-[](https://github.com/nf-core/bamtofastq/actions?query=workflow%3A%22nf-core+CI%22)
-[](https://github.com/nf-core/bamtofastq/actions?query=workflow%3A%22nf-core+linting%22)[](https://nf-co.re/bamtofastq/results)[](https://doi.org/10.5281/zenodo.XXXXXXX)
+
+[](https://github.com/nf-core/bamtofastq/actions/workflows/ci.yml)
+[](https://github.com/nf-core/bamtofastq/actions/workflows/linting.yml)[](https://nf-co.re/bamtofastq/results)[](https://doi.org/10.5281/zenodo.XXXXXXX)
[](https://www.nextflow.io/)
[](https://docs.conda.io/en/latest/)
diff --git a/assets/multiqc_config.yml b/assets/multiqc_config.yml
index a11ef467..42c1cc33 100644
--- a/assets/multiqc_config.yml
+++ b/assets/multiqc_config.yml
@@ -13,3 +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 c22a9b4b..6899f501 100644
--- a/assets/schema_input.json
+++ b/assets/schema_input.json
@@ -10,25 +10,22 @@
"sample": {
"type": "string",
"pattern": "^\\S+$",
- "errorMessage": "Sample name must be provided and cannot contain spaces"
+ "errorMessage": "Sample name must be provided and cannot contain spaces",
+ "meta": ["id"]
},
"fastq_1": {
"type": "string",
+ "format": "file-path",
+ "exists": true,
"pattern": "^\\S+\\.f(ast)?q\\.gz$",
"errorMessage": "FastQ file for reads 1 must be provided, cannot contain spaces and must have extension '.fq.gz' or '.fastq.gz'"
},
"fastq_2": {
- "errorMessage": "FastQ file for reads 2 cannot contain spaces and must have extension '.fq.gz' or '.fastq.gz'",
- "anyOf": [
- {
- "type": "string",
- "pattern": "^\\S+\\.f(ast)?q\\.gz$"
- },
- {
- "type": "string",
- "maxLength": 0
- }
- ]
+ "type": "string",
+ "format": "file-path",
+ "exists": true,
+ "pattern": "^\\S+\\.f(ast)?q\\.gz$",
+ "errorMessage": "FastQ file for reads 2 cannot contain spaces and must have extension '.fq.gz' or '.fastq.gz'"
}
},
"required": ["sample", "fastq_1"]
diff --git a/bin/check_samplesheet.py b/bin/check_samplesheet.py
deleted file mode 100755
index 4a758fe0..00000000
--- a/bin/check_samplesheet.py
+++ /dev/null
@@ -1,259 +0,0 @@
-#!/usr/bin/env python
-
-
-"""Provide a command line tool to validate and transform tabular samplesheets."""
-
-
-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 = (
- ".fq.gz",
- ".fastq.gz",
- )
-
- def __init__(
- self,
- sample_col="sample",
- first_col="fastq_1",
- second_col="fastq_2",
- single_col="single_end",
- **kwargs,
- ):
- """
- Initialize the row checker with the expected column names.
-
- Args:
- sample_col (str): The name of the column that contains the sample name
- (default "sample").
- first_col (str): The name of the column that contains the first (or only)
- FASTQ file path (default "fastq_1").
- second_col (str): The name of the column that contains the second (if any)
- FASTQ file path (default "fastq_2").
- single_col (str): The name of the new column that will be inserted and
- records whether the sample contains single- or paired-end sequencing
- reads (default "single_end").
-
- """
- super().__init__(**kwargs)
- self._sample_col = sample_col
- self._first_col = first_col
- self._second_col = second_col
- self._single_col = single_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_sample(row)
- self._validate_first(row)
- self._validate_second(row)
- self._validate_pair(row)
- self._seen.add((row[self._sample_col], row[self._first_col]))
- self.modified.append(row)
-
- def _validate_sample(self, row):
- """Assert that the sample name exists and convert spaces to underscores."""
- if len(row[self._sample_col]) <= 0:
- raise AssertionError("Sample input is required.")
- # Sanitize samples slightly.
- row[self._sample_col] = row[self._sample_col].replace(" ", "_")
-
- def _validate_first(self, row):
- """Assert that the first FASTQ entry is non-empty and has the right format."""
- if len(row[self._first_col]) <= 0:
- raise AssertionError("At least the first FASTQ file is required.")
- self._validate_fastq_format(row[self._first_col])
-
- def _validate_second(self, row):
- """Assert that the second FASTQ entry has the right format if it exists."""
- if len(row[self._second_col]) > 0:
- self._validate_fastq_format(row[self._second_col])
-
- def _validate_pair(self, row):
- """Assert that read pairs have the same file extension. Report pair status."""
- if row[self._first_col] and row[self._second_col]:
- row[self._single_col] = False
- first_col_suffix = Path(row[self._first_col]).suffixes[-2:]
- second_col_suffix = Path(row[self._second_col]).suffixes[-2:]
- if first_col_suffix != second_col_suffix:
- raise AssertionError("FASTQ pairs must have the same file extensions.")
