-[](https://github.com/nf-core/mhcquant/actions?query=workflow%3A%22nf-core+CI%22)
-[](https://github.com/nf-core/mhcquant/actions?query=workflow%3A%22nf-core+linting%22)[](https://nf-co.re/mhcquant/results)[](https://doi.org/10.5281/zenodo.8427707)
+
+[](https://github.com/nf-core/mhcquant/actions/workflows/ci.yml)
+[](https://github.com/nf-core/mhcquant/actions/workflows/linting.yml)[](https://nf-co.re/mhcquant/results)[](https://doi.org/10.5281/zenodo.8427707)
[](https://www.nextflow.io/)
[](https://docs.conda.io/en/latest/)
diff --git a/assets/multiqc_config.yml b/assets/multiqc_config.yml
index a4906753..5d8e4954 100644
--- a/assets/multiqc_config.yml
+++ b/assets/multiqc_config.yml
@@ -15,3 +15,5 @@ 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 6df68dfd..da298c60 100644
--- a/assets/schema_input.json
+++ b/assets/schema_input.json
@@ -9,35 +9,27 @@
"properties": {
"ID": {
"type": "integer",
- "errorMessage": "Provide an unique identifier for the replicate, must be a numeric value"
+ "errorMessage": "Provide an unique identifier for the replicate, must be a numeric value",
+ "meta": ["id"]
},
"Sample": {
"type": "string",
- "pattern": "^\\S+-?",
- "errorMessage": "Sample name must be provided and cannot contain spaces"
+ "pattern": "^\\S+$",
+ "errorMessage": "Sample name must be provided and cannot contain spaces",
+ "meta": ["sample"]
},
"Condition": {
"type": "string",
"pattern": "^\\S+-?",
- "errorMessage": "Sample condition must be provided and cannot contain spaces"
+ "errorMessage": "Sample condition must be provided and cannot contain spaces",
+ "meta": ["condition"]
},
"ReplicateFileName": {
"type": "string",
- "errorMessage": "MS file spaces and must have extension '.raw'|'.RAW', '.mzml'|'mzML', or '.d'",
- "anyOf": [
- {
- "type": "string",
- "pattern": "^(?i)\\S+-?\\.raw$"
- },
- {
- "type": "string",
- "pattern": "^(?i)\\S+-?\\.mzML$"
- },
- {
- "type": "string",
- "pattern": "^\\S+-?\\.d$"
- }
- ]
+ "format": "file-path",
+ "exists": true,
+ "pattern": "^\\S+-?\\.(raw|RAW|mzML|mzML.gz|d|d.tar|d.tar.gz|d.zip)$",
+ "errorMessage": "MS file cannot contain spaces and must have one of the extensions: raw | RAW | mzML | mzML.gz | d | d.tar | d.tar.gz | d.zip"
}
},
"required": ["ID", "Sample", "Condition", "ReplicateFileName"]
diff --git a/bin/check_samplesheet.py b/bin/check_samplesheet.py
deleted file mode 100755
index 9154eb41..00000000
--- a/bin/check_samplesheet.py
+++ /dev/null
@@ -1,241 +0,0 @@
-#!/usr/bin/env python
-
-# Written by Marissa Dubbelaar and released under MIT license.
-
-"""Provide a command line tool to validate and transform tabular samplesheets."""
-
-import os
-import argparse
-import csv
-import logging
-import sys
-from collections import Counter
-from pathlib import Path
-
-logger = logging.getLogger()
-
-
-class RowChecker:
- """
- Define a service that can validate and transform each given row.
-
- Attributes:
- modified (list): A list of dicts, where each dict corresponds to a previously
- validated and transformed row. The order of rows is maintained.
-
- """
-
- VALID_FORMATS = (".raw", ".mzml", ".d")
-
- def __init__(
- self,
- id_col="ID",
- sample_col="Sample",
- condition_col="Condition",
- filename_col="ReplicateFileName",
- **kwargs,
- ):
- """
- Initialize the row checker with the expected column names.
- Args:
- id_col (int) : An integer that acts as a unique identifier for the
- unique samples.
