diff --git a/.devcontainer/devcontainer.json b/.devcontainer/devcontainer.json
index 4a9bc5c7..4ecfbfe3 100644
--- a/.devcontainer/devcontainer.json
+++ b/.devcontainer/devcontainer.json
@@ -18,11 +18,11 @@
"python.linting.flake8Path": "/opt/conda/bin/flake8",
"python.linting.pycodestylePath": "/opt/conda/bin/pycodestyle",
"python.linting.pydocstylePath": "/opt/conda/bin/pydocstyle",
- "python.linting.pylintPath": "/opt/conda/bin/pylint",
+ "python.linting.pylintPath": "/opt/conda/bin/pylint"
},
// Add the IDs of extensions you want installed when the container is created.
- "extensions": ["ms-python.python", "ms-python.vscode-pylance", "nf-core.nf-core-extensionpack"],
- },
- },
+ "extensions": ["ms-python.python", "ms-python.vscode-pylance", "nf-core.nf-core-extensionpack"]
+ }
+ }
}
diff --git a/.nf-core.yml b/.nf-core.yml
index cfe39173..b67677ae 100644
--- a/.nf-core.yml
+++ b/.nf-core.yml
@@ -3,4 +3,9 @@ lint:
files_unchanged:
- .github/ISSUE_TEMPLATE/bug_report.yml
- pyproject.toml
+ - .github/workflows/branch.yml
+ - .github/workflows/linting_comment.yml
+ - .github/workflows/linting.yml
+ - .github/CONTRIBUTING.md
+ - .github/PULL_REQUEST_TEMPLATE.md
multiqc_config: false
diff --git a/CHANGELOG.md b/CHANGELOG.md
index 175fbef6..1b017b4f 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -25,6 +25,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
- [[#113](https://github.com/nf-core/proteinfold/pull/113)] - Include esmfold dbs for full data sets.
- [[PR #114](https://github.com/nf-core/rnaseq/pull/114)] - Update paths to test dbs.
- [[PR #117](https://github.com/nf-core/proteinfold/pull/117)] - Update pipeline template to [nf-core/tools 2.10](https://github.com/nf-core/tools/releases/tag/2.10).
+- [[PR #132](https://github.com/nf-core/proteinfold/pull/132)] - Remove `lib/` directory.
## 1.0.0 - White Silver Reebok
diff --git a/lib/NfcoreTemplate.groovy b/lib/NfcoreTemplate.groovy
deleted file mode 100755
index e248e4c3..00000000
--- a/lib/NfcoreTemplate.groovy
+++ /dev/null
@@ -1,356 +0,0 @@
-//
-// This file holds several functions used within the nf-core pipeline template.
-//
-
-import org.yaml.snakeyaml.Yaml
-import groovy.json.JsonOutput
-import nextflow.extension.FilesEx
-
-class NfcoreTemplate {
-
- //
- // Check AWS Batch related parameters have been specified correctly
- //
- public static void awsBatch(workflow, params) {
- if (workflow.profile.contains('awsbatch')) {
- // Check params.awsqueue and params.awsregion have been set if running on AWSBatch
- assert (params.awsqueue && params.awsregion) : "Specify correct --awsqueue and --awsregion parameters on AWSBatch!"
- // Check outdir paths to be S3 buckets if running on AWSBatch
- assert params.outdir.startsWith('s3:') : "Outdir not on S3 - specify S3 Bucket to run on AWSBatch!"
- }
- }
-
- //
- // Warn if a -profile or Nextflow config has not been provided to run the pipeline
- //
- public static void checkConfigProvided(workflow, log) {
- if (workflow.profile == 'standard' && workflow.configFiles.size() <= 1) {
- log.warn "[$workflow.manifest.name] You are attempting to run the pipeline without any custom configuration!\n\n" +
- "This will be dependent on your local compute environment but can be achieved via one or more of the following:\n" +
- " (1) Using an existing pipeline profile e.g. `-profile docker` or `-profile singularity`\n" +
- " (2) Using an existing nf-core/configs for your Institution e.g. `-profile crick` or `-profile uppmax`\n" +
- " (3) Using your own local custom config e.g. `-c /path/to/your/custom.config`\n\n" +
- "Please refer to the quick start section and usage docs for the pipeline.\n "
- }
- }
-
- //
- // Generate version string
- //
- public static String version(workflow) {
- String version_string = ""
-
- if (workflow.manifest.version) {
- def prefix_v = workflow.manifest.version[0] != 'v' ? 'v' : ''
- version_string += "${prefix_v}${workflow.manifest.version}"
- }
-
- if (workflow.commitId) {
- def git_shortsha = workflow.commitId.substring(0, 7)
- version_string += "-g${git_shortsha}"
- }
-
- return version_string
- }
-
- //
- // Construct and send completion email
- //
- public static void email(workflow, params, summary_params, projectDir, log, multiqc_report=[]) {
-
- // Set up the e-mail variables
- def subject = "[$workflow.manifest.name] Successful: $workflow.runName"
- if (!workflow.success) {
- subject = "[$workflow.manifest.name] FAILED: $workflow.runName"
- }
-
- def summary = [:]
- for (group in summary_params.keySet()) {
- summary << summary_params[group]
- }
-
- def misc_fields = [:]
- misc_fields['Date Started'] = workflow.start
- misc_fields['Date Completed'] = workflow.complete
- misc_fields['Pipeline script file path'] = workflow.scriptFile
- misc_fields['Pipeline script hash ID'] = workflow.scriptId
- if (workflow.repository) misc_fields['Pipeline repository Git URL'] = workflow.repository
- if (workflow.commitId) misc_fields['Pipeline repository Git Commit'] = workflow.commitId
- if (workflow.revision) misc_fields['Pipeline Git branch/tag'] = workflow.revision
- misc_fields['Nextflow Version'] = workflow.nextflow.version
- misc_fields['Nextflow Build'] = workflow.nextflow.build
- misc_fields['Nextflow Compile Timestamp'] = workflow.nextflow.timestamp
-
- def email_fields = [:]
- email_fields['version'] = NfcoreTemplate.version(workflow)
- email_fields['runName'] = workflow.runName
- email_fields['success'] = workflow.success
- email_fields['dateComplete'] = workflow.complete
- email_fields['duration'] = workflow.duration
- email_fields['exitStatus'] = workflow.exitStatus
- email_fields['errorMessage'] = (workflow.errorMessage ?: 'None')
- email_fields['errorReport'] = (workflow.errorReport ?: 'None')
- email_fields['commandLine'] = workflow.commandLine
- email_fields['projectDir'] = workflow.projectDir
- email_fields['summary'] = summary << misc_fields
-
- // On success try attach the multiqc report
- def mqc_report = null
- try {
- if (workflow.success) {
- mqc_report = multiqc_report.getVal()
- if (mqc_report.getClass() == ArrayList && mqc_report.size() >= 1) {
- if (mqc_report.size() > 1) {
- log.warn "[$workflow.manifest.name] Found multiple reports from process 'MULTIQC', will use only one"
- }
- mqc_report = mqc_report[0]
- }
- }
- } catch (all) {
- if (multiqc_report) {
- log.warn "[$workflow.manifest.name] Could not attach MultiQC report to summary email"
- }
- }
-
- // Check if we are only sending emails on failure
- def email_address = params.email
- if (!params.email && params.email_on_fail && !workflow.success) {
- email_address = params.email_on_fail
- }
-
- // Render the TXT template
- def engine = new groovy.text.GStringTemplateEngine()
- def tf = new File("$projectDir/assets/email_template.txt")
- def txt_template = engine.createTemplate(tf).make(email_fields)
- def email_txt = txt_template.toString()
-
- // Render the HTML template
- def hf = new File("$projectDir/assets/email_template.html")
- def html_template = engine.createTemplate(hf).make(email_fields)
- def email_html = html_template.toString()
-
- // Render the sendmail template
- def max_multiqc_email_size = (params.containsKey('max_multiqc_email_size') ? params.max_multiqc_email_size : 0) as nextflow.util.MemoryUnit
- def smail_fields = [ email: email_address, subject: subject, email_txt: email_txt, email_html: email_html, projectDir: "$projectDir", mqcFile: mqc_report, mqcMaxSize: max_multiqc_email_size.toBytes() ]
- def sf = new File("$projectDir/assets/sendmail_template.txt")
- def sendmail_template = engine.createTemplate(sf).make(smail_fields)
- def sendmail_html = sendmail_template.toString()
-
- // Send the HTML e-mail
- Map colors = logColours(params.monochrome_logs)
- if (email_address) {
- try {
- if (params.plaintext_email) { throw GroovyException('Send plaintext e-mail, not HTML') }
- // Try to send HTML e-mail using sendmail
- def sendmail_tf = new File(workflow.launchDir.toString(), ".sendmail_tmp.html")
- sendmail_tf.withWriter { w -> w << sendmail_html }
- [ 'sendmail', '-t' ].execute() << sendmail_html
- log.info "-${colors.purple}[$workflow.manifest.name]${colors.green} Sent summary e-mail to $email_address (sendmail)-"
- } catch (all) {
- // Catch failures and try with plaintext
- def mail_cmd = [ 'mail', '-s', subject, '--content-type=text/html', email_address ]
- if ( mqc_report != null && mqc_report.size() <= max_multiqc_email_size.toBytes() ) {
- mail_cmd += [ '-A', mqc_report ]
- }
- mail_cmd.execute() << email_html
- log.info "-${colors.purple}[$workflow.manifest.name]${colors.green} Sent summary e-mail to $email_address (mail)-"
- }
- }
-
- // Write summary e-mail HTML to a file
- def output_hf = new File(workflow.launchDir.toString(), ".pipeline_report.html")
- output_hf.withWriter { w -> w << email_html }
- FilesEx.copyTo(output_hf.toPath(), "${params.outdir}/pipeline_info/pipeline_report.html");
- output_hf.delete()
-
- // Write summary e-mail TXT to a file
- def output_tf = new File(workflow.launchDir.toString(), ".pipeline_report.txt")
- output_tf.withWriter { w -> w << email_txt }
- FilesEx.copyTo(output_tf.toPath(), "${params.outdir}/pipeline_info/pipeline_report.txt");
- output_tf.delete()
- }
-
- //
- // Construct and send a notification to a web server as JSON
- // e.g. Microsoft Teams and Slack
- //
- public static void IM_notification(workflow, params, summary_params, projectDir, log) {
- def hook_url = params.hook_url
-
- def summary = [:]
- for (group in summary_params.keySet()) {
- summary << summary_params[group]
- }
-
- def misc_fields = [:]
- misc_fields['start'] = workflow.start
- misc_fields['complete'] = workflow.complete
- misc_fields['scriptfile'] = workflow.scriptFile
- misc_fields['scriptid'] = workflow.scriptId
- if (workflow.repository) misc_fields['repository'] = workflow.repository
- if (workflow.commitId) misc_fields['commitid'] = workflow.commitId
- if (workflow.revision) misc_fields['revision'] = workflow.revision
- misc_fields['nxf_version'] = workflow.nextflow.version
- misc_fields['nxf_build'] = workflow.nextflow.build
- misc_fields['nxf_timestamp'] = workflow.nextflow.timestamp
-
- def msg_fields = [:]
- msg_fields['version'] = NfcoreTemplate.version(workflow)
- msg_fields['runName'] = workflow.runName
- msg_fields['success'] = workflow.success
- msg_fields['dateComplete'] = workflow.complete
- msg_fields['duration'] = workflow.duration
- msg_fields['exitStatus'] = workflow.exitStatus
- msg_fields['errorMessage'] = (workflow.errorMessage ?: 'None')
- msg_fields['errorReport'] = (workflow.errorReport ?: 'None')
- msg_fields['commandLine'] = workflow.commandLine.replaceFirst(/ +--hook_url +[^ ]+/, "")
- msg_fields['projectDir'] = workflow.projectDir
- msg_fields['summary'] = summary << misc_fields
-
- // Render the JSON template
- def engine = new groovy.text.GStringTemplateEngine()
- // Different JSON depending on the service provider
- // Defaults to "Adaptive Cards" (https://adaptivecards.io), except Slack which has its own format
- def json_path = hook_url.contains("hooks.slack.com") ? "slackreport.json" : "adaptivecard.json"
- def hf = new File("$projectDir/assets/${json_path}")
- def json_template = engine.createTemplate(hf).make(msg_fields)
- def json_message = json_template.toString()
-
- // POST
- def post = new URL(hook_url).openConnection();
- post.setRequestMethod("POST")
- post.setDoOutput(true)
- post.setRequestProperty("Content-Type", "application/json")
- post.getOutputStream().write(json_message.getBytes("UTF-8"));
- def postRC = post.getResponseCode();
- if (! postRC.equals(200)) {
- log.warn(post.getErrorStream().getText());
- }
- }
-
- //
- // Dump pipeline parameters in a json file
- //
- public static void dump_parameters(workflow, params) {
- def timestamp = new java.util.Date().format( 'yyyy-MM-dd_HH-mm-ss')
- def filename = "params_${timestamp}.json"
- def temp_pf = new File(workflow.launchDir.toString(), ".${filename}")
- def jsonStr = JsonOutput.toJson(params)
- temp_pf.text = JsonOutput.prettyPrint(jsonStr)
-
- FilesEx.copyTo(temp_pf.toPath(), "${params.outdir}/pipeline_info/params_${timestamp}.json")
- temp_pf.delete()
- }
-
- //
- // Print pipeline summary on completion
- //
- public static void summary(workflow, params, log) {
- Map colors = logColours(params.monochrome_logs)
- if (workflow.success) {
- if (workflow.stats.ignoredCount == 0) {
- log.info "-${colors.purple}[$workflow.manifest.name]${colors.green} Pipeline completed successfully${colors.reset}-"
- } else {
- log.info "-${colors.purple}[$workflow.manifest.name]${colors.yellow} Pipeline completed successfully, but with errored process(es) ${colors.reset}-"
- }
- } else {
- log.info "-${colors.purple}[$workflow.manifest.name]${colors.red} Pipeline completed with errors${colors.reset}-"
- }
- }
-
- //
- // ANSII Colours used for terminal logging
- //
- public static Map logColours(Boolean monochrome_logs) {
- Map colorcodes = [:]
-
- // Reset / Meta
- colorcodes['reset'] = monochrome_logs ? '' : "\033[0m"
- colorcodes['bold'] = monochrome_logs ? '' : "\033[1m"
- colorcodes['dim'] = monochrome_logs ? '' : "\033[2m"
- colorcodes['underlined'] = monochrome_logs ? '' : "\033[4m"
- colorcodes['blink'] = monochrome_logs ? '' : "\033[5m"
- colorcodes['reverse'] = monochrome_logs ? '' : "\033[7m"
- colorcodes['hidden'] = monochrome_logs ? '' : "\033[8m"
-
- // Regular Colors
- colorcodes['black'] = monochrome_logs ? '' : "\033[0;30m"
- colorcodes['red'] = monochrome_logs ? '' : "\033[0;31m"
- colorcodes['green'] = monochrome_logs ? '' : "\033[0;32m"
- colorcodes['yellow'] = monochrome_logs ? '' : "\033[0;33m"
- colorcodes['blue'] = monochrome_logs ? '' : "\033[0;34m"
- colorcodes['purple'] = monochrome_logs ? '' : "\033[0;35m"
- colorcodes['cyan'] = monochrome_logs ? '' : "\033[0;36m"
- colorcodes['white'] = monochrome_logs ? '' : "\033[0;37m"
-
- // Bold
- colorcodes['bblack'] = monochrome_logs ? '' : "\033[1;30m"
- colorcodes['bred'] = monochrome_logs ? '' : "\033[1;31m"
- colorcodes['bgreen'] = monochrome_logs ? '' : "\033[1;32m"
- colorcodes['byellow'] = monochrome_logs ? '' : "\033[1;33m"
- colorcodes['bblue'] = monochrome_logs ? '' : "\033[1;34m"
- colorcodes['bpurple'] = monochrome_logs ? '' : "\033[1;35m"
- colorcodes['bcyan'] = monochrome_logs ? '' : "\033[1;36m"
- colorcodes['bwhite'] = monochrome_logs ? '' : "\033[1;37m"
-
- // Underline
- colorcodes['ublack'] = monochrome_logs ? '' : "\033[4;30m"
- colorcodes['ured'] = monochrome_logs ? '' : "\033[4;31m"
- colorcodes['ugreen'] = monochrome_logs ? '' : "\033[4;32m"
- colorcodes['uyellow'] = monochrome_logs ? '' : "\033[4;33m"
- colorcodes['ublue'] = monochrome_logs ? '' : "\033[4;34m"
- colorcodes['upurple'] = monochrome_logs ? '' : "\033[4;35m"
- colorcodes['ucyan'] = monochrome_logs ? '' : "\033[4;36m"
- colorcodes['uwhite'] = monochrome_logs ? '' : "\033[4;37m"
-
- // High Intensity
- colorcodes['iblack'] = monochrome_logs ? '' : "\033[0;90m"
- colorcodes['ired'] = monochrome_logs ? '' : "\033[0;91m"
- colorcodes['igreen'] = monochrome_logs ? '' : "\033[0;92m"
- colorcodes['iyellow'] = monochrome_logs ? '' : "\033[0;93m"
- colorcodes['iblue'] = monochrome_logs ? '' : "\033[0;94m"
- colorcodes['ipurple'] = monochrome_logs ? '' : "\033[0;95m"
- colorcodes['icyan'] = monochrome_logs ? '' : "\033[0;96m"
- colorcodes['iwhite'] = monochrome_logs ? '' : "\033[0;97m"
-
- // Bold High Intensity
- colorcodes['biblack'] = monochrome_logs ? '' : "\033[1;90m"
- colorcodes['bired'] = monochrome_logs ? '' : "\033[1;91m"
- colorcodes['bigreen'] = monochrome_logs ? '' : "\033[1;92m"
- colorcodes['biyellow'] = monochrome_logs ? '' : "\033[1;93m"
- colorcodes['biblue'] = monochrome_logs ? '' : "\033[1;94m"
- colorcodes['bipurple'] = monochrome_logs ? '' : "\033[1;95m"
- colorcodes['bicyan'] = monochrome_logs ? '' : "\033[1;96m"
- colorcodes['biwhite'] = monochrome_logs ? '' : "\033[1;97m"
-
- return colorcodes
- }
-
- //
- // Does what is says on the tin
- //
- public static String dashedLine(monochrome_logs) {
- Map colors = logColours(monochrome_logs)
- return "-${colors.dim}----------------------------------------------------${colors.reset}-"
- }
-
- //
- // nf-core logo
- //
- public static String logo(workflow, monochrome_logs) {
- Map colors = logColours(monochrome_logs)
- String workflow_version = NfcoreTemplate.version(workflow)
- String.format(
- """\n
- ${dashedLine(monochrome_logs)}
- ${colors.green},--.${colors.black}/${colors.green},-.${colors.reset}
- ${colors.blue} ___ __ __ __ ___ ${colors.green}/,-._.--~\'${colors.reset}
- ${colors.blue} |\\ | |__ __ / ` / \\ |__) |__ ${colors.yellow}} {${colors.reset}
- ${colors.blue} | \\| | \\__, \\__/ | \\ |___ ${colors.green}\\`-._,-`-,${colors.reset}
- ${colors.green}`._,._,\'${colors.reset}
- ${colors.purple} ${workflow.manifest.name} ${workflow_version}${colors.reset}
- ${dashedLine(monochrome_logs)}
- """.stripIndent()
- )
- }
-}
diff --git a/lib/Utils.groovy b/lib/Utils.groovy
deleted file mode 100644
index 8d030f4e..00000000
--- a/lib/Utils.groovy
+++ /dev/null
@@ -1,47 +0,0 @@
-//
-// This file holds several Groovy functions that could be useful for any Nextflow pipeline
-//
-
-import org.yaml.snakeyaml.Yaml
-
-class Utils {
-
- //
- // When running with -profile conda, warn if channels have not been set-up appropriately
- //
- public static void checkCondaChannels(log) {
- Yaml parser = new Yaml()
- def channels = []
- try {
- def config = parser.load("conda config --show channels".execute().text)
- channels = config.channels
- } catch(NullPointerException | IOException e) {
- log.warn "Could not verify conda channel configuration."
