-[](https://github.com/nf-core/epitopeprediction/actions?query=workflow%3A%22nf-core+CI%22)
-[](https://github.com/nf-core/epitopeprediction/actions?query=workflow%3A%22nf-core+linting%22)[](https://nf-co.re/epitopeprediction/results)[](https://doi.org/10.5281/zenodo.3564666)
+
+[](https://github.com/nf-core/epitopeprediction/actions/workflows/ci.yml)
+[](https://github.com/nf-core/epitopeprediction/actions/workflows/linting.yml)[](https://nf-co.re/epitopeprediction/results)[](https://doi.org/10.5281/zenodo.3564666)
[](https://www.nextflow.io/)
[](https://docs.conda.io/en/latest/)
diff --git a/assets/multiqc_config.yml b/assets/multiqc_config.yml
index ad84390..00ebcf7 100644
--- a/assets/multiqc_config.yml
+++ b/assets/multiqc_config.yml
@@ -1,7 +1,9 @@
report_comment: >
+
This report has been generated by the nf-core/epitopeprediction
analysis pipeline. For information about how to interpret these results, please see the
documentation.
+
report_section_order:
"nf-core-epitopeprediction-methods-description":
order: -1000
@@ -11,3 +13,5 @@ report_section_order:
order: -1002
export_plots: true
+
+disable_version_detection: true
diff --git a/assets/schema_input.json b/assets/schema_input.json
index b15dc42..95d5bb4 100644
--- a/assets/schema_input.json
+++ b/assets/schema_input.json
@@ -10,7 +10,8 @@
"sample": {
"type": "string",
"pattern": "^\\S+$",
- "errorMessage": "Sample name must be provided and cannot contain spaces"
+ "errorMessage": "Sample name must be provided and cannot contain spaces",
+ "meta": ["id"]
},
"alleles": {
"anyOf": [
diff --git a/conf/test_grch38.config b/conf/test_grch38.config
index 9729812..0c2bbd0 100644
--- a/conf/test_grch38.config
+++ b/conf/test_grch38.config
@@ -14,5 +14,5 @@ params {
// Input data
input = 'https://raw.githubusercontent.com/nf-core/test-datasets/epitopeprediction/testdata/sample_sheets/sample_sheet_variants.csv'
- genome_version = 'GRCh38'
+ genome_reference = 'grch38'
}
diff --git a/docs/usage.md b/docs/usage.md
index ece95e6..08ff5e3 100644
--- a/docs/usage.md
+++ b/docs/usage.md
@@ -20,7 +20,7 @@ The pipeline currently accepts three different types of input that are genomic v
#### Genomic variants
-The supported file formats for genomic variants are `.vcf`, `.vcf.gz` and `tsv`.
+The supported file formats for genomic variants are `.vcf`, `.vcf.gz`.
> [!IMPORTANT]
> Please note that genomic variants have to be annotated. Currently, we support variants that have been annotated using [SnpEff](http://pcingola.> github.io/SnpEff/) and [VEP](https://www.ensembl.org/info/docs/tools/vep/index.html).
@@ -157,7 +157,7 @@ First, go to the [nf-core/epitopeprediction releases page](https://github.com/nf
This version number will be logged in reports when you run the pipeline, so that you'll know what you used when you look back in the future. For example, at the bottom of the MultiQC reports.
-To further assist in reproducbility, you can use share and re-use [parameter files](#running-the-pipeline) to repeat pipeline runs with the same settings without having to write out a command with every single parameter.
+To further assist in reproducibility, you can use share and re-use [parameter files](#running-the-pipeline) to repeat pipeline runs with the same settings without having to write out a command with every single parameter.
:::tip
If you wish to share such profile (such as upload as supplementary material for academic publications), make sure to NOT include cluster specific paths to files, nor institutional specific profiles.