- sample_col (str): The name of the column that contains the sample name
- (default "sample").
- condition_col (str): This column consists of additional information about
- the sample, could be anything from a "wildtype/disease" description
- to a particular treatment (default "").
- filename_col (str): The name of the column that contains the path to the
- raw or mzMl files ).
- """
- super().__init__(**kwargs)
- self._id_col = id_col
- self._sample_col = sample_col
- self._condition_col = condition_col
- self._filename_col = filename_col
- self._seen = set()
- self.modified = []
-
- def validate_and_transform(self, row):
- """
- Perform all validations on the given row and insert the read pairing status.
- Args:
- row (dict): A mapping from column headers (keys) to elements of that row
- (values).
- """
- self._validate_id(row)
- self._validate_sample(row)
- self._validate_condition(row)
- self._validate_filename(row)
- self._seen.add((row[self._sample_col], row[self._filename_col]))
- self.modified.append(row)
-
- def _validate_id(self, row):
- """Assert that the sample name exists and convert spaces to underscores."""
- assert row[self._id_col].isdigit(), "Make sure that the sample ID is an numeric value"
-
- def _validate_sample(self, row):
- """Assert that the sample name exists and convert spaces to underscores."""
- assert len(row[self._sample_col]) > 0, "Sample input is required."
- # Sanitize samples slightly.
- row[self._sample_col] = row[self._sample_col].replace(" ", "_")
-
- def _validate_condition(self, row):
- """Assert that the condition is provided and convert spaces to underscores."""
- assert len(row[self._condition_col]) > 0, "Sample input is required."
- # Sanitize samples slightly.
- row[self._condition_col] = row[self._condition_col].replace(" ", "_")
-
- def _validate_filename(self, row):
- """Assert that the data entry has the right format if it exists."""
- if len(row[self._filename_col]) > 0:
- self._validate_ms_format(row[self._filename_col])
-
- def _validate_ms_format(self, filename):
- """Assert that a given filename has one of the expected MS extensions."""
- assert any(filename.lower().endswith(extension) for extension in self.VALID_FORMATS), (
- f"The file has an unrecognized extension: {filename}\n"
- f"It should be one of: {', '.join(self.VALID_FORMATS)}"
- )
-
- def validate_unique_samples(self):
- """
- Assert that the combination of sample name and filename is unique.
- In addition to the validation, also rename the sample if more than one sample
- file combination exists.
- """
- assert len(self._seen) == len(self.modified), "The pair of sample name and file must be unique."
- if len({pair[0] for pair in self._seen}) < len(self._seen):
- counts = Counter(pair[0] for pair in self._seen)
- seen = Counter()
- for row in self.modified:
- sample = row[self._sample_col]
- seen[sample] += 1
- if counts[sample] > 1:
- row[self._sample_col] = f"{sample}"
-
-
-def read_head(handle, num_lines=10):
- """Read the specified number of lines from the current position in the file."""
- lines = []
- for idx, line in enumerate(handle):
- if idx == num_lines:
- break
- lines.append(line)
- return "".join(lines)
-
-
-def sniff_format(handle):
- """
- Detect the tabular format.
-
- Args:
- handle (text file): A handle to a `text file`_ object. The read position is
- expected to be at the beginning (index 0).
-
- Returns:
- csv.Dialect: The detected tabular format.
-
- .. _text file:
- https://docs.python.org/3/glossary.html#term-text-file
-
- """
- peek = read_head(handle)
- handle.seek(0)
- sniffer = csv.Sniffer()
- dialect = sniffer.sniff(peek)
- return dialect
-
-
-def check_samplesheet(file_in, file_out):
- """
- Check that the tabular samplesheet has the structure expected by nf-core pipelines.
- Validate the general shape of the table, expected columns, and each row. Also add
- an additional column which records whether one or two FASTQ reads were found.
- Args:
- file_in (pathlib.Path): The given tabular samplesheet. The format can be either
- CSV, TSV, or any other format automatically recognized by ``csv.Sniffer``.