- return
- }
-
- // Check that all channels are present
- // This channel list is ordered by required channel priority.
- def required_channels_in_order = ['conda-forge', 'bioconda', 'defaults']
- def channels_missing = ((required_channels_in_order as Set) - (channels as Set)) as Boolean
-
- // Check that they are in the right order
- def channel_priority_violation = false
- def n = required_channels_in_order.size()
- for (int i = 0; i < n - 1; i++) {
- channel_priority_violation |= !(channels.indexOf(required_channels_in_order[i]) < channels.indexOf(required_channels_in_order[i+1]))
- }
-
- if (channels_missing | channel_priority_violation) {
- log.warn "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n" +
- " There is a problem with your Conda configuration!\n\n" +
- " You will need to set-up the conda-forge and bioconda channels correctly.\n" +
- " Please refer to https://bioconda.github.io/\n" +
- " The observed channel order is \n" +
- " ${channels}\n" +
- " but the following channel order is required:\n" +
- " ${required_channels_in_order}\n" +
- "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~"
- }
- }
-}
diff --git a/lib/WorkflowAlphafold2.groovy b/lib/WorkflowAlphafold2.groovy
deleted file mode 100755
index bcf5f396..00000000
--- a/lib/WorkflowAlphafold2.groovy
+++ /dev/null
@@ -1,100 +0,0 @@
-//
-// This file holds several functions specific to the workflow/proteinfold.nf in the nf-core/proteinfold pipeline
-//
-
-import nextflow.Nextflow
-import groovy.text.SimpleTemplateEngine
-
-class WorkflowAlphafold2 {
-
- //
- // Check and validate parameters
- //
- public static void initialise(params, log) { }
-
- //
- // Get workflow summary for MultiQC
- //
- public static String paramsSummaryMultiqc(workflow, summary) {
- String summary_section = ''
- for (group in summary.keySet()) {
- def group_params = summary.get(group) // This gets the parameters of that particular group
- if (group_params) {
- summary_section += " $group
\n"
- summary_section += " \n"
- for (param in group_params.keySet()) {
- summary_section += " - $param
- ${group_params.get(param) ?: 'N/A'}
\n"
- }
- summary_section += "
\n"
- }
- }
-
- String yaml_file_text = "id: '${workflow.manifest.name.replace('/','-')}-summary'\n"
- yaml_file_text += "description: ' - this information is collected when the pipeline is started.'\n"
- yaml_file_text += "section_name: '${workflow.manifest.name} Workflow Summary'\n"
- yaml_file_text += "section_href: 'https://github.com/${workflow.manifest.name}'\n"
- yaml_file_text += "plot_type: 'html'\n"
- yaml_file_text += "data: |\n"
- yaml_file_text += "${summary_section}"
- return yaml_file_text
- }
-
- //
- // Generate methods description for MultiQC
- //
-
- public static String toolCitationText(params) {
-
- // TODO nf-core: 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., & KΓ€ller, M. (2016). MultiQC: summarize analysis results for multiple tools and samples in a single report. Bioinformatics , 32(19), 3047β3048. 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()
- def description_html = engine.createTemplate(methods_text).make(meta)
-
- return description_html
- }
-}
diff --git a/lib/WorkflowColabfold.groovy b/lib/WorkflowColabfold.groovy
deleted file mode 100755
index e84f9c19..00000000
--- a/lib/WorkflowColabfold.groovy
+++ /dev/null
@@ -1,68 +0,0 @@
-//
-// This file holds several functions specific to the workflow/proteinfold.nf in the nf-core/proteinfold pipeline
-//
-
-import nextflow.Nextflow
-import groovy.text.SimpleTemplateEngine
-
-class WorkflowColabfold {
-
- //
- // Check and validate parameters
- //
- public static void initialise(params, log) { }
-
- //
- // Get workflow summary for MultiQC
- //
- public static String paramsSummaryMultiqc(workflow, summary) {
- String summary_section = ''
- for (group in summary.keySet()) {
- def group_params = summary.get(group) // This gets the parameters of that particular group
- if (group_params) {
- summary_section += " $group
\n"
- summary_section += " \n"
- for (param in group_params.keySet()) {
- summary_section += " - $param
- ${group_params.get(param) ?: 'N/A'}
\n"
- }
- summary_section += "
\n"
- }
- }
-
- String yaml_file_text = "id: '${workflow.manifest.name.replace('/','-')}-summary'\n"
- yaml_file_text += "description: ' - this information is collected when the pipeline is started.'\n"
- yaml_file_text += "section_name: '${workflow.manifest.name} Workflow Summary'\n"
- yaml_file_text += "section_href: 'https://github.com/${workflow.manifest.name}'\n"
- yaml_file_text += "plot_type: 'html'\n"
- yaml_file_text += "data: |\n"
- yaml_file_text += "${summary_section}"
- return yaml_file_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()
- def description_html = engine.createTemplate(methods_text).make(meta)
-
- return description_html
- }
-}
diff --git a/lib/WorkflowEsmfold.groovy b/lib/WorkflowEsmfold.groovy
deleted file mode 100644
index 6c38a2af..00000000
--- a/lib/WorkflowEsmfold.groovy
+++ /dev/null
@@ -1,68 +0,0 @@
-//
-// This file holds several functions specific to the workflow/proteinfold.nf in the nf-core/proteinfold pipeline
-//
-
-import nextflow.Nextflow
-import groovy.text.SimpleTemplateEngine
-
-class WorkflowEsmfold {
-
- //
- // Check and validate parameters
- //
- public static void initialise(params, log) { }
-
- //
- // Get workflow summary for MultiQC
- //
- public static String paramsSummaryMultiqc(workflow, summary) {
- String summary_section = ''
- for (group in summary.keySet()) {
- def group_params = summary.get(group) // This gets the parameters of that particular group
- if (group_params) {
- summary_section += " $group
\n"
- summary_section += " \n"
- for (param in group_params.keySet()) {
- summary_section += " - $param
- ${group_params.get(param) ?: 'N/A'}
\n"
- }
- summary_section += "
\n"
- }
- }
-
- String yaml_file_text = "id: '${workflow.manifest.name.replace('/','-')}-summary'\n"
- yaml_file_text += "description: ' - this information is collected when the pipeline is started.'\n"
- yaml_file_text += "section_name: '${workflow.manifest.name} Workflow Summary'\n"
- yaml_file_text += "section_href: 'https://github.com/${workflow.manifest.name}'\n"
- yaml_file_text += "plot_type: 'html'\n"
- yaml_file_text += "data: |\n"
- yaml_file_text += "${summary_section}"
- return yaml_file_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()
- def description_html = engine.createTemplate(methods_text).make(meta)
-
- return description_html
- }
-}
diff --git a/lib/WorkflowMain.groovy b/lib/WorkflowMain.groovy
deleted file mode 100755
index 0ad73200..00000000
--- a/lib/WorkflowMain.groovy
+++ /dev/null
@@ -1,99 +0,0 @@
-//
-// This file holds several functions specific to the main.nf workflow in the nf-core/proteinfold pipeline
-//
-
-import nextflow.Nextflow
-
-class WorkflowMain {
-
- //
- // Citation string for pipeline
- //
- public static String citation(workflow) {
- return "If you use ${workflow.manifest.name} for your analysis please cite:\n\n" +
- // TODO nf-core: Add Zenodo DOI for pipeline after first release
- //"* The pipeline\n" +
- //" https://doi.org/10.5281/zenodo.XXXXXXX\n\n" +
- "* The nf-core framework\n" +
- " https://doi.org/10.1038/s41587-020-0439-x\n\n" +
- "* Software dependencies\n" +
- " https://github.com/${workflow.manifest.name}/blob/master/CITATIONS.md"
- }
-
-
- //
- // Validate parameters and print summary to screen
- //
- public static void initialise(workflow, params, log, args) {
-
- // Print workflow version and exit on --version
- if (params.version) {
- String workflow_version = NfcoreTemplate.version(workflow)
- log.info "${workflow.manifest.name} ${workflow_version}"
- System.exit(0)
- }
-
- // Check that a -profile or Nextflow config has been provided to run the pipeline
- NfcoreTemplate.checkConfigProvided(workflow, log)
- // Check that the profile doesn't contain spaces and doesn't end with a trailing comma
- checkProfile(workflow.profile, args, log)
-
- // Check that conda channels are set-up correctly
- if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) {
- Utils.checkCondaChannels(log)
- }
-
-
- // Check AWS batch settings
- NfcoreTemplate.awsBatch(workflow, params)
- }
- //
- // Get attribute from genome config file e.g. fasta
- //
- public static Object getGenomeAttribute(params, attribute) {
- if (params.genomes && params.genome && params.genomes.containsKey(params.genome)) {
- if (params.genomes[ params.genome ].containsKey(attribute)) {
- return params.genomes[ params.genome ][ attribute ]
- }
- }
- return null
- }
-
- //
- // Get link to Colabfold Alphafold2 parameters
- //
- public static String getColabfoldAlphafold2Params(params) {
- def link = null
- if (params.colabfold_alphafold2_params_tags) {
- if (params.colabfold_alphafold2_params_tags.containsKey(params.colabfold_model_preset.toString())) {
- link = "https://storage.googleapis.com/alphafold/" + params.colabfold_alphafold2_params_tags[ params.colabfold_model_preset.toString() ] + '.tar'
- }
- }
- return link
- }
-
- //
- // Get path to Colabfold Alphafold2 parameters
- //
- public static String getColabfoldAlphafold2ParamsPath(params) {
- def path = null
- if (params.colabfold_alphafold2_params_tags) {
- if (params.colabfold_alphafold2_params_tags.containsKey(params.colabfold_model_preset.toString())) {
- path = "${params.colabfold_db}/params/" + params.colabfold_alphafold2_params_tags[ params.colabfold_model_preset.toString() ]
- }
- }
- return path
- }
-
- //
- // Exit pipeline if --profile contains spaces
- //
- private static void checkProfile(profile, args, log) {
- if (profile.endsWith(',')) {
- Nextflow.error "Profile cannot end with a trailing comma. Please remove the comma from the end of the profile string.\nHint: A common mistake is to provide multiple values to `-profile` separated by spaces. Please use commas to separate profiles instead,e.g., `-profile docker,test`."
- }
- if (args[0]) {
- log.warn "nf-core pipelines do not accept positional arguments. The positional argument `${args[0]}` has been detected.\n Hint: A common mistake is to provide multiple values to `-profile` separated by spaces. Please use commas to separate profiles instead,e.g., `-profile docker,test`."
- }
- }
-}
diff --git a/main.nf b/main.nf
index 6e974b23..f7000ee6 100644
--- a/main.nf
+++ b/main.nf
@@ -13,36 +13,34 @@ nextflow.enable.dsl = 2
/*
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
- COLABFOLD PARAMETER VALUES
+ IMPORT FUNCTIONS / MODULES / SUBWORKFLOWS / WORKFLOWS
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
*/
-params.colabfold_alphafold2_params = WorkflowMain.getColabfoldAlphafold2Params(params)
-params.colabfold_alphafold2_params_path = WorkflowMain.getColabfoldAlphafold2ParamsPath(params)
+if (params.mode == "alphafold2") {
+ include { PREPARE_ALPHAFOLD2_DBS } from './subworkflows/local/prepare_alphafold2_dbs'
+ include { ALPHAFOLD2 } from './workflows/alphafold2'
+} else if (params.mode == "colabfold") {
+ include { PREPARE_COLABFOLD_DBS } from './subworkflows/local/prepare_colabfold_dbs'
+ include { COLABFOLD } from './workflows/colabfold'
+} else if (params.mode == "esmfold") {
+ include { PREPARE_ESMFOLD_DBS } from './subworkflows/local/prepare_esmfold_dbs'
+ include { ESMFOLD } from './workflows/esmfold'
+}
+
+include { PIPELINE_INITIALISATION } from './subworkflows/local/utils_nfcore_proteinfold_pipeline'
+include { PIPELINE_COMPLETION } from './subworkflows/local/utils_nfcore_proteinfold_pipeline'
+include { getColabfoldAlphafold2Params } from './subworkflows/local/utils_nfcore_proteinfold_pipeline'
+include { getColabfoldAlphafold2ParamsPath } from './subworkflows/local/utils_nfcore_proteinfold_pipeline'
/*
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
- VALIDATE & PRINT PARAMETER SUMMARY
+ COLABFOLD PARAMETER VALUES
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
*/
-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, args)
+params.colabfold_alphafold2_params = getColabfoldAlphafold2Params()
+params.colabfold_alphafold2_params_path = getColabfoldAlphafold2ParamsPath()
/*
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
@@ -50,35 +48,128 @@ WorkflowMain.initialise(workflow, params, log, args)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
*/
-if (params.mode == "alphafold2") {
- include { ALPHAFOLD2 } from './workflows/alphafold2'
-} else if (params.mode == "colabfold") {
- include { COLABFOLD } from './workflows/colabfold'
-} else if (params.mode == "esmfold") {
- include { ESMFOLD } from './workflows/esmfold'
-}
-
+//
+// WORKFLOW: Run main analysis pipeline
+//
workflow NFCORE_PROTEINFOLD {
+
+ main:
+ ch_multiqc = Channel.empty()
+ ch_versions = Channel.empty()
+
//
// WORKFLOW: Run alphafold2
//
if(params.mode == "alphafold2") {
- ALPHAFOLD2 ()
+ //
+ // SUBWORKFLOW: Prepare Alphafold2 DBs
+ //
+ PREPARE_ALPHAFOLD2_DBS (
+ params.alphafold2_db,
+ params.full_dbs,
+ params.bfd_path,
+ params.small_bfd_path,
+ params.alphafold2_params_path,
+ params.mgnify_path,
+ params.pdb70_path,
+ params.pdb_mmcif_path,
+ params.uniref30_alphafold2_path,
+ params.uniref90_path,
+ params.pdb_seqres_path,
+ params.uniprot_path,
+ params.uniprot_sprot,
+ params.uniprot_trembl
+ )
+ ch_versions = ch_versions.mix(PREPARE_ALPHAFOLD2_DBS.out.versions)
+
+ //
+ // WORKFLOW: Run nf-core/alphafold2 workflow
+ //
+ ALPHAFOLD2 (
+ ch_versions,
+ params.full_dbs,
+ params.alphafold2_mode,
+ params.alphafold2_model_preset,
+ PREPARE_ALPHAFOLD2_DBS.out.params,
+ PREPARE_ALPHAFOLD2_DBS.out.bfd.ifEmpty([]),
+ PREPARE_ALPHAFOLD2_DBS.out.small_bfd.ifEmpty([]),
+ PREPARE_ALPHAFOLD2_DBS.out.mgnify,
+ PREPARE_ALPHAFOLD2_DBS.out.pdb70,
+ PREPARE_ALPHAFOLD2_DBS.out.pdb_mmcif,
+ PREPARE_ALPHAFOLD2_DBS.out.uniref30,
+ PREPARE_ALPHAFOLD2_DBS.out.uniref90,
+ PREPARE_ALPHAFOLD2_DBS.out.pdb_seqres,
+ PREPARE_ALPHAFOLD2_DBS.out.uniprot
+ )
+ ch_multiqc = ALPHAFOLD2.out.multiqc_report
+ ch_versions = ch_versions.mix(ALPHAFOLD2.out.versions)
}
//
// WORKFLOW: Run colabfold
//
else if(params.mode == "colabfold") {
- COLABFOLD ()
+ //
+ // SUBWORKFLOW: Prepare Colabfold DBs
+ //
+ PREPARE_COLABFOLD_DBS (
+ params.colabfold_db,
+ params.colabfold_server,
+ params.colabfold_alphafold2_params_path,
+ params.colabfold_db_path,
+ params.uniref30_colabfold_path,
+ params.colabfold_alphafold2_params,
+ params.colabfold_db_link,
+ params.uniref30_colabfold_link,
+ params.create_colabfold_index
+ )
+ ch_versions = ch_versions.mix(PREPARE_COLABFOLD_DBS.out.versions)
+
+ //
+ // WORKFLOW: Run nf-core/colabfold workflow
+ //
+ COLABFOLD (
+ ch_versions,
+ params.colabfold_model_preset,
+ PREPARE_COLABFOLD_DBS.out.params,
+ PREPARE_COLABFOLD_DBS.out.colabfold_db,
+ PREPARE_COLABFOLD_DBS.out.uniref30,
+ params.num_recycle
+ )
+ ch_multiqc = COLABFOLD.out.multiqc_report
+ ch_versions = ch_versions.mix(COLABFOLD.out.versions)
}
//
// WORKFLOW: Run esmfold
//
else if(params.mode == "esmfold") {
- ESMFOLD ()
+ //
+ // SUBWORKFLOW: Prepare esmfold DBs
+ //
+ PREPARE_ESMFOLD_DBS (
+ params.esmfold_db,
+ params.esmfold_params_path,
+ params.esmfold_3B_v1,
+ params.esm2_t36_3B_UR50D,
+ params.esm2_t36_3B_UR50D_contact_regression
+ )
+ ch_versions = ch_versions.mix(PREPARE_ESMFOLD_DBS.out.versions)
+
+ //
+ // WORKFLOW: Run nf-core/esmfold workflow
+ //
+ ESMFOLD (
+ ch_versions,
+ PREPARE_ESMFOLD_DBS.out.params,
+ params.num_recycle
+ )
+ ch_multiqc = ESMFOLD.out.multiqc_report
+ ch_versions = ch_versions.mix(ESMFOLD.out.versions)
}
+ emit:
+ multiqc_report = ch_multiqc // channel: /path/to/multiqc_report.html
+ versions = ch_versions // channel: [version1, version2, ...]
