutput class NfcoreTemplate { @@ -222,6 +223,21 @@ class NfcoreTemplate { } } + // + // Dump pipeline parameters in a json file + // + public static void dump_parameters(workflow, params) { + def output_d = new File("${params.outdir}/pipeline_info/") + if (!output_d.exists()) { + output_d.mkdirs() + } + + def timestamp = new java.util.Date().format( 'yyyy-MM-dd_HH-mm-ss') + def output_pf = new File(output_d, "params_${timestamp}.json") + def jsonStr = JsonOutput.toJson(params) + output_pf.text = JsonOutput.prettyPrint(jsonStr) + } + // // Print pipeline summary on completion // From 14f2c809d3d628cef8f3595abab668e8ac4ddd4c Mon Sep 17 00:00:00 2001 From: Gisela Gabernet Garriga Date: Thu, 12 Oct 2023 20:20:48 -0400 Subject: [PATCH 27/32] temporary inactivate validate params --- main.nf | 9 +++++---- 1 file changed, 5 insertions(+), 4 deletions(-) diff --git a/main.nf b/main.nf index 24de2277..095f148f 100644 --- a/main.nf +++ b/main.nf @@ -17,7 +17,8 @@ nextflow.enable.dsl = 2 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ */ -include { validateParameters; paramsHelp } from 'plugin/nf-validation' +// Commented out as taking too long for big samplesheets +//include { validateParameters; paramsHelp } from 'plugin/nf-validation' // Print help message if needed if (params.help) { @@ -29,9 +30,9 @@ if (params.help) { } // Validate input parameters -if (params.validate_params) { - validateParameters() -} +//if (params.validate_params) { +// validateParameters() +//} WorkflowMain.initialise(workflow, params, log) From e762a6adc9da1421200907082937fe9da7c55ab6 Mon Sep 17 00:00:00 2001 From: Gisela Gabernet Garriga Date: Thu, 12 Oct 2023 20:21:00 -0400 Subject: [PATCH 28/32] dowser clones by cloneby --- conf/modules.config | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/conf/modules.config b/conf/modules.config index d70d052b..91dc666d 100644 --- a/conf/modules.config +++ b/conf/modules.config @@ -454,7 +454,7 @@ process { ext.args = ['outname':'', 'model':'hierarchical', 'method':'nt', 'linkage':'single', 'skip_convergence':true, - 'outputby':'sample_id', 'min_n':30] + 'outputby':'${params.cloneby}', 'min_n':30] } withName: DEFINE_CLONES_REPORT { @@ -466,7 +466,7 @@ process { ext.args = ['outname':'', 'model':'hierarchical', 'method':'nt', 'linkage':'single', 'skip_convergence':false, - 'outputby':'sample_id', 'min_n':30] + 'outputby':'${params.outdir}', 'min_n':30] } withName: DOWSER_LINEAGES { From c20157a92ccbeddb2fc07937346f62bf2cb44051 Mon Sep 17 00:00:00 2001 From: Gisela Gabernet Garriga Date: Thu, 12 Oct 2023 20:21:11 -0400 Subject: [PATCH 29/32] findthreshold optional output --- modules/local/enchantr/find_threshold.nf | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/modules/local/enchantr/find_threshold.nf b/modules/local/enchantr/find_threshold.nf index 8f3a533b..06df734c 100644 --- a/modules/local/enchantr/find_threshold.nf +++ b/modules/local/enchantr/find_threshold.nf @@ -38,7 +38,7 @@ process FIND_THRESHOLD { // tuple val(meta), path("*threshold-pass.tsv"), emit: tab // sequence tsv in AIRR format path("*_command_log.txt"), emit: logs //process logs path "*_report" - path "all_reps_dist_report/tables/*_threshold-summary.tsv", emit: threshold_summary + path "all_reps_dist_report/tables/*_threshold-summary.tsv", emit: threshold_summary, optional:true path "all_reps_dist_report/tables/*_threshold-mean.tsv", emit: mean_threshold path "versions.yml", emit: versions From da21e209439c1b3aad9e1c31f3d39aab088238c3 Mon Sep 17 00:00:00 2001 From: Gisela Gabernet Date: Thu, 12 Oct 2023 20:23:14 -0400 Subject: [PATCH 30/32] report clones by cloneby --- conf/modules.config | 2 +- modules/local/enchantr/define_clones.nf | 1 + 2 files changed, 2 insertions(+), 1 deletion(-) diff --git a/conf/modules.config b/conf/modules.config index d70d052b..3ef1cfd7 100644 --- a/conf/modules.config +++ b/conf/modules.config @@ -466,7 +466,7 @@ process { ext.args = ['outname':'', 'model':'hierarchical', 'method':'nt', 'linkage':'single', 'skip_convergence':false, - 'outputby':'sample_id', 'min_n':30] + 'min_n':30] } withName: DOWSER_LINEAGES { diff --git a/modules/local/enchantr/define_clones.nf b/modules/local/enchantr/define_clones.nf index 8f843516..c127bbc0 100644 --- a/modules/local/enchantr/define_clones.nf +++ b/modules/local/enchantr/define_clones.nf @@ -56,6 +56,7 @@ process DEFINE_CLONES { 'imgt_db'='${imgt_base}', \\ 'species'='auto', \\ 'cloneby'='${params.cloneby}', \\ + 'outputby'='${params.cloneby}', 'force'=FALSE, \\ 'threshold'=${thr}, \\ 'singlecell'='${params.singlecell}','outdir'=getwd(), \\ From 5358d66fa60af3dd16c6ef02ea1ebebf8fcf7e25 Mon Sep 17 00:00:00 2001 From: Gisela Gabernet Date: Thu, 12 Oct 2023 21:14:29 -0400 Subject: [PATCH 31/32] allow whitespace in tissue --- bin/check_samplesheet.py | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/bin/check_samplesheet.py b/bin/check_samplesheet.py index 355caec3..6347db2f 100755 --- a/bin/check_samplesheet.py +++ b/bin/check_samplesheet.py @@ -85,8 +85,7 @@ def check_samplesheet(file_in, assembled): "filename_R2", "subject_id", "species", - "pcr_target_locus", - "tissue", + "pcr_target_locus" ] no_whitespaces_assembled = [ "sample_id", From 5f98b829d5aab0eeb34d9eb3c5d68f058a0d50a2 Mon Sep 17 00:00:00 2001 From: Gisela Gabernet Date: Fri, 13 Oct 2023 21:58:51 -0400 Subject: [PATCH 32/32] fix lint --- bin/check_samplesheet.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/bin/check_samplesheet.py b/bin/check_samplesheet.py index 6347db2f..39c2514e 100755 --- a/bin/check_samplesheet.py +++ b/bin/check_samplesheet.py @@ -85,7 +85,7 @@ def check_samplesheet(file_in, assembled): "filename_R2", "subject_id", "species", - "pcr_target_locus" + "pcr_target_locus", ] no_whitespaces_assembled = [ "sample_id",