- file_out (pathlib.Path): Where the validated and transformed samplesheet should
- be created; always in CSV format.
- Example:
- This function checks that the samplesheet follows the following structure,
- see also the `viral recon samplesheet`_::
- ID Sample Condition ReplicateFileName
- 1 WT A WT_A.raw
- 2 WT B WT_B.raw
- 3 KO A KO_A.raw
- 4 KO B KO_B.raw
- .. _viral recon samplesheet:
- https://raw.githubusercontent.com/nf-core/test-datasets/viralrecon/samplesheet/samplesheet_test_illumina_amplicon.csv
- """
- required_columns = {"ID", "Sample", "Condition", "ReplicateFileName"}
-
- # See https://docs.python.org/3.9/library/csv.html#id3 to read up on `newline=""`.
- with file_in.open(newline="") as in_handle:
- reader = csv.DictReader(in_handle, dialect=sniff_format(in_handle))
- # Validate the existence of the expected header columns.
- if not required_columns.issubset(reader.fieldnames):
- req_cols = ", ".join(required_columns)
- logger.critical(f"The sample sheet **must** contain these column headers: {req_cols}.")
- sys.exit(1)
- # Validate each row.
- checker = RowChecker()
- for i, row in enumerate(reader):
- try:
- checker.validate_and_transform(row)
- except AssertionError as error:
- logger.critical(f"{str(error)} On line {i + 2}.")
- sys.exit(1)
- checker.validate_unique_samples()
- header = list(reader.fieldnames)
- header.insert(4, "Extension")
- # See https://docs.python.org/3.9/library/csv.html#id3 to read up on `newline=""`.
- with file_out.open(mode="w", newline="") as out_handle:
- writer = csv.DictWriter(out_handle, header, delimiter="\t")
- writer.writeheader()
- for row in checker.modified:
- row["Extension"] = os.path.splitext(row["ReplicateFileName"])[1][1:].lower()
- writer.writerow(row)
-
-
-def parse_args(argv=None):
- """Define and immediately parse command line arguments."""
- parser = argparse.ArgumentParser(
- description="Validate and transform a tabular samplesheet.",
- epilog="Example: python check_samplesheet.py samplesheet.csv samplesheet.valid.csv",
- )
- parser.add_argument(
- "file_in",
- metavar="FILE_IN",
- type=Path,
- help="Tabular input samplesheet in CSV or TSV format.",
- )
- parser.add_argument(
- "file_out",
- metavar="FILE_OUT",
- type=Path,
- help="Transformed output samplesheet in CSV format.",
- )
- parser.add_argument(
- "-l",
- "--log-level",
- help="The desired log level (default WARNING).",
- choices=("CRITICAL", "ERROR", "WARNING", "INFO", "DEBUG"),
- default="WARNING",
- )
- return parser.parse_args(argv)
-
-
-def main(argv=None):
- """Coordinate argument parsing and program execution."""
- args = parse_args(argv)
- logging.basicConfig(level=args.log_level, format="[%(levelname)s] %(message)s")
- if not args.file_in.is_file():
- logger.error(f"The given input file {args.file_in} was not found!")