}
/*
@@ -92,7 +183,37 @@ workflow NFCORE_PROTEINFOLD {
// See: https://github.com/nf-core/rnaseq/issues/619
//
workflow {
+
+ main:
+ //
+ // SUBWORKFLOW: Run initialisation tasks
+ //
+ PIPELINE_INITIALISATION (
+ params.version,
+ params.help,
+ params.validate_params,
+ params.monochrome_logs,
+ args,
+ params.outdir
+ )
+
+ //
+ // WORKFLOW: Run main workflow
+ //
NFCORE_PROTEINFOLD ()
+
+ //
+ // SUBWORKFLOW: Run completion tasks
+ //
+ PIPELINE_COMPLETION (
+ params.email,
+ params.email_on_fail,
+ params.plaintext_email,
+ params.outdir,
+ params.monochrome_logs,
+ params.hook_url,
+ NFCORE_PROTEINFOLD.out.multiqc_report
+ )
}
/*
diff --git a/modules.json b/modules.json
index 5f59deaf..c0360e4a 100644
--- a/modules.json
+++ b/modules.json
@@ -42,6 +42,25 @@
"patch": "modules/nf-core/untar/untar.diff"
}
}
+ },
+ "subworkflows": {
+ "nf-core": {
+ "utils_nextflow_pipeline": {
+ "branch": "master",
+ "git_sha": "cd08c91373cd00a73255081340e4914485846ba1",
+ "installed_by": ["subworkflows"]
+ },
+ "utils_nfcore_pipeline": {
+ "branch": "master",
+ "git_sha": "262b17ed2aad591039f914951659177e6c39a8d8",
+ "installed_by": ["subworkflows"]
+ },
+ "utils_nfvalidation_plugin": {
+ "branch": "master",
+ "git_sha": "cd08c91373cd00a73255081340e4914485846ba1",
+ "installed_by": ["subworkflows"]
+ }
+ }
}
}
}
diff --git a/modules/local/run_esmfold.nf b/modules/local/run_esmfold.nf
index 3f8e6c02..4d5645c3 100644
--- a/modules/local/run_esmfold.nf
+++ b/modules/local/run_esmfold.nf
@@ -43,7 +43,7 @@ process RUN_ESMFOLD {
def VERSION = '1.0.3' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions.
"""
touch ./"${fasta.baseName}".pdb
- touch ./"${fasta.baseName}"_mqc.tsv
+ touch ./"${fasta.baseName}"_plddt_mqc.tsv
cat <<-END_VERSIONS > versions.yml
"${task.process}":
diff --git a/subworkflows/local/prepare_alphafold2_dbs.nf b/subworkflows/local/prepare_alphafold2_dbs.nf
index c085d6f4..d3efffbf 100644
--- a/subworkflows/local/prepare_alphafold2_dbs.nf
+++ b/subworkflows/local/prepare_alphafold2_dbs.nf
@@ -18,98 +18,115 @@ include { COMBINE_UNIPROT } from '../../modules/local/combine_uniprot'
include { DOWNLOAD_PDBMMCIF } from '../../modules/local/download_pdbmmcif'
workflow PREPARE_ALPHAFOLD2_DBS {
+
+ take:
+ alphafold2_db // directory: path to alphafold2 DBs
+ full_dbs // boolean: Use full databases (otherwise reduced version)
+ bfd_path // directory: /path/to/bfd/
+ small_bfd_path // directory: /path/to/small_bfd/
+ alphafold2_params_path // directory: /path/to/alphafold2/params/
+ mgnify_path // directory: /path/to/mgnify/
+ pdb70_path // directory: /path/to/pdb70/
+ pdb_mmcif_path // directory: /path/to/pdb_mmcif/
+ uniref30_alphafold2_path // directory: /path/to/uniref30/alphafold2/
+ uniref90_path // directory: /path/to/uniref90/
+ pdb_seqres_path // directory: /path/to/pdb_seqres/
+ uniprot_path // directory: /path/to/uniprot/
+ uniprot_sprot // string: Specifies the link to download uniprot_sprot
+ uniprot_trembl
+
main:
ch_bfd = Channel.empty()
ch_small_bfd = Channel.empty()
ch_versions = Channel.empty()
- if (params.alphafold2_db) {
- if (params.full_dbs) {
- ch_bfd = file( params.bfd_path )
+ if (alphafold2_db) {
+ if (full_dbs) {
+ ch_bfd = file( bfd_path )
ch_small_bfd = file( "${projectDir}/assets/dummy_db" )
}
else {
ch_bfd = file( "${projectDir}/assets/dummy_db" )
- ch_small_bfd = file( params.small_bfd_path )
+ ch_small_bfd = file( small_bfd_path )
}
- ch_params = file( params.alphafold2_params_path )
- ch_mgnify = file( params.mgnify_path )
- ch_pdb70 = file( params.pdb70_path, type: 'dir' )
- ch_mmcif_files = file( params.pdb_mmcif_path, type: 'dir' )
- ch_mmcif_obsolete = file( params.pdb_mmcif_path, type: 'file' )
+ ch_params = file( alphafold2_params_path )
+ ch_mgnify = file( mgnify_path )
+ ch_pdb70 = file( pdb70_path, type: 'dir' )
+ ch_mmcif_files = file( pdb_mmcif_path, type: 'dir' )
+ ch_mmcif_obsolete = file( pdb_mmcif_path, type: 'file' )
ch_mmcif = ch_mmcif_files + ch_mmcif_obsolete
- ch_uniref30 = file( params.uniref30_alphafold2_path, type: 'any' )
- ch_uniref90 = file( params.uniref90_path )
- ch_pdb_seqres = file( params.pdb_seqres_path )
- ch_uniprot = file( params.uniprot_path )
+ ch_uniref30 = file( uniref30_alphafold2_path, type: 'any' )
+ ch_uniref90 = file( uniref90_path )
+ ch_pdb_seqres = file( pdb_seqres_path )
+ ch_uniprot = file( uniprot_path )
}
else {
- if (params.full_dbs) {
+ if (full_dbs) {
ARIA2_BFD(
- params.bfd
+ bfd
)
ch_bfd = ARIA2_BFD.out.db
ch_versions = ch_versions.mix(ARIA2_BFD.out.versions)
} else {
ARIA2_SMALL_BFD(
- params.small_bfd
+ small_bfd
)
ch_small_bfd = ARIA2_SMALL_BFD.out.db
ch_versions = ch_versions.mix(ARIA2_SMALL_BFD.out.versions)
}
ARIA2_ALPHAFOLD2_PARAMS(
- params.alphafold2_params
+ alphafold2_params
)
ch_params = ARIA2_ALPHAFOLD2_PARAMS.out.db
ch_versions = ch_versions.mix(ARIA2_ALPHAFOLD2_PARAMS.out.versions)
ARIA2_MGNIFY(
- params.mgnify
+ mgnify
)
ch_mgnify = ARIA2_MGNIFY.out.db
ch_versions = ch_versions.mix(ARIA2_MGNIFY.out.versions)
ARIA2_PDB70(
- params.pdb70
+ pdb70
)
ch_pdb70 = ARIA2_PDB70.out.db
ch_versions = ch_versions.mix(ARIA2_PDB70.out.versions)
DOWNLOAD_PDBMMCIF(
- params.pdb_mmcif,
- params.pdb_obsolete
+ pdb_mmcif,
+ pdb_obsolete
)
ch_mmcif = DOWNLOAD_PDBMMCIF.out.ch_db
ch_versions = ch_versions.mix(DOWNLOAD_PDBMMCIF.out.versions)
ARIA2_UNIREF30(
- params.uniref30_alphafold2
+ uniref30_alphafold2
)
ch_uniref30 = ARIA2_UNIREF30.out.db
ch_versions = ch_versions.mix(ARIA2_UNIREF30.out.versions)
ARIA2_UNIREF90(
- params.uniref90
+ uniref90
)
ch_uniref90 = ARIA2_UNIREF90.out.db
ch_versions = ch_versions.mix(ARIA2_UNIREF90.out.versions)
ARIA2 (
- params.pdb_seqres
+ pdb_seqres
)
ch_pdb_seqres = ARIA2.out.downloaded_file
ch_versions = ch_versions.mix(ARIA2.out.versions)
ARIA2_UNIPROT_SPROT(
- params.uniprot_sprot
+ uniprot_sprot
)
ch_versions = ch_versions.mix(ARIA2_UNIPROT_SPROT.out.versions)
ARIA2_UNIPROT_TREMBL(
- params.uniprot_trembl
+ uniprot_trembl
)
ch_versions = ch_versions.mix(ARIA2_UNIPROT_TREMBL.out.versions)
COMBINE_UNIPROT (
diff --git a/subworkflows/local/prepare_colabfold_dbs.nf b/subworkflows/local/prepare_colabfold_dbs.nf
index fd189f3c..97a23dad 100644
--- a/subworkflows/local/prepare_colabfold_dbs.nf
+++ b/subworkflows/local/prepare_colabfold_dbs.nf
@@ -11,29 +11,41 @@ include { MMSEQS_TSV2EXPROFILEDB as MMSEQS_TSV2EXPROFILEDB_COLABFOLDDB } from '.
include { MMSEQS_TSV2EXPROFILEDB as MMSEQS_TSV2EXPROFILEDB_UNIPROT30 } from '../../modules/nf-core/mmseqs/tsv2exprofiledb/main'
workflow PREPARE_COLABFOLD_DBS {
+
+ take:
+ colabfold_db // directory: path/to/colabfold/DBs and params
+ colabfold_server // string: Specifies the server to use for colabfold
+ colabfold_alphafold2_params_path // directory: /path/to/colabfold/alphafold2/params/
+ colabfold_db_path // directory: /path/to/colabfold/db/
+ uniref30_colabfold_path // directory: /path/to/uniref30/colabfold/
+ colabfold_alphafold2_params // string: Specifies the link to download colabfold alphafold2 params
+ colabfold_db_link // string: Specifies the link to download colabfold db
+ uniref30_colabfold_link // string: Specifies the link to download uniref30
+ create_colabfold_index // boolean: Create index for colabfold db
+
main:
ch_params = Channel.empty()
ch_colabfold_db = Channel.empty()
ch_uniref30 = Channel.empty()
ch_versions = Channel.empty()
- if (params.colabfold_db) {
- ch_params = file( params.colabfold_alphafold2_params_path, type: 'any' )
- if (params.colabfold_server == 'local') {
- ch_colabfold_db = file( params.colabfold_db_path, type: 'any' )
- ch_uniref30 = file( params.uniref30_colabfold_path , type: 'any' )
+ if (colabfold_db) {
+ ch_params = file( colabfold_alphafold2_params_path, type: 'any' )
+ if (colabfold_server == 'local') {
+ ch_colabfold_db = file( colabfold_db_path, type: 'any' )
+ ch_uniref30 = file( uniref30_colabfold_path , type: 'any' )
}
}
else {
ARIA2_COLABFOLD_PARAMS (
- params.colabfold_alphafold2_params
+ colabfold_alphafold2_params
)
ch_params = ARIA2_COLABFOLD_PARAMS.out.db
ch_versions = ch_versions.mix(ARIA2_COLABFOLD_PARAMS.out.versions)
if (params.colabfold_server == 'local') {
ARIA2_COLABFOLD_DB (
- params.colabfold_db_link
+ colabfold_db_link
)
ch_versions = ch_versions.mix(ARIA2_COLABFOLD_DB.out.versions)
@@ -52,7 +64,7 @@ workflow PREPARE_COLABFOLD_DBS {
}
ARIA2_UNIREF30(
- params.uniref30
+ uniref30_colabfold_link
)
ch_versions = ch_versions.mix(ARIA2_UNIREF30.out.versions)
@@ -62,7 +74,7 @@ workflow PREPARE_COLABFOLD_DBS {
ch_uniref30 = MMSEQS_TSV2EXPROFILEDB_UNIPROT30.out.db_exprofile
ch_versions = ch_versions.mix(MMSEQS_TSV2EXPROFILEDB_UNIPROT30.out.versions)
- if (params.create_colabfold_index) {
+ if (create_colabfold_index) {
MMSEQS_CREATEINDEX_UNIPROT30 (
MMSEQS_TSV2EXPROFILEDB_UNIPROT30.out.db_exprofile
)
diff --git a/subworkflows/local/prepare_esmfold_dbs.nf b/subworkflows/local/prepare_esmfold_dbs.nf
index 864037c3..39c39370 100644
--- a/subworkflows/local/prepare_esmfold_dbs.nf
+++ b/subworkflows/local/prepare_esmfold_dbs.nf
@@ -7,21 +7,29 @@ include { ARIA2 as ARIA2_ESM2_T36_3B_UR50D } from '../../modu
include { ARIA2 as ARIA2_ESM2_T36_3B_UR50D_CONTACT_REGRESSION } from '../../modules/nf-core/aria2/main'
workflow PREPARE_ESMFOLD_DBS {
+
+ take:
+ esmfold_db // directory: /path/to/esmfold/db/
+ esmfold_params_path // directory: /path/to/esmfold/params/
+ esmfold_3B_v1 // string: Specifies the link to download esmfold 3B v1
+ esm2_t36_3B_UR50D // string: Specifies the link to download esm2 t36 3B UR50D
+ esm2_t36_3B_UR50D_contact_regression // string: Specifies the link to download esm2 t36 3B UR50D contact regression
+
main:
ch_versions = Channel.empty()
- if (params.esmfold_db) {
- ch_params = file( params.esmfold_params_path, type: 'file' )
+ if (esmfold_db) {
+ ch_params = file( esmfold_params_path, type: 'file' )
}
else {
ARIA2_ESMFOLD_3B_V1 (
- params.esmfold_3B_v1
+ esmfold_3B_v1
)
ARIA2_ESM2_T36_3B_UR50D (
- params.esm2_t36_3B_UR50D
+ esm2_t36_3B_UR50D
)
ARIA2_ESM2_T36_3B_UR50D_CONTACT_REGRESSION (
- params.esm2_t36_3B_UR50D_contact_regression
+ esm2_t36_3B_UR50D_contact_regression
)
ch_params = ARIA2_ESMFOLD_3B_V1.out.downloaded_file.mix(ARIA2_ESM2_T36_3B_UR50D.out.downloaded_file,ARIA2_ESM2_T36_3B_UR50D_CONTACT_REGRESSION.out.downloaded_file).collect()
ch_versions = ch_versions.mix(ARIA2_ESMFOLD_3B_V1.out.versions)
diff --git a/subworkflows/local/utils_nfcore_proteinfold_pipeline/main.nf b/subworkflows/local/utils_nfcore_proteinfold_pipeline/main.nf
new file mode 100644
index 00000000..4fca9a96
--- /dev/null
+++ b/subworkflows/local/utils_nfcore_proteinfold_pipeline/main.nf
@@ -0,0 +1,202 @@
+//
+// Subworkflow with functionality specific to the nf-core/pipeline pipeline
+//
+
+import groovy.json.JsonSlurper
+
+/*
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+ IMPORT FUNCTIONS / MODULES / SUBWORKFLOWS
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+*/
+
+include { UTILS_NFVALIDATION_PLUGIN } from '../../nf-core/utils_nfvalidation_plugin'
+include { paramsSummaryMap } from 'plugin/nf-validation'
+include { UTILS_NEXTFLOW_PIPELINE } from '../../nf-core/utils_nextflow_pipeline'
+include { completionEmail } from '../../nf-core/utils_nfcore_pipeline'
+include { completionSummary } from '../../nf-core/utils_nfcore_pipeline'
+include { dashedLine } from '../../nf-core/utils_nfcore_pipeline'
+include { nfCoreLogo } from '../../nf-core/utils_nfcore_pipeline'
+include { imNotification } from '../../nf-core/utils_nfcore_pipeline'
+include { UTILS_NFCORE_PIPELINE } from '../../nf-core/utils_nfcore_pipeline'
+include { workflowCitation } from '../../nf-core/utils_nfcore_pipeline'
+
+/*
+========================================================================================
+ SUBWORKFLOW TO INITIALISE PIPELINE
+========================================================================================
+*/
+
+workflow PIPELINE_INITIALISATION {
+
+ take:
+ version // boolean: Display version and exit
+ help // boolean: Display help text
+ validate_params // boolean: Boolean whether to validate parameters against the schema at runtime
+ monochrome_logs // boolean: Do not use coloured log outputs
+ nextflow_cli_args // array: List of positional nextflow CLI args
+ outdir // string: The output directory where the results will be saved
+
+ main:
+ //
+ // Print version and exit if required and dump pipeline parameters to JSON file
+ //
+ UTILS_NEXTFLOW_PIPELINE (
+ version,
+ true,
+ outdir,
+ workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1
+ )
+
+ //
+ // Validate parameters and generate parameter summary to stdout
+ //
+ pre_help_text = nfCoreLogo(monochrome_logs)
+ post_help_text = '\n' + workflowCitation() + '\n' + dashedLine(monochrome_logs)
+ def String workflow_command = "nextflow run ${workflow.manifest.name} -profile --input samplesheet.csv --genome GRCh37 --outdir "
+ UTILS_NFVALIDATION_PLUGIN (
+ help,
+ workflow_command,
+ pre_help_text,
+ post_help_text,
+ validate_params,
+ "nextflow_schema.json"
+ )
+
+//
+ // Check config provided to the pipeline
+ //
+ UTILS_NFCORE_PIPELINE (
+ nextflow_cli_args
+ )
+
+ // // TODO: remove
+ // // Custom validation for pipeline parameters
+ // //
+ // validateInputParameters()
+
+}
+
+/*
+========================================================================================
+ SUBWORKFLOW FOR PIPELINE COMPLETION
+========================================================================================
+*/
+
+workflow PIPELINE_COMPLETION {
+
+ take:
+ email // string: email address
+ email_on_fail // string: email address sent on pipeline failure
+ plaintext_email // boolean: Send plain-text email instead of HTML
+ outdir // path: Path to output directory where results will be published
+ monochrome_logs // boolean: Disable ANSI colour codes in log output
+ hook_url // string: hook URL for notifications
+ multiqc_report // string: Path to MultiQC report
+
+ main:
+
+ summary_params = paramsSummaryMap(workflow, parameters_schema: "nextflow_schema.json")
+
+ //
+ // Completion email and summary
+ //
+ workflow.onComplete {
+ if (email || email_on_fail) {
+ completionEmail(summary_params, email, email_on_fail, plaintext_email, outdir, monochrome_logs, multiqc_report.toList())
+ }
+
+ completionSummary(monochrome_logs)
+
+ if (hook_url) {
+ imNotification(summary_params, hook_url)
+ }
+ }
+}
+
+/*
+========================================================================================
+ FUNCTIONS
+========================================================================================
+*/
+
+//
+// Get link to Colabfold Alphafold2 parameters
+//
+def getColabfoldAlphafold2Params() {
+ def link = null
+ if (params.colabfold_alphafold2_params_tags) {
+ if (params.colabfold_alphafold2_params_tags.containsKey(params.colabfold_model_preset.toString())) {
+ link = "https://storage.googleapis.com/alphafold/" + params.colabfold_alphafold2_params_tags[ params.colabfold_model_preset.toString() ] + '.tar'
+ }
+ }
+ return link
+}
+
+//
+// Get path to Colabfold Alphafold2 parameters
+//
+def getColabfoldAlphafold2ParamsPath() {
+ def path = null
+ params.colabfold_model_preset.toString()
+ if (params.colabfold_alphafold2_params_tags) {
+ if (params.colabfold_alphafold2_params_tags.containsKey(params.colabfold_model_preset.toString())) {
+ path = "${params.colabfold_db}/params/" + params.colabfold_alphafold2_params_tags[ params.colabfold_model_preset.toString() ]
+ }
+ }
+ return path
+}
+
+//
+// Generate methods description for MultiQC
+//
+def toolCitationText() {
+ // TODO nf-core: 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
+}
+
+def toolBibliographyText() {
+ // TODO nf-core: 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., & KΓ€ller, M. (2016). MultiQC: summarize analysis results for multiple tools and samples in a single report. Bioinformatics , 32(19), 3047β3048. doi: /10.1093/bioinformatics/btw354"
+ ].join(' ').trim()
+
+ return reference_text
+}
+
+def methodsDescriptionText(mqc_methods_yaml) {
+ // 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 = workflow.toMap()
+ meta["manifest_map"] = workflow.manifest.toMap()
+
+ // Pipeline DOI
+ meta["doi_text"] = meta.manifest_map.doi ? "(doi: ${meta.manifest_map.doi})" : ""
+ meta["nodoi_text"] = meta.manifest_map.doi ? "": "If available, make sure to update the text to include the Zenodo DOI of version of the pipeline used. "
+
+ // Tool references
+ meta["tool_citations"] = ""
+ meta["tool_bibliography"] = ""
+
+ // TODO nf-core: Only uncomment below if logic in toolCitationText/toolBibliographyText has been filled!