- else:
- row[self._single_col] = True
-
- def _validate_fastq_format(self, filename):
- """Assert that a given filename has one of the expected FASTQ extensions."""
- if not any(filename.endswith(extension) for extension in self.VALID_FORMATS):
- raise AssertionError(
- f"The FASTQ 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 FASTQ filename is unique.
-
- In addition to the validation, also rename all samples to have a suffix of _T{n}, where n is the
- number of times the same sample exist, but with different FASTQ files, e.g., multiple runs per experiment.
-
- """
- if len(self._seen) != len(self.modified):
- raise AssertionError("The pair of sample name and FASTQ must be unique.")
- seen = Counter()
- for row in self.modified:
- sample = row[self._sample_col]
- seen[sample] += 1
- row[self._sample_col] = f"{sample}_T{seen[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`_::
-
- sample,fastq_1,fastq_2
- SAMPLE_PE,SAMPLE_PE_RUN1_1.fastq.gz,SAMPLE_PE_RUN1_2.fastq.gz
- SAMPLE_PE,SAMPLE_PE_RUN2_1.fastq.gz,SAMPLE_PE_RUN2_2.fastq.gz
- SAMPLE_SE,SAMPLE_SE_RUN1_1.fastq.gz,
-
- .. _viral recon samplesheet:
- https://raw.githubusercontent.com/nf-core/test-datasets/viralrecon/samplesheet/samplesheet_test_illumina_amplicon.csv
-
- """
- required_columns = {"sample", "fastq_1", "fastq_2"}
- # 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(1, "single_end")
- # 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=",")
- writer.writeheader()
- for row in checker.modified:
- 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/conf/modules.config b/conf/modules.config
index d91c6aba..e3ea8fa6 100644
--- a/conf/modules.config
+++ b/conf/modules.config
@@ -18,14 +18,6 @@ process {
saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
]
- withName: SAMPLESHEET_CHECK {
- publishDir = [
- path: { "${params.outdir}/pipeline_info" },
- mode: params.publish_dir_mode,
- saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
- ]
- }
-
withName: FASTQC {
ext.args = '--quiet'
}
diff --git a/lib/NfcoreTemplate.groovy b/lib/NfcoreTemplate.groovy
deleted file mode 100755
index e248e4c3..00000000
--- a/lib/NfcoreTemplate.groovy
+++ /dev/null
@@ -1,356 +0,0 @@
-//
-// This file holds several functions used within the nf-core pipeline template.
-//
-
-import org.yaml.snakeyaml.Yaml
-import groovy.json.JsonOutput
-import nextflow.extension.FilesEx
-
-class NfcoreTemplate {
-
- //
- // Check AWS Batch related parameters have been specified correctly
- //
- public static void awsBatch(workflow, params) {
- if (workflow.profile.contains('awsbatch')) {
- // Check params.awsqueue and params.awsregion have been set if running on AWSBatch
- assert (params.awsqueue && params.awsregion) : "Specify correct --awsqueue and --awsregion parameters on AWSBatch!"
- // Check outdir paths to be S3 buckets if running on AWSBatch
- assert params.outdir.startsWith('s3:') : "Outdir not on S3 - specify S3 Bucket to run on AWSBatch!"
- }
- }
-
- //
- // Warn if a -profile or Nextflow config has not been provided to run the pipeline
- //
- public static void checkConfigProvided(workflow, log) {
- if (workflow.profile == 'standard' && workflow.configFiles.size() <= 1) {
- log.warn "[$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/WorkflowBamtofastq.groovy b/lib/WorkflowBamtofastq.groovy
deleted file mode 100755
index 88fd9fe1..00000000
--- a/lib/WorkflowBamtofastq.groovy
+++ /dev/null
@@ -1,122 +0,0 @@
-//
-// This file holds several functions specific to the workflow/bamtofastq.nf in the nf-core/bamtofastq pipeline
-//
-
-import nextflow.Nextflow
-import groovy.text.SimpleTemplateEngine
-
-class WorkflowBamtofastq {
-
- //
- // Check and validate parameters
- //
- public static void initialise(params, log) {
-
- genomeExistsError(params, log)
-
-
- if (!params.fasta) {
- Nextflow.error "Genome fasta file not specified with e.g. '--fasta genome.fa' or via a detectable config file."
- }
- }
-
- //
- // 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/fastqc/tests/main.nf.test b/modules/nf-core/fastqc/tests/main.nf.test index 1f21c664..70edae4d 100644 --- a/modules/nf-core/fastqc/tests/main.nf.test +++ b/modules/nf-core/fastqc/tests/main.nf.test @@ -33,7 +33,7 @@ nextflow_process { { assert process.out.zip[0][1] ==~ ".*/test_fastqc.zip" }, { assert path(process.out.html[0][1]).text.contains("|
| File type | Conventional base calls | |
| File type | Conventional base calls | |
| File type | Conventional base calls | |
| File type | Conventional base calls | |
| File type | Conventional base calls | |
| File type | Conventional base calls | |
| File type | Conventional base calls | |
| File type | Conventional base calls |