- sys.exit(2)
- args.file_out.parent.mkdir(parents=True, exist_ok=True)
- check_samplesheet(args.file_in, args.file_out)
-
-
-if __name__ == "__main__":
- sys.exit(main())
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/WorkflowMain.groovy b/lib/WorkflowMain.groovy
deleted file mode 100644
index 2f2008fb..00000000
--- a/lib/WorkflowMain.groovy
+++ /dev/null
@@ -1,68 +0,0 @@
-//
-// This file holds several functions specific to the main.nf workflow in the nf-core/mhcquant pipeline
-//
-
-import nextflow.Nextflow
-
-class WorkflowMain {
-
- //
- // Citation string for pipeline
- //
- public static String citation(workflow) {
- return "If you use ${workflow.manifest.name} for your analysis please cite:\n\n" +
- "* The pipeline publication\n" +
- " https://doi.org/10.1021/acs.jproteome.9b00313\n\n" +
- "* The pipeline\n" +
- " https://doi.org/10.5281/zenodo.1569909\n\n" +
- "* The nf-core framework\n" +
- " https://doi.org/10.1038/s41587-020-0439-x\n\n" +
- "* Software dependencies\n" +
- " https://github.com/${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} ${workflow_version}"
- System.exit(0)
- }
-
- // Check that a -profile or Nextflow config has been provided to run the pipeline
- NfcoreTemplate.checkConfigProvided(workflow, log)
- // Check that the profile doesn't contain spaces and doesn't end with a trailing comma
- checkProfile(workflow.profile, args, log)
-
- // Check that conda channels are set-up correctly
- if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) {
- Utils.checkCondaChannels(log)
- }
-
- // Check AWS batch settings
- NfcoreTemplate.awsBatch(workflow, params)
-
- // Check input has been provided
- if (!params.input) {
- log.error "Please provide an input samplesheet to the pipeline e.g. '--input samplesheet.tsv'"
- System.exit(1)
- }
- }
-
- //
- // Exit pipeline if --profile contains spaces
- //
- private static void checkProfile(profile, args, log) {
- if (profile.endsWith(',')) {
- Nextflow.error "Profile cannot end with a trailing comma. Please remove the comma from the end of the profile string.\nHint: A common mistake is to provide multiple values to `-profile` separated by spaces. Please use commas to separate profiles instead,e.g., `-profile docker,test`."
- }
- if (args[0]) {
- log.warn "nf-core pipelines do not accept positional arguments. The positional argument `${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/lib/WorkflowMhcquant.groovy b/lib/WorkflowMhcquant.groovy
deleted file mode 100644
index a99924b3..00000000
--- a/lib/WorkflowMhcquant.groovy
+++ /dev/null
@@ -1,214 +0,0 @@
-//
-// This file holds several functions specific to the workflow/mhcquant.nf in the nf-core/mhcquant pipeline
-//
-
-import nextflow.Nextflow
-import groovy.text.SimpleTemplateEngine
-
-class WorkflowMhcquant {
-
- //
- // Check and validate parameters
- //
- public static void initialise(params, log) {
-
- // Error raise when the database fasta is not included
- if (!params.fasta) {
- log.error "No database fasta was provided, make sure you have used the '--fasta' option."
- System.exit(1)
- }
-
- // Warning for the outpout dir (when not defined)
- if (!params.outdir) {
- outdirWarn(log)
- }
-
- // Database options
- if (params.skip_decoy_generation) {
- skipDecoyWarn(log)
- }
-
- // FDR Scoring
- if (params.klammer && params.description_correct_features == 0) {
- klammerConflictWarn(log)
- }
-
- // Quantification options
- if (params.quantification_fdr) {
- enabledFDRWarn(log)
- }
-
- // Allele sheet
- if ( ( params.predict_class_1 || params.predict_class_2 ) && !params.allele_sheet) {
- // If no allele sheet is provided
- noAllelesError(log)
- System.exit(1)
- }
-
- if ( params.include_proteins_from_vcf && !params.vcf_sheet) {
- // If no vcf sheet is provided
- noVcfError(log)
- System.exit(1)
- }
- }
-
- //
- // Print a warning when the output directory is undefined