+ // meta["tool_citations"] = toolCitationText().replaceAll(", \\.", ".").replaceAll("\\. \\.", ".").replaceAll(", \\.", ".")
+ // meta["tool_bibliography"] = toolBibliographyText()
+ def methods_text = mqc_methods_yaml.text
+
+ def engine = new groovy.text.SimpleTemplateEngine()
+ def description_html = engine.createTemplate(methods_text).make(meta)
+
+ return description_html.toString()
+}
diff --git a/subworkflows/nf-core/utils_nextflow_pipeline/main.nf b/subworkflows/nf-core/utils_nextflow_pipeline/main.nf
new file mode 100644
index 00000000..ac31f28f
--- /dev/null
+++ b/subworkflows/nf-core/utils_nextflow_pipeline/main.nf
@@ -0,0 +1,126 @@
+//
+// Subworkflow with functionality that may be useful for any Nextflow pipeline
+//
+
+import org.yaml.snakeyaml.Yaml
+import groovy.json.JsonOutput
+import nextflow.extension.FilesEx
+
+/*
+========================================================================================
+ SUBWORKFLOW DEFINITION
+========================================================================================
+*/
+
+workflow UTILS_NEXTFLOW_PIPELINE {
+
+ take:
+ print_version // boolean: print version
+ dump_parameters // boolean: dump parameters
+ outdir // path: base directory used to publish pipeline results
+ check_conda_channels // boolean: check conda channels
+
+ main:
+
+ //
+ // Print workflow version and exit on --version
+ //
+ if (print_version) {
+ log.info "${workflow.manifest.name} ${getWorkflowVersion()}"
+ System.exit(0)
+ }
+
+ //
+ // Dump pipeline parameters to a JSON file
+ //
+ if (dump_parameters && outdir) {
+ dumpParametersToJSON(outdir)
+ }
+
+ //
+ // When running with Conda, warn if channels have not been set-up appropriately
+ //
+ if (check_conda_channels) {
+ checkCondaChannels()
+ }
+
+ emit:
+ dummy_emit = true
+}
+
+/*
+========================================================================================
+ FUNCTIONS
+========================================================================================
+*/
+
+//
+// Generate version string
+//
+def getWorkflowVersion() {
+ String version_string = ""
+ if (workflow.manifest.version) {
+ def prefix_v = workflow.manifest.version[0] != 'v' ? 'v' : ''
+ version_string += "${prefix_v}${workflow.manifest.version}"
+ }
+
+ if (workflow.commitId) {
+ def git_shortsha = workflow.commitId.substring(0, 7)
+ version_string += "-g${git_shortsha}"
+ }
+
+ return version_string
+}
+
+//
+// Dump pipeline parameters to a JSON file
+//
+def dumpParametersToJSON(outdir) {
+ def timestamp = new java.util.Date().format( 'yyyy-MM-dd_HH-mm-ss')
+ def filename = "params_${timestamp}.json"
+ def temp_pf = new File(workflow.launchDir.toString(), ".${filename}")
+ def jsonStr = JsonOutput.toJson(params)
+ temp_pf.text = JsonOutput.prettyPrint(jsonStr)
+
+ FilesEx.copyTo(temp_pf.toPath(), "${outdir}/pipeline_info/params_${timestamp}.json")
+ temp_pf.delete()
+}
+
+//
+// When running with -profile conda, warn if channels have not been set-up appropriately
+//
+def checkCondaChannels() {
+ Yaml parser = new Yaml()
+ def channels = []
+ try {
+ def config = parser.load("conda config --show channels".execute().text)
+ channels = config.channels
+ } catch(NullPointerException | IOException e) {
+ log.warn "Could not verify conda channel configuration."
+ return
+ }
+
+ // Check that all channels are present
+ // This channel list is ordered by required channel priority.
+ def required_channels_in_order = ['conda-forge', 'bioconda', 'defaults']
+ def channels_missing = ((required_channels_in_order as Set) - (channels as Set)) as Boolean
+
+ // Check that they are in the right order
+ def channel_priority_violation = false
+ def n = required_channels_in_order.size()
+ for (int i = 0; i < n - 1; i++) {
+ channel_priority_violation |= !(channels.indexOf(required_channels_in_order[i]) < channels.indexOf(required_channels_in_order[i+1]))
+ }
+
+ if (channels_missing | channel_priority_violation) {
+ log.warn "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n" +
+ " There is a problem with your Conda configuration!\n\n" +
+ " You will need to set-up the conda-forge and bioconda channels correctly.\n" +
+ " Please refer to https://bioconda.github.io/\n" +
+ " The observed channel order is \n" +
+ " ${channels}\n" +
+ " but the following channel order is required:\n" +
+ " ${required_channels_in_order}\n" +
+ "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~"
+ }
+}
diff --git a/subworkflows/nf-core/utils_nextflow_pipeline/meta.yml b/subworkflows/nf-core/utils_nextflow_pipeline/meta.yml
new file mode 100644
index 00000000..e5c3a0a8
--- /dev/null
+++ b/subworkflows/nf-core/utils_nextflow_pipeline/meta.yml
@@ -0,0 +1,38 @@
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/subworkflows/yaml-schema.json
+name: "UTILS_NEXTFLOW_PIPELINE"
+description: Subworkflow with functionality that may be useful for any Nextflow pipeline
+keywords:
+ - utility
+ - pipeline
+ - initialise
+ - version
+components: []
+input:
+ - print_version:
+ type: boolean
+ description: |
+ Print the version of the pipeline and exit
+ - dump_parameters:
+ type: boolean
+ description: |
+ Dump the parameters of the pipeline to a JSON file
+ - output_directory:
+ type: directory
+ description: Path to output dir to write JSON file to.
+ pattern: "results/"
+ - check_conda_channel:
+ type: boolean
+ description: |
+ Check if the conda channel priority is correct.
+output:
+ - dummy_emit:
+ type: boolean
+ description: |
+ Dummy emit to make nf-core subworkflows lint happy
+authors:
+ - "@adamrtalbot"
+ - "@drpatelh"
+maintainers:
+ - "@adamrtalbot"
+ - "@drpatelh"
+ - "@maxulysse"
diff --git a/subworkflows/nf-core/utils_nextflow_pipeline/tests/main.function.nf.test b/subworkflows/nf-core/utils_nextflow_pipeline/tests/main.function.nf.test
new file mode 100644
index 00000000..68718e4f
--- /dev/null
+++ b/subworkflows/nf-core/utils_nextflow_pipeline/tests/main.function.nf.test
@@ -0,0 +1,54 @@
+
+nextflow_function {
+
+ name "Test Functions"
+ script "subworkflows/nf-core/utils_nextflow_pipeline/main.nf"
+ config "subworkflows/nf-core/utils_nextflow_pipeline/tests/nextflow.config"
+ tag 'subworkflows'
+ tag 'utils_nextflow_pipeline'
+ tag 'subworkflows/utils_nextflow_pipeline'
+
+ test("Test Function getWorkflowVersion") {
+
+ function "getWorkflowVersion"
+
+ then {
+ assertAll(
+ { assert function.success },
+ { assert snapshot(function.result).match() }
+ )
+ }
+ }
+
+ test("Test Function dumpParametersToJSON") {
+
+ function "dumpParametersToJSON"
+
+ when {
+ function {
+ """
+ // define inputs of the function here. Example:
+ input[0] = "$outputDir"
+ """.stripIndent()
+ }
+ }
+
+ then {
+ assertAll(
+ { assert function.success }
+ )
+ }
+ }
+
+ test("Test Function checkCondaChannels") {
+
+ function "checkCondaChannels"
+
+ then {
+ assertAll(
+ { assert function.success },
+ { assert snapshot(function.result).match() }
+ )
+ }
+ }
+}
diff --git a/subworkflows/nf-core/utils_nextflow_pipeline/tests/main.function.nf.test.snap b/subworkflows/nf-core/utils_nextflow_pipeline/tests/main.function.nf.test.snap
new file mode 100644
index 00000000..db2030f8
--- /dev/null
+++ b/subworkflows/nf-core/utils_nextflow_pipeline/tests/main.function.nf.test.snap
@@ -0,0 +1,12 @@
+{
+ "Test Function getWorkflowVersion": {
+ "content": [
+ "v9.9.9"
+ ],
+ "timestamp": "2024-01-19T11:32:36.031083"
+ },
+ "Test Function checkCondaChannels": {
+ "content": null,
+ "timestamp": "2024-01-19T11:32:50.456"
+ }
+}
\ No newline at end of file
diff --git a/subworkflows/nf-core/utils_nextflow_pipeline/tests/main.workflow.nf.test b/subworkflows/nf-core/utils_nextflow_pipeline/tests/main.workflow.nf.test
new file mode 100644
index 00000000..f7c54bc6
--- /dev/null
+++ b/subworkflows/nf-core/utils_nextflow_pipeline/tests/main.workflow.nf.test
@@ -0,0 +1,123 @@
+nextflow_workflow {
+
+ name "Test Workflow UTILS_NEXTFLOW_PIPELINE"
+ script "../main.nf"
+ config "subworkflows/nf-core/utils_nextflow_pipeline/tests/nextflow.config"
+ workflow "UTILS_NEXTFLOW_PIPELINE"
+ tag 'subworkflows'
+ tag 'utils_nextflow_pipeline'
+ tag 'subworkflows/utils_nextflow_pipeline'
+
+ test("Should run no inputs") {
+
+ when {
+ params {
+ outdir = "tests/results"
+ }
+ workflow {
+ """
+ print_version = false
+ dump_parameters = false
+ outdir = null
+ check_conda_channels = false
+
+ input[0] = print_version
+ input[1] = dump_parameters
+ input[2] = outdir
+ input[3] = check_conda_channels
+ """
+ }
+ }
+
+ then {
+ assertAll(
+ { assert workflow.success }
+ )
+ }
+ }
+
+ test("Should print version") {
+
+ when {
+ params {
+ outdir = "tests/results"
+ }
+ workflow {
+ """
+ print_version = true
+ dump_parameters = false
+ outdir = null
+ check_conda_channels = false
+
+ input[0] = print_version
+ input[1] = dump_parameters
+ input[2] = outdir
+ input[3] = check_conda_channels
+ """
+ }
+ }
+
+ then {
+ assertAll(
+ { assert workflow.success },
+ { assert workflow.stdout.contains("nextflow_workflow v9.9.9") }
+ )
+ }
+ }
+
+ test("Should dump params") {
+
+ when {
+ params {
+ outdir = "$outputDir"
+ }
+ workflow {
+ """
+ print_version = false
+ dump_parameters = true
+ outdir = params.outdir
+ check_conda_channels = false
+
+ input[0] = false
+ input[1] = true
+ input[2] = params.outdir
+ input[3] = false
+ """
+ }
+ }
+
+ then {
+ assertAll(
+ { assert workflow.success }
+ )
+ }
+ }
+
+ test("Should not create params JSON if no output directory") {
+
+ when {
+ params {
+ outdir = "$outputDir"
+ }
+ workflow {
+ """
+ print_version = false
+ dump_parameters = true
+ outdir = params.outdir
+ check_conda_channels = false
+
+ input[0] = false
+ input[1] = true
+ input[2] = null
+ input[3] = false
+ """
+ }
+ }
+
+ then {
+ assertAll(
+ { assert workflow.success }
+ )
+ }
+ }
+}
diff --git a/subworkflows/nf-core/utils_nextflow_pipeline/tests/nextflow.config b/subworkflows/nf-core/utils_nextflow_pipeline/tests/nextflow.config
new file mode 100644
index 00000000..d0a926bf
--- /dev/null
+++ b/subworkflows/nf-core/utils_nextflow_pipeline/tests/nextflow.config
@@ -0,0 +1,9 @@
+manifest {
+ name = 'nextflow_workflow'
+ author = """nf-core"""
+ homePage = 'https://127.0.0.1'
+ description = """Dummy pipeline"""
+ nextflowVersion = '!>=23.04.0'
+ version = '9.9.9'
+ doi = 'https://doi.org/10.5281/zenodo.5070524'
+}
diff --git a/subworkflows/nf-core/utils_nextflow_pipeline/tests/tags.yml b/subworkflows/nf-core/utils_nextflow_pipeline/tests/tags.yml
new file mode 100644
index 00000000..f8476112
--- /dev/null
+++ b/subworkflows/nf-core/utils_nextflow_pipeline/tests/tags.yml
@@ -0,0 +1,2 @@
+subworkflows/utils_nextflow_pipeline:
+ - subworkflows/nf-core/utils_nextflow_pipeline/**
diff --git a/subworkflows/nf-core/utils_nfcore_pipeline/main.nf b/subworkflows/nf-core/utils_nfcore_pipeline/main.nf
new file mode 100644
index 00000000..a8b55d6f
--- /dev/null
+++ b/subworkflows/nf-core/utils_nfcore_pipeline/main.nf
@@ -0,0 +1,440 @@
+//
+// Subworkflow with utility functions specific to the nf-core pipeline template
+//
+
+import org.yaml.snakeyaml.Yaml
+import nextflow.extension.FilesEx
+
+/*
+========================================================================================
+ SUBWORKFLOW DEFINITION
+========================================================================================
+*/
+
+workflow UTILS_NFCORE_PIPELINE {
+
+ take:
+ nextflow_cli_args
+
+ main:
+ valid_config = checkConfigProvided()
+ checkProfileProvided(nextflow_cli_args)
+
+ emit:
+ valid_config
+}
+
+/*
+========================================================================================
+ FUNCTIONS
+========================================================================================
+*/
+
+//
+// Warn if a -profile or Nextflow config has not been provided to run the pipeline
+//
+def checkConfigProvided() {
+ valid_config = true
+ if (workflow.profile == 'standard' && workflow.configFiles.size() <= 1) {
+ log.warn "[$workflow.manifest.name] You are attempting to run the pipeline without any custom configuration!\n\n" +
+ "This will be dependent on your local compute environment but can be achieved via one or more of the following:\n" +
+ " (1) Using an existing pipeline profile e.g. `-profile docker` or `-profile singularity`\n" +
+ " (2) Using an existing nf-core/configs for your Institution e.g. `-profile crick` or `-profile uppmax`\n" +
+ " (3) Using your own local custom config e.g. `-c /path/to/your/custom.config`\n\n" +
+ "Please refer to the quick start section and usage docs for the pipeline.\n "
+ valid_config = false
+ }
+ return valid_config
+}
+
+//
+// Exit pipeline if --profile contains spaces
+//
+def checkProfileProvided(nextflow_cli_args) {
+ if (workflow.profile.endsWith(',')) {
+ error "The `-profile` option cannot end with a trailing comma, please remove it and re-run the pipeline!\n" +
+ "HINT: A common mistake is to provide multiple values separated by spaces e.g. `-profile test, docker`.\n"
+ }
+ if (nextflow_cli_args[0]) {
+ log.warn "nf-core pipelines do not accept positional arguments. The positional argument `${nextflow_cli_args[0]}` has been detected.\n" +
+ "HINT: A common mistake is to provide multiple values separated by spaces e.g. `-profile test, docker`.\n"
+ }
+}
+
+//
+// Citation string for pipeline
+//
+def workflowCitation() {
+ return "If you use ${workflow.manifest.name} for your analysis please cite:\n\n" +
+ "* The pipeline\n" +
+ " ${workflow.manifest.doi}\n\n" +
+ "* The nf-core framework\n" +
+ " https://doi.org/10.1038/s41587-020-0439-x\n\n" +