diff --git a/lib/NfcoreTemplate.groovy b/lib/NfcoreTemplate.groovy
deleted file mode 100755
index e248e4c..0000000
--- 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 8d030f4..0000000
--- 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/WorkflowEpitopeprediction.groovy b/lib/WorkflowEpitopeprediction.groovy
deleted file mode 100755
index 5f54640..0000000
--- a/lib/WorkflowEpitopeprediction.groovy
+++ /dev/null
@@ -1,117 +0,0 @@
-//
-// This file holds several functions specific to the workflow/epitopeprediction.nf in the nf-core/epitopeprediction pipeline
-//
-
-import nextflow.Nextflow
-import groovy.text.SimpleTemplateEngine
-
-class WorkflowEpitopeprediction {
-
- //
- // Check and validate parameters
- //
- public static void initialise(params, log) {
-
- genomeExistsError(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 += " $group
\n" - summary_section += "| Process Name | -Software | -Version | -
|---|---|---|
| {process if (i == 0) else ''} | -{tool} | -{version} | -
| Process Name | \\n\\", - " \\ Software | \\nVersion | \\n
|---|---|---|
| CUSTOM_DUMPSOFTWAREVERSIONS | \\npython | \\n\\", - " \\3.11.7 | \\n
| \\n \\", - " \\ | yaml | \\n5.4.1 | \\n
| TOOL1 | \\ntool1 | \\n\\", - " \\0.11.9 | \\n
| TOOL2 | \\n\\", - " \\tool2 | \\n1.9 | \\n
| Workflow | \\nNextflow | \\n\\" - ], - [ - "CUSTOM_DUMPSOFTWAREVERSIONS:", - " python: 3.11.7", - " yaml: 5.4.1", - "TOOL1:", - " tool1: 0.11.9", - "TOOL2:", - " tool2: '1.9'", - "Workflow:" - ] - ], - "timestamp": "2024-01-09T23:01:18.710682" - } -} \ No newline at end of file diff --git a/modules/nf-core/custom/dumpsoftwareversions/tests/tags.yml b/modules/nf-core/custom/dumpsoftwareversions/tests/tags.yml deleted file mode 100644 index 405aa24..0000000 --- a/modules/nf-core/custom/dumpsoftwareversions/tests/tags.yml +++ /dev/null @@ -1,2 +0,0 @@ -custom/dumpsoftwareversions: - - modules/nf-core/custom/dumpsoftwareversions/** diff --git a/modules/nf-core/multiqc/environment.yml b/modules/nf-core/multiqc/environment.yml index 7625b75..2212096 100644 --- a/modules/nf-core/multiqc/environment.yml +++ b/modules/nf-core/multiqc/environment.yml @@ -4,4 +4,4 @@ channels: - bioconda - defaults dependencies: - - bioconda::multiqc=1.19 + - bioconda::multiqc=1.20 diff --git a/modules/nf-core/multiqc/main.nf b/modules/nf-core/multiqc/main.nf index 1b9f7c4..354f443 100644 --- a/modules/nf-core/multiqc/main.nf +++ b/modules/nf-core/multiqc/main.nf @@ -3,8 +3,8 @@ process MULTIQC { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/multiqc:1.19--pyhdfd78af_0' : - 'biocontainers/multiqc:1.19--pyhdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/multiqc:1.20--pyhdfd78af_0' : + 'biocontainers/multiqc:1.20--pyhdfd78af_0' }" input: path multiqc_files, stageAs: "?/*" diff --git a/modules/nf-core/multiqc/tests/main.nf.test.snap b/modules/nf-core/multiqc/tests/main.nf.test.snap index 549ba79..c204b48 100644 --- a/modules/nf-core/multiqc/tests/main.nf.test.snap +++ b/modules/nf-core/multiqc/tests/main.nf.test.snap @@ -2,14 +2,14 @@ "multiqc_versions_single": { "content": [ [ - "versions.yml:md5,14e9a2661241abd828f4f06a7b5c222d" + "versions.yml:md5,d320d4c37e349c5588e07e7a31cd4186" ] ], "meta": { "nf-test": "0.8.4", "nextflow": "23.10.1" }, - "timestamp": "2024-01-31T17:43:40.529579" + "timestamp": "2024-02-14T09:28:51.744211298" }, "multiqc_stub": { "content": [ @@ -17,25 +17,25 @@ "multiqc_report.html", "multiqc_data", "multiqc_plots", - "versions.yml:md5,14e9a2661241abd828f4f06a7b5c222d" + "versions.yml:md5,d320d4c37e349c5588e07e7a31cd4186" ] ], "meta": { "nf-test": "0.8.4", "nextflow": "23.10.1" }, - "timestamp": "2024-01-31T17:45:09.605359" + "timestamp": "2024-02-14T09:29:28.847433492" }, "multiqc_versions_config": { "content": [ [ - "versions.yml:md5,14e9a2661241abd828f4f06a7b5c222d" + "versions.yml:md5,d320d4c37e349c5588e07e7a31cd4186" ] ], "meta": { "nf-test": "0.8.4", "nextflow": "23.10.1" }, - "timestamp": "2024-01-31T17:44:53.535994" + "timestamp": "2024-02-14T09:29:13.223621555" } } \ No newline at end of file diff --git a/nextflow.config b/nextflow.config index e93b877..8308702 100644 --- a/nextflow.config +++ b/nextflow.config @@ -18,44 +18,42 @@ params { // References genome_reference = 'grch37' - genome = null - fasta = null // Options: Predictions - tools = 'syfpeithi' - tool_thresholds = null + tools = 'syfpeithi' + tool_thresholds = null use_affinity_thresholds = false // Options: Filtering - filter_self = false + filter_self = false show_supported_models = false // External tools external_tools_meta = "${projectDir}/assets/external_tools_meta.json" - netmhc_system = 'linux' - netmhcpan_path = null - netmhc_path = null - netmhciipan_path = null - netmhcii_path = null + netmhc_system = 'linux' + netmhcpan_path = null + netmhc_path = null + netmhciipan_path = null + netmhcii_path = null // Options: Peptides - max_peptide_length = 11 - min_peptide_length = 8 + max_peptide_length = 11 + min_peptide_length = 8 max_peptide_length_class2 = 16 min_peptide_length_class2 = 15 // Options: Annotation - proteome = null + proteome = null wild_type = false // Options: Output fasta_output = false // MultiQC options - multiqc_config = null - multiqc_title = null - multiqc_logo = "$projectDir/assets/nf-core-epitopeprediction_logo_light.png" - max_multiqc_email_size = '25.MB' + multiqc_config = null + multiqc_title = null + multiqc_logo = "$projectDir/assets/nf-core-epitopeprediction_logo_light.png" + max_multiqc_email_size = '25.MB' multiqc_methods_description = null // Boilerplate options @@ -79,7 +77,6 @@ params { custom_config_base = "https://raw.githubusercontent.com/nf-core/configs/${params.custom_config_version}" config_profile_contact = null config_profile_url = null - config_profile_name = null // Max resource options // Defaults only, expecting to be overwritten diff --git a/nextflow_schema.json b/nextflow_schema.json index 7f0a65b..45cdd20 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -16,8 +16,6 @@ "type": "string", "format": "file-path", "exists": true, - "mimetype": "text/csv", - "pattern": "^\\S+\\.csv$", "schema": "assets/schema_input.json", "description": "Path to comma-separated file containing information about the samples in the experiment.", "help_text": "You will need to create a design file with information about the samples in your experiment before running the pipeline. Use this parameter to specify its location. It has to be a comma-separated file with 3 columns, and a header row. See [usage docs](https://nf-co.re/epitopeprediction/usage#samplesheet-input).", @@ -52,6 +50,7 @@ "genome_reference": { "type": "string", "default": "grch37", + "enum": ["grch37", "grch38"], "help_text": "This defines against which human Ensembl genome reference the pipeline performs the analysis including the incorporation of genetic variants e.g.. If `grch37` or `grch38` are specified the most recent Ensembl Biomart version for genome versions will be used. Alternatively, an Ensembl Biomart (archive) version can be specified, e.g. http://jan2020.archive.ensembl.org/.", "description": "Specifies the Ensembl genome reference version that will be used." }, @@ -68,22 +67,6 @@ "fa_icon": "fas fa-dna", "description": "Reference genome related files and options required for the workflow.", "properties": { - "genome": { - "type": "string", - "description": "Name of iGenomes reference.", - "fa_icon": "fas fa-book", - "help_text": "If using a reference genome configured in the pipeline using iGenomes, use this parameter to give the ID for the reference. This is then used to build the full paths for all required reference genome files e.g. `--genome GRCh38`. \n\nSee the [nf-core website docs](https://nf-co.re/usage/reference_genomes) for more details." - }, - "fasta": { - "type": "string", - "format": "file-path", - "exists": true, - "mimetype": "text/plain", - "pattern": "^\\S+\\.fn?a(sta)?(\\.gz)?$", - "description": "Path to FASTA genome file.", - "help_text": "This parameter is *mandatory* if `--genome` is not specified. If you don't have a BWA index available this will be generated for you automatically. Combine with `--save_reference` to save BWA index for future runs.", - "fa_icon": "far fa-file-code" - }, "igenomes_ignore": { "type": "boolean", "description": "Do not load the iGenomes reference config.", diff --git a/pyproject.toml b/pyproject.toml index 7d08e1c..5611062 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -3,11 +3,13 @@ [tool.ruff] line-length = 120 target-version = "py38" -select = ["I", "E1", "E4", "E7", "E9", "F", "UP", "N"] cache-dir = "~/.cache/ruff" -[tool.ruff.isort] +[tool.ruff.lint] +select = ["I", "E1", "E4", "E7", "E9", "F", "UP", "N"] + +[tool.ruff.lint.isort] known-first-party = ["nf_core"] -[tool.ruff.per-file-ignores] +[tool.ruff.lint.per-file-ignores] "__init__.py" = ["E402", "F401"] diff --git a/subworkflows/local/utils_nfcore_epitopeprediction_pipeline/main.nf b/subworkflows/local/utils_nfcore_epitopeprediction_pipeline/main.nf new file mode 100644 index 0000000..e62cbd1 --- /dev/null +++ b/subworkflows/local/utils_nfcore_epitopeprediction_pipeline/main.nf @@ -0,0 +1,232 @@ +// +// Subworkflow with functionality specific to the nf-core/pipeline pipeline +// + +/* +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + IMPORT FUNCTIONS / MODULES / SUBWORKFLOWS +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +*/ + +include { UTILS_NFVALIDATION_PLUGIN } from '../../nf-core/utils_nfvalidation_plugin' +include { paramsSummaryMap } from 'plugin/nf-validation' +include { fromSamplesheet } 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 + input // string: Path to input samplesheet + + main: + + ch_versions = Channel.empty() + + // + // 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