- //
- private static void outdirWarn(log) {
- log.warn "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n" +
- " Results into \'./results\'.\n" +
- " If you want to define a result directory, please use the --outdir option" +
- "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~"
- }
-
- //
- // Print a warning when the parameter skip_decoy_generation is used
- //
- private static void skipDecoyWarn(log) {
- log.warn "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n" +
- " Be aware: skipping decoy generation will prevent generating variants and subset FDR refinement\n" +
- " Decoys have to be named with DECOY_ as prefix in your fasta database\n" +
- "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~"
- }
-
- //
- // Print a warning when the parameter skip_decoy_generation is used
- //
- private static void klammerConflictWarn(log) {
- log.warn "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n" +
- " Quantification FDR enabled\n" +
- "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~"
- }
-
- //
- // Print a warning when the parameter skip_decoy_generation is used
- //
- private static void enabledFDRWarn(log) {
- log.warn "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n" +
- " Klammer was specified, but description of correct features was still 0\n."+
- " Please provide a description of correct features greater than 0.\n" +
- " Klammer has been turned off!\n" +
- "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~"
- }
-
- //
- // Print an error when the no allele_sheet is provided
- //
- private static void noAllelesError(log) {
- log.error "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n" +
- " --predict_class_1 or --predict_class_2 was used but no allele sheet has been provided. \n" +
- " Make sure you have used the '--allele_sheet' option and include an allele sheet.\n" +
- "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~"
- }
-
- //
- // Print an error when there is no vcf_sheet provided
- //
- private static void noVcfError(log) {
- log.error "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n" +
- " --include_proteins_from_vcf was used but no vcf sheet has been provided. \n" +
- " Make sure you have used the '--vcf_sheet' option and include an vcf sheet.\n" +
- "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~"
- }
-
- //
- // 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 += " $group
\n" - summary_section += "| Process Name | -Software | -Version | -
|---|---|---|
| {process if (i == 0) else ''} | -{tool} | -{version} | -
| Process Name | \\n\\", - " \\ Software | \\nVersion | \\n
|---|---|---|
| CUSTOM_DUMPSOFTWAREVERSIONS | \\npython | \\n\\", - " \\3.11.7 | \\n
| \\n \\", - " \\ | yaml | \\n5.4.1 | \\n
| TOOL1 | \\ntool1 | \\n\\", - " \\0.11.9 | \\n
| TOOL2 | \\n\\", - " \\tool2 | \\n1.9 | \\n
| Workflow | \\nNextflow | \\n\\" - ], - [ - "CUSTOM_DUMPSOFTWAREVERSIONS:", - " python: 3.11.7", - " yaml: 5.4.1", - "TOOL1:", - " tool1: 0.11.9", - "TOOL2:", - " tool2: '1.9'", - "Workflow:" - ] - ], - "timestamp": "2024-01-09T23:01:18.710682" - } -} \ No newline at end of file diff --git a/modules/nf-core/custom/dumpsoftwareversions/tests/tags.yml b/modules/nf-core/custom/dumpsoftwareversions/tests/tags.yml deleted file mode 100644 index 405aa24a..00000000 --- a/modules/nf-core/custom/dumpsoftwareversions/tests/tags.yml +++ /dev/null @@ -1,2 +0,0 @@ -custom/dumpsoftwareversions: - - modules/nf-core/custom/dumpsoftwareversions/** diff --git a/modules/nf-core/multiqc/environment.yml b/modules/nf-core/multiqc/environment.yml index 7625b752..2212096a 100644 --- a/modules/nf-core/multiqc/environment.yml +++ b/modules/nf-core/multiqc/environment.yml @@ -4,4 +4,4 @@ channels: - bioconda - defaults dependencies: - - bioconda::multiqc=1.19 + - bioconda::multiqc=1.20 diff --git a/modules/nf-core/multiqc/main.nf