+ "* Software dependencies\n" +
+ " https://github.com/${workflow.manifest.name}/blob/master/CITATIONS.md"
+}
+
+//
+// Generate workflow version string
+//
+def getWorkflowVersion() {
+ String version_string = ""
+ if (workflow.manifest.version) {
+ def prefix_v = workflow.manifest.version[0] != 'v' ? 'v' : ''
+ version_string += "${prefix_v}${workflow.manifest.version}"
+ }
+
+ if (workflow.commitId) {
+ def git_shortsha = workflow.commitId.substring(0, 7)
+ version_string += "-g${git_shortsha}"
+ }
+
+ return version_string
+}
+
+//
+// Get software versions for pipeline
+//
+def processVersionsFromYAML(yaml_file) {
+ Yaml yaml = new Yaml()
+ versions = yaml.load(yaml_file).collectEntries { k, v -> [ k.tokenize(':')[-1], v ] }
+ return yaml.dumpAsMap(versions).trim()
+}
+
+//
+// Get workflow version for pipeline
+//
+def workflowVersionToYAML() {
+ return """
+ Workflow:
+ $workflow.manifest.name: ${getWorkflowVersion()}
+ Nextflow: $workflow.nextflow.version
+ """.stripIndent().trim()
+}
+
+//
+// Get channel of software versions used in pipeline in YAML format
+//
+def softwareVersionsToYAML(ch_versions) {
+ return ch_versions
+ .unique()
+ .map { processVersionsFromYAML(it) }
+ .unique()
+ .mix(Channel.of(workflowVersionToYAML()))
+}
+
+//
+// Get workflow summary for MultiQC
+//
+def paramsSummaryMultiqc(summary_params) {
+ def summary_section = ''
+ for (group in summary_params.keySet()) {
+ def group_params = summary_params.get(group) // This gets the parameters of that particular group
+ if (group_params) {
+ summary_section += " $group
\n"
+ summary_section += " \n"
+ for (param in group_params.keySet()) {
+ summary_section += " - $param
- ${group_params.get(param) ?: 'N/A'}
\n"
+ }
+ summary_section += "
\n"
+ }
+ }
+
+ String yaml_file_text = "id: '${workflow.manifest.name.replace('/','-')}-summary'\n"
+ yaml_file_text += "description: ' - this information is collected when the pipeline is started.'\n"
+ yaml_file_text += "section_name: '${workflow.manifest.name} Workflow Summary'\n"
+ yaml_file_text += "section_href: 'https://github.com/${workflow.manifest.name}'\n"
+ yaml_file_text += "plot_type: 'html'\n"
+ yaml_file_text += "data: |\n"
+ yaml_file_text += "${summary_section}"
+
+ return yaml_file_text
+}
+
+//
+// nf-core logo
+//
+def nfCoreLogo(monochrome_logs=true) {
+ Map colors = logColours(monochrome_logs)
+ String.format(
+ """\n
+ ${dashedLine(monochrome_logs)}
+ ${colors.green},--.${colors.black}/${colors.green},-.${colors.reset}
+ ${colors.blue} ___ __ __ __ ___ ${colors.green}/,-._.--~\'${colors.reset}
+ ${colors.blue} |\\ | |__ __ / ` / \\ |__) |__ ${colors.yellow}} {${colors.reset}
+ ${colors.blue} | \\| | \\__, \\__/ | \\ |___ ${colors.green}\\`-._,-`-,${colors.reset}
+ ${colors.green}`._,._,\'${colors.reset}
+ ${colors.purple} ${workflow.manifest.name} ${getWorkflowVersion()}${colors.reset}
+ ${dashedLine(monochrome_logs)}
+ """.stripIndent()
+ )
+}
+
+//
+// Return dashed line
+//
+def dashedLine(monochrome_logs=true) {
+ Map colors = logColours(monochrome_logs)
+ return "-${colors.dim}----------------------------------------------------${colors.reset}-"
+}
+
+//
+// ANSII colours used for terminal logging
+//
+def logColours(monochrome_logs=true) {
+ Map colorcodes = [:]
+
+ // Reset / Meta
+ colorcodes['reset'] = monochrome_logs ? '' : "\033[0m"
+ colorcodes['bold'] = monochrome_logs ? '' : "\033[1m"
+ colorcodes['dim'] = monochrome_logs ? '' : "\033[2m"
+ colorcodes['underlined'] = monochrome_logs ? '' : "\033[4m"
+ colorcodes['blink'] = monochrome_logs ? '' : "\033[5m"
+ colorcodes['reverse'] = monochrome_logs ? '' : "\033[7m"
+ colorcodes['hidden'] = monochrome_logs ? '' : "\033[8m"
+
+ // Regular Colors
+ colorcodes['black'] = monochrome_logs ? '' : "\033[0;30m"
+ colorcodes['red'] = monochrome_logs ? '' : "\033[0;31m"
+ colorcodes['green'] = monochrome_logs ? '' : "\033[0;32m"
+ colorcodes['yellow'] = monochrome_logs ? '' : "\033[0;33m"
+ colorcodes['blue'] = monochrome_logs ? '' : "\033[0;34m"
+ colorcodes['purple'] = monochrome_logs ? '' : "\033[0;35m"
+ colorcodes['cyan'] = monochrome_logs ? '' : "\033[0;36m"
+ colorcodes['white'] = monochrome_logs ? '' : "\033[0;37m"
+
+ // Bold
+ colorcodes['bblack'] = monochrome_logs ? '' : "\033[1;30m"
+ colorcodes['bred'] = monochrome_logs ? '' : "\033[1;31m"
+ colorcodes['bgreen'] = monochrome_logs ? '' : "\033[1;32m"
+ colorcodes['byellow'] = monochrome_logs ? '' : "\033[1;33m"
+ colorcodes['bblue'] = monochrome_logs ? '' : "\033[1;34m"
+ colorcodes['bpurple'] = monochrome_logs ? '' : "\033[1;35m"
+ colorcodes['bcyan'] = monochrome_logs ? '' : "\033[1;36m"
+ colorcodes['bwhite'] = monochrome_logs ? '' : "\033[1;37m"
+
+ // Underline
+ colorcodes['ublack'] = monochrome_logs ? '' : "\033[4;30m"
+ colorcodes['ured'] = monochrome_logs ? '' : "\033[4;31m"
+ colorcodes['ugreen'] = monochrome_logs ? '' : "\033[4;32m"
+ colorcodes['uyellow'] = monochrome_logs ? '' : "\033[4;33m"
+ colorcodes['ublue'] = monochrome_logs ? '' : "\033[4;34m"
+ colorcodes['upurple'] = monochrome_logs ? '' : "\033[4;35m"
+ colorcodes['ucyan'] = monochrome_logs ? '' : "\033[4;36m"
+ colorcodes['uwhite'] = monochrome_logs ? '' : "\033[4;37m"
+
+ // High Intensity
+ colorcodes['iblack'] = monochrome_logs ? '' : "\033[0;90m"
+ colorcodes['ired'] = monochrome_logs ? '' : "\033[0;91m"
+ colorcodes['igreen'] = monochrome_logs ? '' : "\033[0;92m"
+ colorcodes['iyellow'] = monochrome_logs ? '' : "\033[0;93m"
+ colorcodes['iblue'] = monochrome_logs ? '' : "\033[0;94m"
+ colorcodes['ipurple'] = monochrome_logs ? '' : "\033[0;95m"
+ colorcodes['icyan'] = monochrome_logs ? '' : "\033[0;96m"
+ colorcodes['iwhite'] = monochrome_logs ? '' : "\033[0;97m"
+
+ // Bold High Intensity
+ colorcodes['biblack'] = monochrome_logs ? '' : "\033[1;90m"
+ colorcodes['bired'] = monochrome_logs ? '' : "\033[1;91m"
+ colorcodes['bigreen'] = monochrome_logs ? '' : "\033[1;92m"
+ colorcodes['biyellow'] = monochrome_logs ? '' : "\033[1;93m"
+ colorcodes['biblue'] = monochrome_logs ? '' : "\033[1;94m"
+ colorcodes['bipurple'] = monochrome_logs ? '' : "\033[1;95m"
+ colorcodes['bicyan'] = monochrome_logs ? '' : "\033[1;96m"
+ colorcodes['biwhite'] = monochrome_logs ? '' : "\033[1;97m"
+
+ return colorcodes
+}
+
+//
+// Attach the multiqc report to email
+//
+def attachMultiqcReport(multiqc_report) {
+ def mqc_report = null
+ try {
+ if (workflow.success) {
+ mqc_report = multiqc_report.getVal()
+ if (mqc_report.getClass() == ArrayList && mqc_report.size() >= 1) {
+ if (mqc_report.size() > 1) {
+ log.warn "[$workflow.manifest.name] Found multiple reports from process 'MULTIQC', will use only one"
+ }
+ mqc_report = mqc_report[0]
+ }
+ }
+ } catch (all) {
+ if (multiqc_report) {
+ log.warn "[$workflow.manifest.name] Could not attach MultiQC report to summary email"
+ }
+ }
+ return mqc_report
+}
+
+//
+// Construct and send completion email
+//
+def completionEmail(summary_params, email, email_on_fail, plaintext_email, outdir, monochrome_logs=true, multiqc_report=null) {
+
+ // Set up the e-mail variables
+ def subject = "[$workflow.manifest.name] Successful: $workflow.runName"
+ if (!workflow.success) {
+ subject = "[$workflow.manifest.name] FAILED: $workflow.runName"
+ }
+
+ def summary = [:]
+ for (group in summary_params.keySet()) {
+ summary << summary_params[group]
+ }
+
+ def misc_fields = [:]
+ misc_fields['Date Started'] = workflow.start
+ misc_fields['Date Completed'] = workflow.complete
+ misc_fields['Pipeline script file path'] = workflow.scriptFile
+ misc_fields['Pipeline script hash ID'] = workflow.scriptId
+ if (workflow.repository) misc_fields['Pipeline repository Git URL'] = workflow.repository
+ if (workflow.commitId) misc_fields['Pipeline repository Git Commit'] = workflow.commitId
+ if (workflow.revision) misc_fields['Pipeline Git branch/tag'] = workflow.revision
+ misc_fields['Nextflow Version'] = workflow.nextflow.version
+ misc_fields['Nextflow Build'] = workflow.nextflow.build
+ misc_fields['Nextflow Compile Timestamp'] = workflow.nextflow.timestamp
+
+ def email_fields = [:]
+ email_fields['version'] = getWorkflowVersion()
+ email_fields['runName'] = workflow.runName
+ email_fields['success'] = workflow.success
+ email_fields['dateComplete'] = workflow.complete
+ email_fields['duration'] = workflow.duration
+ email_fields['exitStatus'] = workflow.exitStatus
+ email_fields['errorMessage'] = (workflow.errorMessage ?: 'None')
+ email_fields['errorReport'] = (workflow.errorReport ?: 'None')
+ email_fields['commandLine'] = workflow.commandLine
+ email_fields['projectDir'] = workflow.projectDir
+ email_fields['summary'] = summary << misc_fields
+
+ // On success try attach the multiqc report
+ def mqc_report = attachMultiqcReport(multiqc_report)
+
+ // Check if we are only sending emails on failure
+ def email_address = email
+ if (!email && email_on_fail && !workflow.success) {
+ email_address = email_on_fail
+ }
+
+ // Render the TXT template
+ def engine = new groovy.text.GStringTemplateEngine()
+ def tf = new File("${workflow.projectDir}/assets/email_template.txt")
+ def txt_template = engine.createTemplate(tf).make(email_fields)
+ def email_txt = txt_template.toString()
+
+ // Render the HTML template
+ def hf = new File("${workflow.projectDir}/assets/email_template.html")
+ def html_template = engine.createTemplate(hf).make(email_fields)
+ def email_html = html_template.toString()
+
+ // Render the sendmail template
+ def max_multiqc_email_size = (params.containsKey('max_multiqc_email_size') ? params.max_multiqc_email_size : 0) as nextflow.util.MemoryUnit
+ def smail_fields = [ email: email_address, subject: subject, email_txt: email_txt, email_html: email_html, projectDir: "${workflow.projectDir}", mqcFile: mqc_report, mqcMaxSize: max_multiqc_email_size.toBytes() ]
+ def sf = new File("${workflow.projectDir}/assets/sendmail_template.txt")
+ def sendmail_template = engine.createTemplate(sf).make(smail_fields)
+ def sendmail_html = sendmail_template.toString()
+
+ // Send the HTML e-mail
+ Map colors = logColours(monochrome_logs)
+ if (email_address) {
+ try {
+ if (plaintext_email) { throw GroovyException('Send plaintext e-mail, not HTML') }
+ // Try to send HTML e-mail using sendmail
+ def sendmail_tf = new File(workflow.launchDir.toString(), ".sendmail_tmp.html")
+ sendmail_tf.withWriter { w -> w << sendmail_html }
+ [ 'sendmail', '-t' ].execute() << sendmail_html
+ log.info "-${colors.purple}[$workflow.manifest.name]${colors.green} Sent summary e-mail to $email_address (sendmail)-"
+ } catch (all) {
+ // Catch failures and try with plaintext
+ def mail_cmd = [ 'mail', '-s', subject, '--content-type=text/html', email_address ]
+ mail_cmd.execute() << email_html
+ log.info "-${colors.purple}[$workflow.manifest.name]${colors.green} Sent summary e-mail to $email_address (mail)-"
+ }
+ }
+
+ // Write summary e-mail HTML to a file
+ def output_hf = new File(workflow.launchDir.toString(), ".pipeline_report.html")
+ output_hf.withWriter { w -> w << email_html }
+ FilesEx.copyTo(output_hf.toPath(), "${outdir}/pipeline_info/pipeline_report.html");
+ output_hf.delete()
+
+ // Write summary e-mail TXT to a file
+ def output_tf = new File(workflow.launchDir.toString(), ".pipeline_report.txt")
+ output_tf.withWriter { w -> w << email_txt }
+ FilesEx.copyTo(output_tf.toPath(), "${outdir}/pipeline_info/pipeline_report.txt");
+ output_tf.delete()
+}
+
+//
+// Print pipeline summary on completion
+//
+def completionSummary(monochrome_logs=true) {
+ Map colors = logColours(monochrome_logs)
+ if (workflow.success) {
+ if (workflow.stats.ignoredCount == 0) {
+ log.info "-${colors.purple}[$workflow.manifest.name]${colors.green} Pipeline completed successfully${colors.reset}-"
+ } else {
+ log.info "-${colors.purple}[$workflow.manifest.name]${colors.yellow} Pipeline completed successfully, but with errored process(es) ${colors.reset}-"
+ }
+ } else {
+ log.info "-${colors.purple}[$workflow.manifest.name]${colors.red} Pipeline completed with errors${colors.reset}-"
+ }
+}
+
+//
+// Construct and send a notification to a web server as JSON e.g. Microsoft Teams and Slack
+//
+def imNotification(summary_params, hook_url) {
+ def summary = [:]
+ for (group in summary_params.keySet()) {
+ summary << summary_params[group]
+ }
+
+ def misc_fields = [:]
+ misc_fields['start'] = workflow.start
+ misc_fields['complete'] = workflow.complete
+ misc_fields['scriptfile'] = workflow.scriptFile
+ misc_fields['scriptid'] = workflow.scriptId
+ if (workflow.repository) misc_fields['repository'] = workflow.repository
+ if (workflow.commitId) misc_fields['commitid'] = workflow.commitId
+ if (workflow.revision) misc_fields['revision'] = workflow.revision
+ misc_fields['nxf_version'] = workflow.nextflow.version
+ misc_fields['nxf_build'] = workflow.nextflow.build
+ misc_fields['nxf_timestamp'] = workflow.nextflow.timestamp
+
+ def msg_fields = [:]
+ msg_fields['version'] = getWorkflowVersion()
+ msg_fields['runName'] = workflow.runName
+ msg_fields['success'] = workflow.success
+ msg_fields['dateComplete'] = workflow.complete
+ msg_fields['duration'] = workflow.duration
+ msg_fields['exitStatus'] = workflow.exitStatus
+ msg_fields['errorMessage'] = (workflow.errorMessage ?: 'None')
+ msg_fields['errorReport'] = (workflow.errorReport ?: 'None')
+ msg_fields['commandLine'] = workflow.commandLine.replaceFirst(/ +--hook_url +[^ ]+/, "")
+ msg_fields['projectDir'] = workflow.projectDir
+ msg_fields['summary'] = summary << misc_fields
+
+ // Render the JSON template
+ def engine = new groovy.text.GStringTemplateEngine()
+ // Different JSON depending on the service provider
+ // Defaults to "Adaptive Cards" (https://adaptivecards.io), except Slack which has its own format
+ def json_path = hook_url.contains("hooks.slack.com") ? "slackreport.json" : "adaptivecard.json"
+ def hf = new File("${workflow.projectDir}/assets/${json_path}")
+ def json_template = engine.createTemplate(hf).make(msg_fields)
+ def json_message = json_template.toString()
+
+ // POST
+ def post = new URL(hook_url).openConnection();
+ post.setRequestMethod("POST")
+ post.setDoOutput(true)
+ post.setRequestProperty("Content-Type", "application/json")
+ post.getOutputStream().write(json_message.getBytes("UTF-8"));
+ def postRC = post.getResponseCode();
+ if (! postRC.equals(200)) {
+ log.warn(post.getErrorStream().getText());
+ }
+}
diff --git a/subworkflows/nf-core/utils_nfcore_pipeline/meta.yml b/subworkflows/nf-core/utils_nfcore_pipeline/meta.yml
new file mode 100644
index 00000000..d08d2434
--- /dev/null
+++ b/subworkflows/nf-core/utils_nfcore_pipeline/meta.yml
@@ -0,0 +1,24 @@
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/subworkflows/yaml-schema.json
+name: "UTILS_NFCORE_PIPELINE"
+description: Subworkflow with utility functions specific to the nf-core pipeline template
+keywords:
+ - utility
+ - pipeline
+ - initialise
+ - version
+components: []
+input:
+ - nextflow_cli_args:
+ type: list
+ description: |
+ Nextflow CLI positional arguments
+output:
+ - success:
+ type: boolean
+ description: |
+ Dummy output to indicate success
+authors:
+ - "@adamrtalbot"
+maintainers:
+ - "@adamrtalbot"
+ - "@maxulysse"
diff --git a/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.function.nf.test b/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.function.nf.test
new file mode 100644
index 00000000..1dc317f8
--- /dev/null
+++ b/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.function.nf.test
@@ -0,0 +1,134 @@
+
+nextflow_function {
+
+ name "Test Functions"
+ script "../main.nf"
+ config "subworkflows/nf-core/utils_nfcore_pipeline/tests/nextflow.config"
+ tag "subworkflows"
+ tag "subworkflows_nfcore"
+ tag "utils_nfcore_pipeline"
+ tag "subworkflows/utils_nfcore_pipeline"
+
+ test("Test Function checkConfigProvided") {
+
+ function "checkConfigProvided"
+
+ then {
+ assertAll(
+ { assert function.success },
+ { assert snapshot(function.result).match() }
+ )
+ }
+ }
+
+ test("Test Function checkProfileProvided") {
+
+ function "checkProfileProvided"
+
+ when {
+ function {
+ """
+ input[0] = []
+ """
+ }
+ }
+
+ then {
+ assertAll(
+ { assert function.success },
+ { assert snapshot(function.result).match() }
+ )
+ }
+ }
+
+ test("Test Function workflowCitation") {
+
+ function "workflowCitation"
+
+ then {
+ assertAll(
+ { assert function.success },
+ { assert snapshot(function.result).match() }
+ )
+ }
+ }
+
+ test("Test Function nfCoreLogo") {
+
+ function "nfCoreLogo"
+
+ when {
+ function {
+ """
+ input[0] = false
+ """
+ }
+ }
+
+ then {
+ assertAll(
+ { assert function.success },
+ { assert snapshot(function.result).match() }
+ )
+ }
+ }
+
+ test("Test Function dashedLine") {
+
+ function "dashedLine"
+
+ when {
+ function {
+ """
+ input[0] = false
+ """
+ }
+ }
+
+ then {
+ assertAll(
+ { assert function.success },
+ { assert snapshot(function.result).match() }
+ )
+ }
+ }
+
+ test("Test Function without logColours") {
+
+ function "logColours"
+
+ when {
+ function {
+ """
+ input[0] = true
+ """
+ }
+ }
+
+ then {
+ assertAll(
+ { assert function.success },
+ { assert snapshot(function.result).match() }
+ )
+ }
+ }
+
+ test("Test Function with logColours") {
+ function "logColours"
+
+ when {
+ function {
+ """
+ input[0] = false
+ """
+ }
+ }
+
+ then {
+ assertAll(
+ { assert function.success },
+ { assert snapshot(function.result).match() }
+ )
+ }
+ }
+}
diff --git a/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.function.nf.test.snap b/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.function.nf.test.snap
new file mode 100644
index 00000000..10f948e6
--- /dev/null
+++ b/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.function.nf.test.snap
@@ -0,0 +1,138 @@
+{
+ "Test Function checkProfileProvided": {
+ "content": null,
+ "timestamp": "2024-02-09T15:43:55.145717"
+ },
+ "Test Function checkConfigProvided": {
+ "content": [
+ true
+ ],
+ "timestamp": "2024-01-19T11:34:13.548431224"
+ },
+ "Test Function nfCoreLogo": {
+ "content": [
+ "\n\n-\u001b[2m----------------------------------------------------\u001b[0m-\n \u001b[0;32m,--.\u001b[0;30m/\u001b[0;32m,-.\u001b[0m\n\u001b[0;34m ___ __ __ __ ___ \u001b[0;32m/,-._.--~'\u001b[0m\n\u001b[0;34m |\\ | |__ __ / ` / \\ |__) |__ \u001b[0;33m} {\u001b[0m\n\u001b[0;34m | \\| | \\__, \\__/ | \\ |___ \u001b[0;32m\\`-._,-`-,\u001b[0m\n \u001b[0;32m`._,._,'\u001b[0m\n\u001b[0;35m nextflow_workflow v9.9.9\u001b[0m\n-\u001b[2m----------------------------------------------------\u001b[0m-\n"
+ ],
+ "timestamp": "2024-01-19T11:34:38.840454873"
+ },
+ "Test Function workflowCitation": {
+ "content": [
+ "If you use nextflow_workflow for your analysis please cite:\n\n* The pipeline\n https://doi.org/10.5281/zenodo.5070524\n\n* The nf-core framework\n https://doi.org/10.1038/s41587-020-0439-x\n\n* Software dependencies\n https://github.com/nextflow_workflow/blob/master/CITATIONS.md"
+ ],
+ "timestamp": "2024-01-19T11:34:22.24352016"
+ },
+ "Test Function without logColours": {
+ "content": [
+ {
+ "reset": "",
+ "bold": "",
+ "dim": "",
+ "underlined": "",
+ "blink": "",
+ "reverse": "",
+ "hidden": "",
+ "black": "",
+ "red": "",
+ "green": "",
+ "yellow": "",
+ "blue": "",
+ "purple": "",
+ "cyan": "",
+ "white": "",
+ "bblack": "",
+ "bred": "",
+ "bgreen": "",
+ "byellow": "",
+ "bblue": "",
+ "bpurple": "",
+ "bcyan": "",
+ "bwhite": "",
+ "ublack": "",
+ "ured": "",
+ "ugreen": "",
+ "uyellow": "",
+ "ublue": "",
+ "upurple": "",
+ "ucyan": "",
+ "uwhite": "",
+ "iblack": "",
+ "ired": "",
+ "igreen": "",
+ "iyellow": "",
+ "iblue": "",
+ "ipurple": "",
+ "icyan": "",
+ "iwhite": "",
+ "biblack": "",
+ "bired": "",
+ "bigreen": "",
+ "biyellow": "",
+ "biblue": "",
+ "bipurple": "",
+ "bicyan": "",
+ "biwhite": ""
+ }
+ ],
+ "timestamp": "2024-01-19T11:35:04.418416984"
+ },
+ "Test Function dashedLine": {
+ "content": [
+ "-\u001b[2m----------------------------------------------------\u001b[0m-"
+ ],
+ "timestamp": "2024-01-19T11:34:55.420000755"
+ },
+ "Test Function with logColours": {
+ "content": [
+ {
+ "reset": "\u001b[0m",
+ "bold": "\u001b[1m",
+ "dim": "\u001b[2m",
+ "underlined": "\u001b[4m",
+ "blink": "\u001b[5m",
+ "reverse": "\u001b[7m",
+ "hidden": "\u001b[8m",
+ "black": "\u001b[0;30m",
+ "red": "\u001b[0;31m",
+ "green": "\u001b[0;32m",
+ "yellow": "\u001b[0;33m",
+ "blue": "\u001b[0;34m",
+ "purple": "\u001b[0;35m",
+ "cyan": "\u001b[0;36m",
+ "white": "\u001b[0;37m",
+ "bblack": "\u001b[1;30m",
+ "bred": "\u001b[1;31m",
+ "bgreen": "\u001b[1;32m",
+ "byellow": "\u001b[1;33m",
+ "bblue": "\u001b[1;34m",
+ "bpurple": "\u001b[1;35m",
+ "bcyan": "\u001b[1;36m",
+ "bwhite": "\u001b[1;37m",
+ "ublack": "\u001b[4;30m",
+ "ured": "\u001b[4;31m",
+ "ugreen": "\u001b[4;32m",
+ "uyellow": "\u001b[4;33m",
+ "ublue": "\u001b[4;34m",
+ "upurple": "\u001b[4;35m",
+ "ucyan": "\u001b[4;36m",
+ "uwhite": "\u001b[4;37m",
+ "iblack": "\u001b[0;90m",
+ "ired": "\u001b[0;91m",
+ "igreen": "\u001b[0;92m",
+ "iyellow": "\u001b[0;93m",
+ "iblue": "\u001b[0;94m",
+ "ipurple": "\u001b[0;95m",
+ "icyan": "\u001b[0;96m",
+ "iwhite": "\u001b[0;97m",
+ "biblack": "\u001b[1;90m",
+ "bired": "\u001b[1;91m",
+ "bigreen": "\u001b[1;92m",
+ "biyellow": "\u001b[1;93m",
+ "biblue": "\u001b[1;94m",
+ "bipurple": "\u001b[1;95m",
+ "bicyan": "\u001b[1;96m",
+ "biwhite": "\u001b[1;97m"
+ }
+ ],
+ "timestamp": "2024-01-19T11:35:13.436366565"
+ }
+}
\ No newline at end of file
diff --git a/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.workflow.nf.test b/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.workflow.nf.test
new file mode 100644
index 00000000..8940d32d
--- /dev/null
+++ b/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.workflow.nf.test
@@ -0,0 +1,29 @@
+nextflow_workflow {
+
+ name "Test Workflow UTILS_NFCORE_PIPELINE"
+ script "../main.nf"
+ config "subworkflows/nf-core/utils_nfcore_pipeline/tests/nextflow.config"
+ workflow "UTILS_NFCORE_PIPELINE"
+ tag "subworkflows"
+ tag "subworkflows_nfcore"
+ tag "utils_nfcore_pipeline"
+ tag "subworkflows/utils_nfcore_pipeline"
+
+ test("Should run without failures") {
+
+ when {
+ workflow {
+ """
+ input[0] = []
+ """
+ }
+ }
+
+ then {
+ assertAll(
+ { assert workflow.success },
+ { assert snapshot(workflow.out).match() }
+ )
+ }
+ }
+}
diff --git a/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.workflow.nf.test.snap b/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.workflow.nf.test.snap
new file mode 100644
index 00000000..d07ce54c
--- /dev/null
+++ b/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.workflow.nf.test.snap
@@ -0,0 +1,15 @@
+{
+ "Should run without failures": {
+ "content": [
+ {
+ "0": [
+ true
+ ],
+ "valid_config": [
+ true
+ ]
+ }
+ ],
+ "timestamp": "2024-01-19T11:35:22.538940073"
+ }
+}
\ No newline at end of file
diff --git a/subworkflows/nf-core/utils_nfcore_pipeline/tests/nextflow.config b/subworkflows/nf-core/utils_nfcore_pipeline/tests/nextflow.config
new file mode 100644
index 00000000..d0a926bf
--- /dev/null
+++ b/subworkflows/nf-core/utils_nfcore_pipeline/tests/nextflow.config
@@ -0,0 +1,9 @@
+manifest {
+ name = 'nextflow_workflow'
+ author = """nf-core"""
+ homePage = 'https://127.0.0.1'
+ description = """Dummy pipeline"""
+ nextflowVersion = '!>=23.04.0'
+ version = '9.9.9'
+ doi = 'https://doi.org/10.5281/zenodo.5070524'
+}
diff --git a/subworkflows/nf-core/utils_nfcore_pipeline/tests/tags.yml b/subworkflows/nf-core/utils_nfcore_pipeline/tests/tags.yml
new file mode 100644
index 00000000..ac8523c9
--- /dev/null
+++ b/subworkflows/nf-core/utils_nfcore_pipeline/tests/tags.yml
@@ -0,0 +1,2 @@
+subworkflows/utils_nfcore_pipeline:
+ - subworkflows/nf-core/utils_nfcore_pipeline/**
diff --git a/subworkflows/nf-core/utils_nfvalidation_plugin/main.nf b/subworkflows/nf-core/utils_nfvalidation_plugin/main.nf
new file mode 100644
index 00000000..2585b65d
--- /dev/null
+++ b/subworkflows/nf-core/utils_nfvalidation_plugin/main.nf
@@ -0,0 +1,62 @@
+//
+// Subworkflow that uses the nf-validation plugin to render help text and parameter summary
+//
+
+/*
+========================================================================================
+ IMPORT NF-VALIDATION PLUGIN
+========================================================================================
+*/
+
+include { paramsHelp } from 'plugin/nf-validation'
+include { paramsSummaryLog } from 'plugin/nf-validation'
+include { validateParameters } from 'plugin/nf-validation'
+
+/*
+========================================================================================
+ SUBWORKFLOW DEFINITION
+========================================================================================
+*/
+
+workflow UTILS_NFVALIDATION_PLUGIN {
+
+ take:
+ print_help // boolean: print help
+ workflow_command // string: default commmand used to run pipeline
+ pre_help_text // string: string to be printed before help text and summary log
+ post_help_text // string: string to be printed after help text and summary log
+ validate_params // boolean: validate parameters
+ schema_filename // path: JSON schema file, null to use default value
+
+ main:
+
+ log.debug "Using schema file: ${schema_filename}"
+
+ // Default values for strings
+ pre_help_text = pre_help_text ?: ''
+ post_help_text = post_help_text ?: ''
+ workflow_command = workflow_command ?: ''
+
+ //
+ // Print help message if needed
+ //
+ if (print_help) {
+ log.info pre_help_text + paramsHelp(workflow_command, parameters_schema: schema_filename) + post_help_text
+ System.exit(0)
+ }
+
+ //
+ // Print parameter summary to stdout
+ //
+ log.info pre_help_text + paramsSummaryLog(workflow, parameters_schema: schema_filename) + post_help_text
+
+ //
+ // Validate parameters relative to the parameter JSON schema
+ //
+ if (validate_params){
+ validateParameters(parameters_schema: schema_filename)
+ }
+
+ emit:
+ dummy_emit = true
+}
diff --git a/subworkflows/nf-core/utils_nfvalidation_plugin/meta.yml b/subworkflows/nf-core/utils_nfvalidation_plugin/meta.yml
new file mode 100644
index 00000000..3d4a6b04
--- /dev/null
+++ b/subworkflows/nf-core/utils_nfvalidation_plugin/meta.yml
@@ -0,0 +1,44 @@
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/subworkflows/yaml-schema.json
+name: "UTILS_NFVALIDATION_PLUGIN"
+description: Use nf-validation to initiate and validate a pipeline
+keywords:
+ - utility
+ - pipeline
+ - initialise
+ - validation
+components: []
+input:
+ - print_help:
+ type: boolean
+ description: |
+ Print help message and exit
+ - workflow_command:
+ type: string
+ description: |
+ The command to run the workflow e.g. "nextflow run main.nf"
+ - pre_help_text:
+ type: string
+ description: |
+ Text to print before the help message
+ - post_help_text:
+ type: string
+ description: |
+ Text to print after the help message
+ - validate_params:
+ type: boolean
+ description: |
+ Validate the parameters and error if invalid.
+ - schema_filename:
+ type: string
+ description: |
+ The filename of the schema to validate against.