b/modules/nf-core/multiqc/main.nf index 1b9f7c43..354f4430 100644 --- a/modules/nf-core/multiqc/main.nf +++ b/modules/nf-core/multiqc/main.nf @@ -3,8 +3,8 @@ process MULTIQC { conda "${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 b/modules/nf-core/multiqc/tests/main.nf.test index d0438eda..f1c4242e 100644 --- a/modules/nf-core/multiqc/tests/main.nf.test +++ b/modules/nf-core/multiqc/tests/main.nf.test @@ -3,6 +3,7 @@ nextflow_process { name "Test Process MULTIQC" script "../main.nf" process "MULTIQC" + tag "modules" tag "modules_nfcore" tag "multiqc" @@ -12,7 +13,7 @@ nextflow_process { when { process { """ - input[0] = Channel.of([file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz_fastqc_zip'], checkIfExists: true)]) + input[0] = Channel.of(file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastqc/test_fastqc.zip', checkIfExists: true)) input[1] = [] input[2] = [] input[3] = [] @@ -25,7 +26,7 @@ nextflow_process { { assert process.success }, { assert process.out.report[0] ==~ ".*/multiqc_report.html" }, { assert process.out.data[0] ==~ ".*/multiqc_data" }, - { assert snapshot(process.out.versions).match("versions") } + { assert snapshot(process.out.versions).match("multiqc_versions_single") } ) } @@ -36,7 +37,7 @@ nextflow_process { when { process { """ - input[0] = Channel.of([file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz_fastqc_zip'], checkIfExists: true)]) + input[0] = Channel.of(file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastqc/test_fastqc.zip', checkIfExists: true)) input[1] = Channel.of(file("https://github.com/nf-core/tools/raw/dev/nf_core/pipeline-template/assets/multiqc_config.yml", checkIfExists: true)) input[2] = [] input[3] = [] @@ -49,7 +50,7 @@ nextflow_process { { assert process.success }, { assert process.out.report[0] ==~ ".*/multiqc_report.html" }, { assert process.out.data[0] ==~ ".*/multiqc_data" }, - { assert snapshot(process.out.versions).match("versions") } + { assert snapshot(process.out.versions).match("multiqc_versions_config") } ) } } @@ -61,7 +62,7 @@ nextflow_process { when { process { """ - input[0] = Channel.of([file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz_fastqc_zip'], checkIfExists: true)]) + input[0] = Channel.of(file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastqc/test_fastqc.zip', checkIfExists: true)) input[1] = [] input[2] = [] input[3] = [] @@ -75,7 +76,7 @@ nextflow_process { { assert snapshot(process.out.report.collect { file(it).getName() } + process.out.data.collect { file(it).getName() } + process.out.plots.collect { file(it).getName() } + - process.out.versions ).match() } + process.out.versions ).match("multiqc_stub") } ) } diff --git a/modules/nf-core/multiqc/tests/main.nf.test.snap b/modules/nf-core/multiqc/tests/main.nf.test.snap index d37e7304..c204b488 100644 --- a/modules/nf-core/multiqc/tests/main.nf.test.snap +++ b/modules/nf-core/multiqc/tests/main.nf.test.snap @@ -1,21 +1,41 @@ { - "versions": { + "multiqc_versions_single": { "content": [ [ - "versions.yml:md5,14e9a2661241abd828f4f06a7b5c222d" + "versions.yml:md5,d320d4c37e349c5588e07e7a31cd4186" ] ], - "timestamp": "2024-01-09T23:02:49.911994" + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-02-14T09:28:51.744211298" }, - "sarscov2 single-end [fastqc] - stub": { + "multiqc_stub": { "content": [ [ "multiqc_report.html", "multiqc_data", "multiqc_plots", - "versions.yml:md5,14e9a2661241abd828f4f06a7b5c222d" + "versions.yml:md5,d320d4c37e349c5588e07e7a31cd4186" ] ], - "timestamp": "2024-01-09T23:03:14.524346" + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-02-14T09:29:28.847433492" + }, + "multiqc_versions_config": { + "content": [ + [ + "versions.yml:md5,d320d4c37e349c5588e07e7a31cd4186" + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-02-14T09:29:13.223621555" } } \ No newline at end of