+output:
+ - dummy_emit:
+ type: boolean
+ description: |
+ Dummy emit to make nf-core subworkflows lint happy
+authors:
+ - "@adamrtalbot"
+maintainers:
+ - "@adamrtalbot"
+ - "@maxulysse"
diff --git a/subworkflows/nf-core/utils_nfvalidation_plugin/tests/main.nf.test b/subworkflows/nf-core/utils_nfvalidation_plugin/tests/main.nf.test
new file mode 100644
index 00000000..5784a33f
--- /dev/null
+++ b/subworkflows/nf-core/utils_nfvalidation_plugin/tests/main.nf.test
@@ -0,0 +1,200 @@
+nextflow_workflow {
+
+ name "Test Workflow UTILS_NFVALIDATION_PLUGIN"
+ script "../main.nf"
+ workflow "UTILS_NFVALIDATION_PLUGIN"
+ tag "subworkflows"
+ tag "subworkflows_nfcore"
+ tag "plugin/nf-validation"
+ tag "'plugin/nf-validation'"
+ tag "utils_nfvalidation_plugin"
+ tag "subworkflows/utils_nfvalidation_plugin"
+
+ test("Should run nothing") {
+
+ when {
+
+ params {
+ monochrome_logs = true
+ test_data = ''
+ }
+
+ workflow {
+ """
+ help = false
+ workflow_command = null
+ pre_help_text = null
+ post_help_text = null
+ validate_params = false
+ schema_filename = "$moduleTestDir/nextflow_schema.json"
+
+ input[0] = help
+ input[1] = workflow_command
+ input[2] = pre_help_text
+ input[3] = post_help_text
+ input[4] = validate_params
+ input[5] = schema_filename
+ """
+ }
+ }
+
+ then {
+ assertAll(
+ { assert workflow.success }
+ )
+ }
+ }
+
+ test("Should run help") {
+
+
+ when {
+
+ params {
+ monochrome_logs = true
+ test_data = ''
+ }
+ workflow {
+ """
+ help = true
+ workflow_command = null
+ pre_help_text = null
+ post_help_text = null
+ validate_params = false
+ schema_filename = "$moduleTestDir/nextflow_schema.json"
+
+ input[0] = help
+ input[1] = workflow_command
+ input[2] = pre_help_text
+ input[3] = post_help_text
+ input[4] = validate_params
+ input[5] = schema_filename
+ """
+ }
+ }
+
+ then {
+ assertAll(
+ { assert workflow.success },
+ { assert workflow.exitStatus == 0 },
+ { assert workflow.stdout.any { it.contains('Input/output options') } },
+ { assert workflow.stdout.any { it.contains('--outdir') } }
+ )
+ }
+ }
+
+ test("Should run help with command") {
+
+ when {
+
+ params {
+ monochrome_logs = true
+ test_data = ''
+ }
+ workflow {
+ """
+ help = true
+ workflow_command = "nextflow run noorg/doesntexist"
+ pre_help_text = null
+ post_help_text = null
+ validate_params = false
+ schema_filename = "$moduleTestDir/nextflow_schema.json"
+
+ input[0] = help
+ input[1] = workflow_command
+ input[2] = pre_help_text
+ input[3] = post_help_text
+ input[4] = validate_params
+ input[5] = schema_filename
+ """
+ }
+ }
+
+ then {
+ assertAll(
+ { assert workflow.success },
+ { assert workflow.exitStatus == 0 },
+ { assert workflow.stdout.any { it.contains('nextflow run noorg/doesntexist') } },
+ { assert workflow.stdout.any { it.contains('Input/output options') } },
+ { assert workflow.stdout.any { it.contains('--outdir') } }
+ )
+ }
+ }
+
+ test("Should run help with extra text") {
+
+
+ when {
+
+ params {
+ monochrome_logs = true
+ test_data = ''
+ }
+ workflow {
+ """
+ help = true
+ workflow_command = "nextflow run noorg/doesntexist"
+ pre_help_text = "pre-help-text"
+ post_help_text = "post-help-text"
+ validate_params = false
+ schema_filename = "$moduleTestDir/nextflow_schema.json"
+
+ input[0] = help
+ input[1] = workflow_command
+ input[2] = pre_help_text
+ input[3] = post_help_text
+ input[4] = validate_params
+ input[5] = schema_filename
+ """
+ }
+ }
+
+ then {
+ assertAll(
+ { assert workflow.success },
+ { assert workflow.exitStatus == 0 },
+ { assert workflow.stdout.any { it.contains('pre-help-text') } },
+ { assert workflow.stdout.any { it.contains('nextflow run noorg/doesntexist') } },
+ { assert workflow.stdout.any { it.contains('Input/output options') } },
+ { assert workflow.stdout.any { it.contains('--outdir') } },
+ { assert workflow.stdout.any { it.contains('post-help-text') } }
+ )
+ }
+ }
+
+ test("Should validate params") {
+
+ when {
+
+ params {
+ monochrome_logs = true
+ test_data = ''
+ outdir = 1
+ }
+ workflow {
+ """
+ help = false
+ workflow_command = null
+ pre_help_text = null
+ post_help_text = null
+ validate_params = true
+ schema_filename = "$moduleTestDir/nextflow_schema.json"
+
+ input[0] = help
+ input[1] = workflow_command
+ input[2] = pre_help_text
+ input[3] = post_help_text
+ input[4] = validate_params
+ input[5] = schema_filename
+ """
+ }
+ }
+
+ then {
+ assertAll(
+ { assert workflow.failed },
+ { assert workflow.stdout.any { it.contains('ERROR ~ ERROR: Validation of pipeline parameters failed!') } }
+ )
+ }
+ }
+}
diff --git a/subworkflows/nf-core/utils_nfvalidation_plugin/tests/nextflow_schema.json b/subworkflows/nf-core/utils_nfvalidation_plugin/tests/nextflow_schema.json
new file mode 100644
index 00000000..7626c1c9
--- /dev/null
+++ b/subworkflows/nf-core/utils_nfvalidation_plugin/tests/nextflow_schema.json
@@ -0,0 +1,96 @@
+{
+ "$schema": "http://json-schema.org/draft-07/schema",
+ "$id": "https://raw.githubusercontent.com/./master/nextflow_schema.json",
+ "title": ". pipeline parameters",
+ "description": "",
+ "type": "object",
+ "definitions": {
+ "input_output_options": {
+ "title": "Input/output options",
+ "type": "object",
+ "fa_icon": "fas fa-terminal",
+ "description": "Define where the pipeline should find input data and save output data.",
+ "required": ["outdir"],
+ "properties": {
+ "validate_params": {
+ "type": "boolean",
+ "description": "Validate parameters?",
+ "default": true,
+ "hidden": true
+ },
+ "outdir": {
+ "type": "string",
+ "format": "directory-path",
+ "description": "The output directory where the results will be saved. You have to use absolute paths to storage on Cloud infrastructure.",
+ "fa_icon": "fas fa-folder-open"
+ },
+ "test_data_base": {
+ "type": "string",
+ "default": "https://raw.githubusercontent.com/nf-core/test-datasets/modules",
+ "description": "Base for test data directory",
+ "hidden": true
+ },
+ "test_data": {
+ "type": "string",
+ "description": "Fake test data param",
+ "hidden": true
+ }
+ }
+ },
+ "generic_options": {
+ "title": "Generic options",
+ "type": "object",
+ "fa_icon": "fas fa-file-import",
+ "description": "Less common options for the pipeline, typically set in a config file.",
+ "help_text": "These options are common to all nf-core pipelines and allow you to customise some of the core preferences for how the pipeline runs.\n\nTypically these options would be set in a Nextflow config file loaded for all pipeline runs, such as `~/.nextflow/config`.",
+ "properties": {
+ "help": {
+ "type": "boolean",
+ "description": "Display help text.",
+ "fa_icon": "fas fa-question-circle",
+ "hidden": true
+ },
+ "version": {
+ "type": "boolean",
+ "description": "Display version and exit.",
+ "fa_icon": "fas fa-question-circle",
+ "hidden": true
+ },
+ "logo": {
+ "type": "boolean",
+ "default": true,
+ "description": "Display nf-core logo in console output.",
+ "fa_icon": "fas fa-image",
+ "hidden": true
+ },
+ "singularity_pull_docker_container": {
+ "type": "boolean",
+ "description": "Pull Singularity container from Docker?",
+ "hidden": true
+ },
+ "publish_dir_mode": {
+ "type": "string",
+ "default": "copy",
+ "description": "Method used to save pipeline results to output directory.",
+ "help_text": "The Nextflow `publishDir` option specifies which intermediate files should be saved to the output directory. This option tells the pipeline what method should be used to move these files. See [Nextflow docs](https://www.nextflow.io/docs/latest/process.html#publishdir) for details.",
+ "fa_icon": "fas fa-copy",
+ "enum": ["symlink", "rellink", "link", "copy", "copyNoFollow", "move"],
+ "hidden": true
+ },
+ "monochrome_logs": {
+ "type": "boolean",
+ "description": "Use monochrome_logs",
+ "hidden": true
+ }
+ }
+ }
+ },
+ "allOf": [
+ {
+ "$ref": "#/definitions/input_output_options"
+ },
+ {
+ "$ref": "#/definitions/generic_options"
+ }
+ ]
+}
diff --git a/subworkflows/nf-core/utils_nfvalidation_plugin/tests/tags.yml b/subworkflows/nf-core/utils_nfvalidation_plugin/tests/tags.yml
new file mode 100644
index 00000000..60b1cfff
--- /dev/null
+++ b/subworkflows/nf-core/utils_nfvalidation_plugin/tests/tags.yml
@@ -0,0 +1,2 @@
+subworkflows/utils_nfvalidation_plugin:
+ - subworkflows/nf-core/utils_nfvalidation_plugin/**
diff --git a/workflows/alphafold2.nf b/workflows/alphafold2.nf
index 45f7405d..43752a8f 100644
--- a/workflows/alphafold2.nf
+++ b/workflows/alphafold2.nf
@@ -1,32 +1,3 @@
-/*
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
- VALIDATE INPUTS
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-*/
-
-include { paramsSummaryLog; paramsSummaryMap; fromSamplesheet } from 'plugin/nf-validation'
-
-def logo = NfcoreTemplate.logo(workflow, params.monochrome_logs)
-def citation = '\n' + WorkflowMain.citation(workflow) + '\n'
-def summary_params = paramsSummaryMap(workflow)
-
-// Print parameter summary log to screen
-log.info logo + paramsSummaryLog(workflow) + citation
-
-// Validate input parameters
-WorkflowAlphafold2.initialise(params, log)
-
-/*
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
- CONFIG FILES
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-*/
-
-ch_multiqc_config = Channel.fromPath("$projectDir/assets/multiqc_config.yml", checkIfExists: true)
-ch_multiqc_custom_config = params.multiqc_config ? Channel.fromPath( params.multiqc_config ) : Channel.empty()
-ch_multiqc_logo = params.multiqc_logo ? Channel.fromPath( params.multiqc_logo ) : Channel.empty()
-ch_multiqc_custom_methods_description = params.multiqc_methods_description ? file(params.multiqc_methods_description) : file("$projectDir/assets/methods_description_template.yml", checkIfExists: true)
-
/*
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
IMPORT LOCAL MODULES/SUBWORKFLOWS
@@ -34,12 +5,7 @@ ch_multiqc_custom_methods_description = params.multiqc_methods_description ? fil
*/
//
-// SUBWORKFLOW: Consisting of a mix of local and nf-core/modules
-//
-include { PREPARE_ALPHAFOLD2_DBS } from '../subworkflows/local/prepare_alphafold2_dbs'
-
-//
-// MODULE: Local to the pipeline
+// MODULE: Loaded from modules/local/
//
include { RUN_ALPHAFOLD2 } from '../modules/local/run_alphafold2'
include { RUN_ALPHAFOLD2_MSA } from '../modules/local/run_alphafold2_msa'
@@ -54,8 +20,16 @@ include { RUN_ALPHAFOLD2_PRED } from '../modules/local/run_alphafold2_pred'
//
// MODULE: Installed directly from nf-core/modules
//
-include { MULTIQC } from '../modules/nf-core/multiqc/main'
-include { CUSTOM_DUMPSOFTWAREVERSIONS } from '../modules/nf-core/custom/dumpsoftwareversions/main'
+include { MULTIQC } from '../modules/nf-core/multiqc/main'
+
+//
+// SUBWORKFLOW: Consisting entirely of nf-core/modules
+//
+include { paramsSummaryMap } from 'plugin/nf-validation'
+include { fromSamplesheet } from 'plugin/nf-validation'
+include { paramsSummaryMultiqc } from '../subworkflows/nf-core/utils_nfcore_pipeline'
+include { softwareVersionsToYAML } from '../subworkflows/nf-core/utils_nfcore_pipeline'
+include { methodsDescriptionText } from '../subworkflows/local/utils_nfcore_proteinfold_pipeline'
/*
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
@@ -63,12 +37,26 @@ include { CUSTOM_DUMPSOFTWAREVERSIONS } from '../modules/nf-core/custom/dumpsoft
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
*/
-// Info required for completion email and summary
-def multiqc_report = []
-
workflow ALPHAFOLD2 {
- ch_versions = Channel.empty()
+ take:
+ ch_versions // channel: [ path(versions.yml) ]
+ full_dbs // boolean: Use full databases (otherwise reduced version)
+ alphafold2_mode // string: Mode to run Alphafold2 in
+ alphafold2_model_preset // string: Specifies the model preset to use for Alphafold2
+ ch_alphafold2_params // channel: path(alphafold2_params)
+ ch_bfd // channel: path(bfd)
+ ch_small_bfd // channel: path(small_bfd)
+ ch_mgnify // channel: path(mgnify)
+ ch_pdb70 // channel: path(pdb70)
+ ch_pdb_mmcif // channel: path(pdb_mmcif)
+ ch_uniref30 // channel: path(uniref30)
+ ch_uniref90 // channel: path(uniref90)
+ ch_pdb_seqres // channel: path(pdb_seqres)
+ ch_uniprot // channel: path(uniprot)
+
+ main:
+ ch_multiqc_files = Channel.empty()
//
// Create input channel from input file provided through params.input
@@ -77,7 +65,7 @@ workflow ALPHAFOLD2 {
.fromSamplesheet("input")
.set { ch_fasta }
- if (params.alphafold2_model_preset != 'multimer') {
+ if (alphafold2_model_preset != 'multimer') {
ch_fasta
.map {
meta, fasta ->
@@ -87,96 +75,92 @@ workflow ALPHAFOLD2 {
.set { ch_fasta }
}
- //
- // SUBWORKFLOW: Download databases and params for Alphafold2
- //
- PREPARE_ALPHAFOLD2_DBS ( )
- ch_versions = ch_versions.mix(PREPARE_ALPHAFOLD2_DBS.out.versions)
-
- if (params.alphafold2_mode == 'standard') {
+ if (alphafold2_mode == 'standard') {
//
// SUBWORKFLOW: Run Alphafold2 standard mode
//
RUN_ALPHAFOLD2 (
ch_fasta,
- params.full_dbs,
- params.alphafold2_model_preset,
- PREPARE_ALPHAFOLD2_DBS.out.params,
- PREPARE_ALPHAFOLD2_DBS.out.bfd.ifEmpty([]),
- PREPARE_ALPHAFOLD2_DBS.out.small_bfd.ifEmpty([]),
- PREPARE_ALPHAFOLD2_DBS.out.mgnify,
- PREPARE_ALPHAFOLD2_DBS.out.pdb70,
- PREPARE_ALPHAFOLD2_DBS.out.pdb_mmcif,
- PREPARE_ALPHAFOLD2_DBS.out.uniref30,
- PREPARE_ALPHAFOLD2_DBS.out.uniref90,
- PREPARE_ALPHAFOLD2_DBS.out.pdb_seqres,
- PREPARE_ALPHAFOLD2_DBS.out.uniprot,
+ full_dbs,
+ alphafold2_model_preset,
+ ch_alphafold2_params,
+ ch_bfd,
+ ch_small_bfd,
+ ch_mgnify,
+ ch_pdb70,
+ ch_pdb_mmcif,
+ ch_uniref30,
+ ch_uniref90,
+ ch_pdb_seqres,
+ ch_uniprot
)
- ch_versions = ch_versions.mix(RUN_ALPHAFOLD2.out.versions)
ch_multiqc_rep = RUN_ALPHAFOLD2.out.multiqc.collect()
- } else if (params.alphafold2_mode == 'split_msa_prediction') {
+ ch_versions = ch_versions.mix(RUN_ALPHAFOLD2.out.versions)
+
+ } else if (alphafold2_mode == 'split_msa_prediction') {
//
// SUBWORKFLOW: Run Alphafold2 split mode, MSA and predicition
//
RUN_ALPHAFOLD2_MSA (
ch_fasta,
- params.full_dbs,
- params.alphafold2_model_preset,
- PREPARE_ALPHAFOLD2_DBS.out.params,
- PREPARE_ALPHAFOLD2_DBS.out.bfd.ifEmpty([]),
- PREPARE_ALPHAFOLD2_DBS.out.small_bfd.ifEmpty([]),
- PREPARE_ALPHAFOLD2_DBS.out.mgnify,
- PREPARE_ALPHAFOLD2_DBS.out.pdb70,
- PREPARE_ALPHAFOLD2_DBS.out.pdb_mmcif,
- PREPARE_ALPHAFOLD2_DBS.out.uniref30,
- PREPARE_ALPHAFOLD2_DBS.out.uniref90,
- PREPARE_ALPHAFOLD2_DBS.out.pdb_seqres,
- PREPARE_ALPHAFOLD2_DBS.out.uniprot
-
+ full_dbs,
+ alphafold2_model_preset,
+ ch_alphafold2_params,
+ ch_bfd,
+ ch_small_bfd,
+ ch_mgnify,
+ ch_pdb70,
+ ch_pdb_mmcif,
+ ch_uniref30,
+ ch_uniref90,
+ ch_pdb_seqres,
+ ch_uniprot
)
- ch_versions = ch_versions.mix(RUN_ALPHAFOLD2_MSA.out.versions)
+ ch_versions = ch_versions.mix(RUN_ALPHAFOLD2_MSA.out.versions)
RUN_ALPHAFOLD2_PRED (
ch_fasta,
- params.full_dbs,
- params.alphafold2_model_preset,
- PREPARE_ALPHAFOLD2_DBS.out.params,
- PREPARE_ALPHAFOLD2_DBS.out.bfd.ifEmpty([]),
- PREPARE_ALPHAFOLD2_DBS.out.small_bfd.ifEmpty([]),
- PREPARE_ALPHAFOLD2_DBS.out.mgnify,
- PREPARE_ALPHAFOLD2_DBS.out.pdb70,
- PREPARE_ALPHAFOLD2_DBS.out.pdb_mmcif,
- PREPARE_ALPHAFOLD2_DBS.out.uniref30,
- PREPARE_ALPHAFOLD2_DBS.out.uniref90,
- PREPARE_ALPHAFOLD2_DBS.out.pdb_seqres,
- PREPARE_ALPHAFOLD2_DBS.out.uniprot,
+ full_dbs,
+ alphafold2_model_preset,
+ ch_alphafold2_params,
+ ch_bfd,
+ ch_small_bfd,
+ ch_mgnify,
+ ch_pdb70,
+ ch_pdb_mmcif,
+ ch_uniref30,
+ ch_uniref90,
+ ch_pdb_seqres,
+ ch_uniprot,
RUN_ALPHAFOLD2_MSA.out.features
-
)
- ch_versions = ch_versions.mix(RUN_ALPHAFOLD2_PRED.out.versions)
ch_multiqc_rep = RUN_ALPHAFOLD2_PRED.out.multiqc.collect()
+ ch_versions = ch_versions.mix(RUN_ALPHAFOLD2_PRED.out.versions)
}
//
- // MODULE: Pipeline reporting
+ // Collate and save software versions
//
- CUSTOM_DUMPSOFTWAREVERSIONS (
- ch_versions.unique().collectFile(name: 'collated_versions.yml')
- )
+ softwareVersionsToYAML(ch_versions)
+ .collectFile(storeDir: "${params.outdir}/pipeline_info", name: 'nf_core_proteinfold_software_mqc_versions.yml', sort: true, newLine: true)
+ .set { ch_collated_versions }
//
// MODULE: MultiQC
//
- workflow_summary = WorkflowAlphafold2.paramsSummaryMultiqc(workflow, summary_params)
- ch_workflow_summary = Channel.value(workflow_summary)
-
- methods_description = WorkflowAlphafold2.methodsDescriptionText(workflow, ch_multiqc_custom_methods_description, params)
- ch_methods_description = Channel.value(methods_description)
+ ch_multiqc_report = Channel.empty()
+ ch_multiqc_config = Channel.fromPath("$projectDir/assets/multiqc_config.yml", checkIfExists: true)
+ ch_multiqc_custom_config = params.multiqc_config ? Channel.fromPath( params.multiqc_config ) : Channel.empty()
+ ch_multiqc_logo = params.multiqc_logo ? Channel.fromPath( params.multiqc_logo ) : Channel.empty()
+ summary_params = paramsSummaryMap(workflow, parameters_schema: "nextflow_schema.json")
+ ch_workflow_summary = Channel.value(paramsSummaryMultiqc(summary_params))
+ ch_multiqc_custom_methods_description = params.multiqc_methods_description ? file(params.multiqc_methods_description, checkIfExists: true) : file("$projectDir/assets/methods_description_template.yml", checkIfExists: true)
+ ch_methods_description = Channel.value(methodsDescriptionText(ch_multiqc_custom_methods_description))
ch_multiqc_files = Channel.empty()