file diff --git a/modules/nf-core/openms/idfilter/main.nf b/modules/nf-core/openms/idfilter/main.nf index fdc9c13f..7bf16569 100644 --- a/modules/nf-core/openms/idfilter/main.nf +++ b/modules/nf-core/openms/idfilter/main.nf @@ -4,8 +4,8 @@ process OPENMS_IDFILTER { conda "bioconda::openms=3.1.0" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/openms:3.1.0--h8964181_3' : - 'biocontainers/openms:3.1.0--h8964181_3' }" + 'https://depot.galaxyproject.org/singularity/openms:3.1.0--h8964181_2' : + 'biocontainers/openms:3.1.0--h8964181_2' }" input: tuple val(meta), path(id_file), path(filter_file) diff --git a/nextflow.config b/nextflow.config index ea7a0f65..e126464d 100644 --- a/nextflow.config +++ b/nextflow.config @@ -76,12 +76,11 @@ params { deeplc_calibration_set_size = 0.15 // MultiQC options - skip_multiqc = false - multiqc_config = null - multiqc_title = null - multiqc_logo = null - max_multiqc_email_size = '25.MB' - multiqc_methods_description = null + multiqc_config = null + multiqc_title = null + multiqc_logo = null + max_multiqc_email_size = '25.MB' + multiqc_methods_description = null // Boilerplate options publish_dir_mode = 'copy' @@ -101,7 +100,6 @@ params { config_profile_contact = null config_profile_url = null - // Max resource options // Defaults only, expecting to be overwritten max_memory = '128.GB' diff --git a/nextflow_schema.json b/nextflow_schema.json index 9ee2aa80..5ebbcc7f 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -18,10 +18,9 @@ "help_text": "Use this to specify a sample sheet table including your input raw or mzml files as well as their meta information such as SampleID and Condition. For example:\n\n| ID | Sample | Condition | ReplicateFileName |\n| -----|:------------:| ----------:|------------------------------------------:|\n| 1 | MM15_Melanom | A | data/MM15_Melanom_W_1_A_standard.raw |\n| 2 | MM15_Melanom | B | data/MM15_Melanom_W_1_B_standard.raw |\n| 3 | MM17_Melanom | B | data/MM17_Melanom_W_1_B_standard.raw |\n\n```bash\n--input 'path/samples.tsv'\n```", "format": "file-path", "exists": true, - "mimetype": "text/csv", - "pattern": "^\\S+\\.tsv$", "schema": "assets/schema_input.json", - "fa_icon": "fas fa-file-csv" + "mimetype": "text/csv", + "pattern": "^\\S+\\.tsv$" }, "outdir": { "type": "string", @@ -457,13 +456,6 @@ "hidden": true, "fa_icon": "fas fa-users-cog" }, - "skip_multiqc": { - "type": "boolean", - "description": "Skip MultiQC.", - "fa_icon": "fas fa-fast-forward", - "hidden": true, - "default": false - }, "custom_config_base": { "type": "string", "description": "Base directory for Institutional configs.", diff --git a/pyproject.toml b/pyproject.toml index 7d08e1c8..56110621 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/input_check.nf b/subworkflows/local/input_check.nf deleted file mode 100644 index 835d7ae0..00000000 --- a/subworkflows/local/input_check.nf +++ /dev/null @@ -1,51 +0,0 @@ -// -// Check input samplesheet and get read channels -// - -include { SAMPLESHEET_CHECK } from '../../modules/local/samplesheet_check' - -workflow INPUT_CHECK { - take: - samplesheet // file: /path/to/samplesheet.csv - - main: - // Process the samplesheet and get the initial channels - def initial_channels = SAMPLESHEET_CHECK ( samplesheet ) - .csv - .splitCsv(header:true, sep:'\t') - .map { row -> [row.Sample + '_' + row.Condition, row] } - - // Group by sample_condition and count - def count_channels = initial_channels - .groupTuple() - .map { key, rows -> [rows, rows.size()] } - .flatMap { rows, count -> rows.collect { [it, count] } } - - ms_runs = count_channels.map { row, group_count -> create_ms_channel(row, group_count) } - - emit: - ms_runs // channel: [ val(meta), [ runs ] ] - versions = SAMPLESHEET_CHECK.out.versions // channel: [ versions.yml ] -} - -// Function to get list of [ meta, filenames ] -def create_ms_channel(LinkedHashMap row, int group_count) { - def meta = [:] - - meta.id = row.ID - meta.sample = row.Sample - meta.condition = row.Condition - meta.ext = row.Extension - meta.group_count = group_count - - // add path(s) of the data file(s) to the meta map - def ms_file = file(row.ReplicateFileName) - if (!ms_file.exists()) { - exit 1, "ERROR: Please check input samplesheet -> MS file does not exist!\n${row.ReplicateFileName}" - } - - meta.spectra = ms_file.baseName - ms_meta = [ meta, [ ms_file ] ] - - return ms_meta -} diff --git a/subworkflows/local/process_feature.nf b/subworkflows/local/process_feature.nf index 0e55e618..2b20b5f4 100644 --- a/subworkflows/local/process_feature.nf +++ b/subworkflows/local/process_feature.nf @@ -15,7 +15,7 @@ workflow PROCESS_FEATURE { // Quantify identifications using targeted feature extraction OPENMS_FEATUREFINDERIDENTIFICATION(ch_runs_to_be_quantified).featurexml - .map { meta, featurexml -> [ groupKey([id: meta.sample + '_' + meta.condition], meta.group_count), featurexml] } + .map { meta, featurexml -> [ groupKey([id: "${meta.sample}_${meta.condition}"], meta.group_count), featurexml] } .groupTuple() .set { ch_features_grouped } ch_versions = ch_versions.mix(OPENMS_FEATUREFINDERIDENTIFICATION.out.versions) diff --git a/subworkflows/local/quant.nf b/subworkflows/local/quant.nf index f72a98a5..a7dda954 100644 --- a/subworkflows/local/quant.nf +++ b/subworkflows/local/quant.nf @@ -50,14 +50,14 @@ workflow QUANT { // Manipulate such that [meta_run1, idxml_run1, pout_group1], [meta_run2, idxml_run2, pout_group1] ... ch_runs_score_switched // Nextflow can only combine/join on the exact groupKey object, merge_id is not sufficient - .map { meta, idxml -> [groupKey([id: meta.sample + '_' + meta.condition], meta.group_count) , meta, idxml] } + .map { meta, idxml -> [groupKey([id: "${meta.sample}_${meta.condition}"], meta.group_count) , meta, idxml] } .combine(filter_q_value, by:0) .map { group_meta, meta, idxml, q_value -> [meta, idxml, q_value] } .set { ch_runs_to_filter} // Filter runs based on fdr filtered coprocessed percolator output. OPENMS_IDFILTER_QUANT( ch_runs_to_filter ).filtered - .map { meta, idxml -> [ groupKey([id:meta.sample + '_' + meta.condition], meta.group_count), idxml] } + .map { meta, idxml -> [ groupKey([id:"${meta.sample}_${meta.condition}"], meta.group_count), idxml] } .groupTuple() .set { ch_runs_to_be_aligned } ch_versions = ch_versions.mix(OPENMS_IDFILTER_QUANT.out.versions) @@ -72,14 +72,14 @@ workflow QUANT { // We need to merge groupwise the aligned idxml files together to use them as id_ext in featurefinder OPENMS_IDMERGER_QUANT( MAP_ALIGNMENT.out.aligned_idxml - .map { meta, aligned_idxml -> [ groupKey([id: meta.sample + '_' + meta.condition], meta.group_count), aligned_idxml] } + .map { meta, aligned_idxml -> [ groupKey([id: "${meta.sample}_${meta.condition}"], meta.group_count), aligned_idxml] } .groupTuple()) ch_versions = ch_versions.mix(OPENMS_IDMERGER_QUANT.out.versions) // Manipulate channels such that we end up with : [meta, mzml, run_idxml, merged_runs_idxml] MAP_ALIGNMENT.out.aligned_mzml .join( MAP_ALIGNMENT.out.aligned_idxml ) - .map { meta, mzml, idxml -> [ groupKey([id: meta.sample + '_' + meta.condition], meta.group_count), meta, mzml, idxml] } + .map { meta, mzml, idxml -> [ groupKey([id: "${meta.sample}_${meta.condition}"], meta.group_count), meta, mzml, idxml] } .groupTuple() .map { group_meta, meta, mzml, idxml -> [group_meta, meta, mzml, idxml] } .join( OPENMS_IDMERGER_QUANT.out.idxml ) diff --git a/subworkflows/local/utils_nfcore_mhcquant_pipeline/main.nf b/subworkflows/local/utils_nfcore_mhcquant_pipeline/main.nf new file mode 100644 index 00000000..42a110f2 --- /dev/null +++ b/subworkflows/local/utils_nfcore_mhcquant_pipeline/main.nf @@ -0,0 +1,244 @@ +// +// 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