ch_multiqc_files = ch_multiqc_files.mix(ch_workflow_summary.collectFile(name: 'workflow_summary_mqc.yaml'))
ch_multiqc_files = ch_multiqc_files.mix(ch_methods_description.collectFile(name: 'methods_description_mqc.yaml'))
- ch_multiqc_files = ch_multiqc_files.mix(CUSTOM_DUMPSOFTWAREVERSIONS.out.mqc_yml.collect())
+ ch_multiqc_files = ch_multiqc_files.mix(ch_collated_versions)
ch_multiqc_files = ch_multiqc_files.mix(ch_multiqc_rep)
MULTIQC (
@@ -185,24 +169,11 @@ workflow ALPHAFOLD2 {
ch_multiqc_custom_config.toList(),
ch_multiqc_logo.toList()
)
- multiqc_report = MULTIQC.out.report.toList()
-}
-
-/*
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
- COMPLETION EMAIL AND SUMMARY
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-*/
+ ch_multiqc_report = MULTIQC.out.report.toList()
-workflow.onComplete {
- if (params.email || params.email_on_fail) {
- NfcoreTemplate.email(workflow, params, summary_params, projectDir, log, multiqc_report)
- }
- NfcoreTemplate.dump_parameters(workflow, params)
- NfcoreTemplate.summary(workflow, params, log)
- if (params.hook_url) {
- NfcoreTemplate.adaptivecard(workflow, params, summary_params, projectDir, log)
- }
+ emit:
+ multiqc_report = ch_multiqc_report // channel: /path/to/multiqc_report.html
+ versions = ch_versions // channel: [ path(versions.yml) ]
}
/*
diff --git a/workflows/colabfold.nf b/workflows/colabfold.nf
index f07495eb..dd38fd0f 100644
--- a/workflows/colabfold.nf
+++ b/workflows/colabfold.nf
@@ -1,32 +1,3 @@
-/*
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
- VALIDATE INPUTS
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-*/
-
-include { paramsSummaryLog; paramsSummaryMap; fromSamplesheet } from 'plugin/nf-validation'
-
-def logo = NfcoreTemplate.logo(workflow, params.monochrome_logs)
-def citation = '\n' + WorkflowMain.citation(workflow) + '\n'
-def summary_params = paramsSummaryMap(workflow)
-
-// Print parameter summary log to screen
-log.info logo + paramsSummaryLog(workflow) + citation
-
-// Validate input parameters
-WorkflowColabfold.initialise(params, log)
-
-/*
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
- CONFIG FILES
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-*/
-
-ch_multiqc_config = Channel.fromPath("$projectDir/assets/multiqc_config.yml", checkIfExists: true)
-ch_multiqc_custom_config = params.multiqc_config ? Channel.fromPath( params.multiqc_config ) : Channel.empty()
-ch_multiqc_logo = params.multiqc_logo ? Channel.fromPath( params.multiqc_logo ) : Channel.empty()
-ch_multiqc_custom_methods_description = params.multiqc_methods_description ? file(params.multiqc_methods_description) : file("$projectDir/assets/methods_description_template.yml", checkIfExists: true)
-
/*
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
IMPORT LOCAL MODULES/SUBWORKFLOWS
@@ -34,12 +5,7 @@ ch_multiqc_custom_methods_description = params.multiqc_methods_description ? fil
*/
//
-// SUBWORKFLOW: Consisting of a mix of local and nf-core/modules
-//
-include { PREPARE_COLABFOLD_DBS } from '../subworkflows/local/prepare_colabfold_dbs'
-
-//
-// MODULE: Local to the pipeline
+// MODULE: Loaded from modules/local/
//
include { COLABFOLD_BATCH } from '../modules/local/colabfold_batch'
include { MMSEQS_COLABFOLDSEARCH } from '../modules/local/mmseqs_colabfoldsearch'
@@ -54,8 +20,16 @@ include { MULTIFASTA_TO_CSV } from '../modules/local/multifasta_to_csv'
//
// MODULE: Installed directly from nf-core/modules
//
-include { MULTIQC } from '../modules/nf-core/multiqc/main'
-include { CUSTOM_DUMPSOFTWAREVERSIONS } from '../modules/nf-core/custom/dumpsoftwareversions/main'
+include { MULTIQC } from '../modules/nf-core/multiqc/main'
+
+//
+// SUBWORKFLOW: Consisting entirely of nf-core/modules
+//
+include { paramsSummaryMap } from 'plugin/nf-validation'
+include { fromSamplesheet } from 'plugin/nf-validation'
+include { paramsSummaryMultiqc } from '../subworkflows/nf-core/utils_nfcore_pipeline'
+include { softwareVersionsToYAML } from '../subworkflows/nf-core/utils_nfcore_pipeline'
+include { methodsDescriptionText } from '../subworkflows/local/utils_nfcore_proteinfold_pipeline'
/*
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
@@ -63,12 +37,18 @@ include { CUSTOM_DUMPSOFTWAREVERSIONS } from '../modules/nf-core/custom/dumpsoft
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
*/
-// Info required for completion email and summary
-def multiqc_report = []
-
workflow COLABFOLD {
- ch_versions = Channel.empty()
+ take:
+ ch_versions // channel: [ path(versions.yml) ]
+ colabfold_model_preset // string: Specifies the model preset to use for colabfold
+ ch_colabfold_params // channel: path(colabfold_params)
+ ch_colabfold_db // channel: path(colabfold_db)
+ ch_uniref30 // channel: path(uniref30)
+ num_recycle // int: Number of recycles for esmfold
+
+ main:
+ ch_multiqc_files = Channel.empty()
//
// Create input channel from input file provided through params.input
@@ -77,9 +57,6 @@ workflow COLABFOLD {
.fromSamplesheet("input")
.set { ch_fasta }
- PREPARE_COLABFOLD_DBS ( )
- ch_versions = ch_versions.mix(PREPARE_COLABFOLD_DBS.out.versions)
-
if (params.colabfold_server == 'webserver') {
//
// MODULE: Run colabfold
@@ -91,21 +68,21 @@ workflow COLABFOLD {
ch_versions = ch_versions.mix(MULTIFASTA_TO_CSV.out.versions)
COLABFOLD_BATCH(
MULTIFASTA_TO_CSV.out.input_csv,
- params.colabfold_model_preset,
- PREPARE_COLABFOLD_DBS.out.params,
+ colabfold_model_preset,
+ ch_colabfold_params,
[],
[],
- params.num_recycle
+ num_recycle
)
ch_versions = ch_versions.mix(COLABFOLD_BATCH.out.versions)
} else {
COLABFOLD_BATCH(
ch_fasta,
- params.colabfold_model_preset,
- PREPARE_COLABFOLD_DBS.out.params,
+ colabfold_model_preset,
+ ch_colabfold_params,
[],
[],
- params.num_recycle
+ num_recycle
)
ch_versions = ch_versions.mix(COLABFOLD_BATCH.out.versions)
}
@@ -121,17 +98,17 @@ workflow COLABFOLD {
ch_versions = ch_versions.mix(MULTIFASTA_TO_CSV.out.versions)
MMSEQS_COLABFOLDSEARCH (
MULTIFASTA_TO_CSV.out.input_csv,
- PREPARE_COLABFOLD_DBS.out.params,
- PREPARE_COLABFOLD_DBS.out.colabfold_db,
- PREPARE_COLABFOLD_DBS.out.uniref30,
+ ch_colabfold_params,
+ ch_colabfold_db,
+ ch_uniref30
)
ch_versions = ch_versions.mix(MMSEQS_COLABFOLDSEARCH.out.versions)
} else {
MMSEQS_COLABFOLDSEARCH (
ch_fasta,
- PREPARE_COLABFOLD_DBS.out.params,
- PREPARE_COLABFOLD_DBS.out.colabfold_db,
- PREPARE_COLABFOLD_DBS.out.uniref30,
+ ch_colabfold_params,
+ ch_colabfold_db,
+ ch_uniref30
)
ch_versions = ch_versions.mix(MMSEQS_COLABFOLDSEARCH.out.versions)
}
@@ -141,35 +118,38 @@ workflow COLABFOLD {
//
COLABFOLD_BATCH(
MMSEQS_COLABFOLDSEARCH.out.a3m,
- params.colabfold_model_preset,
- PREPARE_COLABFOLD_DBS.out.params,
- PREPARE_COLABFOLD_DBS.out.colabfold_db,
- PREPARE_COLABFOLD_DBS.out.uniref30,
- params.num_recycle
+ colabfold_model_preset,
+ ch_colabfold_params,
+ ch_colabfold_db,
+ ch_uniref30,
+ num_recycle
)
ch_versions = ch_versions.mix(COLABFOLD_BATCH.out.versions)
}
//
- // MODULE: Pipeline reporting
+ // Collate and save software versions
//
- CUSTOM_DUMPSOFTWAREVERSIONS (
- ch_versions.unique().collectFile(name: 'collated_versions.yml')
- )
+ softwareVersionsToYAML(ch_versions)
+ .collectFile(storeDir: "${params.outdir}/pipeline_info", name: 'nf_core_proteinfold_software_mqc_versions.yml', sort: true, newLine: true)
+ .set { ch_collated_versions }
//
// MODULE: MultiQC
//
- workflow_summary = WorkflowColabfold.paramsSummaryMultiqc(workflow, summary_params)
- ch_workflow_summary = Channel.value(workflow_summary)
-
- methods_description = WorkflowColabfold.methodsDescriptionText(workflow, ch_multiqc_custom_methods_description, params)
- ch_methods_description = Channel.value(methods_description)
+ ch_multiqc_report = Channel.empty()
+ ch_multiqc_config = Channel.fromPath("$projectDir/assets/multiqc_config.yml", checkIfExists: true)
+ ch_multiqc_custom_config = params.multiqc_config ? Channel.fromPath( params.multiqc_config ) : Channel.empty()
+ ch_multiqc_logo = params.multiqc_logo ? Channel.fromPath( params.multiqc_logo ) : Channel.empty()
+ summary_params = paramsSummaryMap(workflow, parameters_schema: "nextflow_schema.json")
+ ch_workflow_summary = Channel.value(paramsSummaryMultiqc(summary_params))
+ ch_multiqc_custom_methods_description = params.multiqc_methods_description ? file(params.multiqc_methods_description, checkIfExists: true) : file("$projectDir/assets/methods_description_template.yml", checkIfExists: true)
+ ch_methods_description = Channel.value(methodsDescriptionText(ch_multiqc_custom_methods_description))
ch_multiqc_files = Channel.empty()
ch_multiqc_files = ch_multiqc_files.mix(ch_workflow_summary.collectFile(name: 'workflow_summary_mqc.yaml'))
ch_multiqc_files = ch_multiqc_files.mix(ch_methods_description.collectFile(name: 'methods_description_mqc.yaml'))
- ch_multiqc_files = ch_multiqc_files.mix(CUSTOM_DUMPSOFTWAREVERSIONS.out.mqc_yml.collect())
+ ch_multiqc_files = ch_multiqc_files.mix(ch_collated_versions)
ch_multiqc_files = ch_multiqc_files.mix(COLABFOLD_BATCH.out.multiqc.collect())
MULTIQC (
@@ -178,24 +158,11 @@ workflow COLABFOLD {
ch_multiqc_custom_config.toList(),
ch_multiqc_logo.toList()
)
- multiqc_report = MULTIQC.out.report.toList()
-}
-
-/*
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
- COMPLETION EMAIL AND SUMMARY
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-*/
+ ch_multiqc_report = MULTIQC.out.report.toList()
-workflow.onComplete {
- if (params.email || params.email_on_fail) {
- NfcoreTemplate.email(workflow, params, summary_params, projectDir, log, multiqc_report)
- }
- NfcoreTemplate.dump_parameters(workflow, params)
- NfcoreTemplate.summary(workflow, params, log)
- if (params.hook_url) {
- NfcoreTemplate.IM_notification(workflow, params, summary_params, projectDir, log)
- }
+ emit:
+ multiqc_report = ch_multiqc_report // channel: /path/to/multiqc_report.html
+ versions = ch_versions // channel: [ path(versions.yml) ]
}
/*
diff --git a/workflows/esmfold.nf b/workflows/esmfold.nf
index 70b64fc3..4bf7e2a4 100644
--- a/workflows/esmfold.nf
+++ b/workflows/esmfold.nf
@@ -1,32 +1,3 @@
-/*
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
- PRINT PARAMS SUMMARY
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-*/
-
-include { paramsSummaryLog; paramsSummaryMap; fromSamplesheet } from 'plugin/nf-validation'
-
-def logo = NfcoreTemplate.logo(workflow, params.monochrome_logs)
-def citation = '\n' + WorkflowMain.citation(workflow) + '\n'
-def summary_params = paramsSummaryMap(workflow)
-
-// Print parameter summary log to screen
-log.info logo + paramsSummaryLog(workflow) + citation
-
-// Validate input parameters
-WorkflowEsmfold.initialise(params, log)
-
-/*
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
- CONFIG FILES
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-*/
-
-ch_multiqc_config = Channel.fromPath("$projectDir/assets/multiqc_config.yml", checkIfExists: true)
-ch_multiqc_custom_config = params.multiqc_config ? Channel.fromPath( params.multiqc_config ) : Channel.empty()
-ch_multiqc_logo = params.multiqc_logo ? Channel.fromPath( params.multiqc_logo ) : Channel.empty()
-ch_multiqc_custom_methods_description = params.multiqc_methods_description ? file(params.multiqc_methods_description) : file("$projectDir/assets/methods_description_template.yml", checkIfExists: true)
-
/*
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
IMPORT LOCAL MODULES/SUBWORKFLOWS
@@ -34,12 +5,7 @@ ch_multiqc_custom_methods_description = params.multiqc_methods_description ? fil
*/
//
-// SUBWORKFLOW: Consisting of a mix of local and nf-core/modules
-//
-include { PREPARE_ESMFOLD_DBS } from '../subworkflows/local/prepare_esmfold_dbs'
-
-//
-// MODULE: Local to the pipeline
+// MODULE: Loaded from modules/local/
//
include { RUN_ESMFOLD } from '../modules/local/run_esmfold'
include { MULTIFASTA_TO_SINGLEFASTA } from '../modules/local/multifasta_to_singlefasta'
@@ -53,8 +19,16 @@ include { MULTIFASTA_TO_SINGLEFASTA } from '../modules/local/multifasta_to_singl
//
// MODULE: Installed directly from nf-core/modules
//
-include { MULTIQC } from '../modules/nf-core/multiqc/main'
-include { CUSTOM_DUMPSOFTWAREVERSIONS } from '../modules/nf-core/custom/dumpsoftwareversions/main'
+include { MULTIQC } from '../modules/nf-core/multiqc/main'
+
+//
+// SUBWORKFLOW: Consisting entirely of nf-core/modules
+//
+include { paramsSummaryMap } from 'plugin/nf-validation'
+include { fromSamplesheet } from 'plugin/nf-validation'
+include { paramsSummaryMultiqc } from '../subworkflows/nf-core/utils_nfcore_pipeline'
+include { softwareVersionsToYAML } from '../subworkflows/nf-core/utils_nfcore_pipeline'
+include { methodsDescriptionText } from '../subworkflows/local/utils_nfcore_proteinfold_pipeline'
/*
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
@@ -62,12 +36,15 @@ include { CUSTOM_DUMPSOFTWAREVERSIONS } from '../modules/nf-core/custom/dumpsoft
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
*/
-// Info required for completion email and summary
-def multiqc_report = []
-
workflow ESMFOLD {
- ch_versions = Channel.empty()
+ take:
+ ch_versions // channel: [ path(versions.yml) ]
+ ch_esmfold_params // directory: /path/to/esmfold/params/
+ ch_num_recycle // int: Number of recycles for esmfold
+
+ main:
+ ch_multiqc_files = Channel.empty()
//
// Create input channel from input file provided through params.input
@@ -76,9 +53,6 @@ workflow ESMFOLD {
.fromSamplesheet("input")
.set { ch_fasta }
- PREPARE_ESMFOLD_DBS( )
- ch_versions = ch_versions.mix(PREPARE_ESMFOLD_DBS.out.versions)
-
//
// MODULE: Run esmfold
//
@@ -89,39 +63,42 @@ workflow ESMFOLD {
ch_versions = ch_versions.mix(MULTIFASTA_TO_SINGLEFASTA.out.versions)
RUN_ESMFOLD(
MULTIFASTA_TO_SINGLEFASTA.out.input_fasta,
- PREPARE_ESMFOLD_DBS.out.params,
- params.num_recycles
+ ch_esmfold_params,
+ ch_num_recycle
)
ch_versions = ch_versions.mix(RUN_ESMFOLD.out.versions)
} else {
RUN_ESMFOLD(
ch_fasta,
- PREPARE_ESMFOLD_DBS.out.params,
- params.num_recycles
+ ch_esmfold_params,
+ ch_num_recycle
)
ch_versions = ch_versions.mix(RUN_ESMFOLD.out.versions)
}
//
- // MODULE: Pipeline reporting
+ // Collate and save software versions
//
- CUSTOM_DUMPSOFTWAREVERSIONS (
- ch_versions.unique().collectFile(name: 'collated_versions.yml')
- )
+ softwareVersionsToYAML(ch_versions)
+ .collectFile(storeDir: "${params.outdir}/pipeline_info", name: 'nf_core_proteinfold_software_mqc_versions.yml', sort: true, newLine: true)
+ .set { ch_collated_versions }
//
// MODULE: MultiQC
//
- workflow_summary = WorkflowEsmfold.paramsSummaryMultiqc(workflow, summary_params)
- ch_workflow_summary = Channel.value(workflow_summary)
-
- methods_description = WorkflowEsmfold.methodsDescriptionText(workflow, ch_multiqc_custom_methods_description, params)
- ch_methods_description = Channel.value(methods_description)
+ ch_multiqc_report = Channel.empty()
+ ch_multiqc_config = Channel.fromPath("$projectDir/assets/multiqc_config.yml", checkIfExists: true)
+ ch_multiqc_custom_config = params.multiqc_config ? Channel.fromPath( params.multiqc_config ) : Channel.empty()
+ ch_multiqc_logo = params.multiqc_logo ? Channel.fromPath( params.multiqc_logo ) : Channel.empty()
+ summary_params = paramsSummaryMap(workflow, parameters_schema: "nextflow_schema.json")
+ ch_workflow_summary = Channel.value(paramsSummaryMultiqc(summary_params))
+ ch_multiqc_methods_description = params.multiqc_methods_description ? file(params.multiqc_methods_description, checkIfExists: true) : file("$projectDir/assets/methods_description_template.yml", checkIfExists: true)
+ ch_methods_description = Channel.value(methodsDescriptionText(ch_multiqc_methods_description))
ch_multiqc_files = Channel.empty()
ch_multiqc_files = ch_multiqc_files.mix(ch_workflow_summary.collectFile(name: 'workflow_summary_mqc.yaml'))
ch_multiqc_files = ch_multiqc_files.mix(ch_methods_description.collectFile(name: 'methods_description_mqc.yaml'))
- ch_multiqc_files = ch_multiqc_files.mix(CUSTOM_DUMPSOFTWAREVERSIONS.out.mqc_yml.collect())
+ ch_multiqc_files = ch_multiqc_files.mix(ch_collated_versions)
ch_multiqc_files = ch_multiqc_files.mix(RUN_ESMFOLD.out.multiqc.collect())
MULTIQC (
@@ -130,31 +107,10 @@ workflow ESMFOLD {
ch_multiqc_custom_config.toList(),
ch_multiqc_logo.toList()
)
- multiqc_report = MULTIQC.out.report.toList()
-}
-
-/*
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
- COMPLETION EMAIL AND SUMMARY
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-*/
-
-workflow.onComplete {
- if (params.email || params.email_on_fail) {
- NfcoreTemplate.email(workflow, params, summary_params, projectDir, log, multiqc_report)
- }
- NfcoreTemplate.dump_parameters(workflow, params)
- NfcoreTemplate.summary(workflow, params, log)
- if (params.hook_url) {
- NfcoreTemplate.IM_notification(workflow, params, summary_params, projectDir, log)
- }
-}
-
-workflow.onError {
- if (workflow.errorReport.contains("Process requirement exceeds available memory")) {
- println("π Default resources exceed availability π ")
- println("π‘ See here on how to configure pipeline: https://nf-co.re/docs/usage/configuration#tuning-workflow-resources π‘")
- }
+ ch_multiqc_report = MULTIQC.out.report.toList()
+ emit:
+ multiqc_report = ch_multiqc_report // channel: /path/to/multiqc_report.html
+ versions = ch_versions // channel: [ path(versions.yml) ]
}
/*