diff --git a/modules.json b/modules.json
index ea627ba..9d1ddfb 100644
--- a/modules.json
+++ b/modules.json
@@ -7,12 +7,12 @@
"nf-core": {
"fastqc": {
"branch": "master",
- "git_sha": "46eca555142d6e597729fcb682adcc791796f514",
+ "git_sha": "b49b8992e5271ce427f3a7cdb29628fc58400eb5",
"installed_by": ["modules"]
},
"multiqc": {
"branch": "master",
- "git_sha": "b80f5fd12ff7c43938f424dd76392a2704fa2396",
+ "git_sha": "19ca321db5d8bd48923262c2eca6422359633491",
"installed_by": ["modules"]
},
"quartonotebook": {
@@ -37,12 +37,12 @@
"nf-core": {
"utils_nextflow_pipeline": {
"branch": "master",
- "git_sha": "5caf7640a9ef1d18d765d55339be751bb0969dfa",
+ "git_sha": "d20fb2a9cc3e2835e9d067d1046a63252eb17352",
"installed_by": ["subworkflows"]
},
"utils_nfcore_pipeline": {
"branch": "master",
- "git_sha": "92de218a329bfc9a9033116eb5f65fd270e72ba3",
+ "git_sha": "2fdce49d30c0254f76bc0f13c55c17455c1251ab",
"installed_by": ["subworkflows"]
},
"utils_nfvalidation_plugin": {
diff --git a/modules/nf-core/fastqc/main.nf b/modules/nf-core/fastqc/main.nf
index d79f1c8..d8989f4 100644
--- a/modules/nf-core/fastqc/main.nf
+++ b/modules/nf-core/fastqc/main.nf
@@ -26,7 +26,10 @@ process FASTQC {
def rename_to = old_new_pairs*.join(' ').join(' ')
def renamed_files = old_new_pairs.collect{ old_name, new_name -> new_name }.join(' ')
- def memory_in_mb = MemoryUnit.of("${task.memory}").toUnit('MB')
+ // The total amount of allocated RAM by FastQC is equal to the number of threads defined (--threads) time the amount of RAM defined (--memory)
+ // https://github.com/s-andrews/FastQC/blob/1faeea0412093224d7f6a07f777fad60a5650795/fastqc#L211-L222
+ // Dividing the task.memory by task.cpu allows to stick to requested amount of RAM in the label
+ def memory_in_mb = MemoryUnit.of("${task.memory}").toUnit('MB') / task.cpus
// FastQC memory value allowed range (100 - 10000)
def fastqc_memory = memory_in_mb > 10000 ? 10000 : (memory_in_mb < 100 ? 100 : memory_in_mb)
diff --git a/modules/nf-core/multiqc/environment.yml b/modules/nf-core/multiqc/environment.yml
index 2121492..a31464c 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=1.23
+ - bioconda::multiqc=1.24.1
diff --git a/modules/nf-core/multiqc/main.nf b/modules/nf-core/multiqc/main.nf
index 459dfea..ceaec13 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:1.23--pyhdfd78af_0' :
- 'biocontainers/multiqc:1.23--pyhdfd78af_0' }"
+ 'https://depot.galaxyproject.org/singularity/multiqc:1.24.1--pyhdfd78af_0' :
+ 'biocontainers/multiqc:1.24.1--pyhdfd78af_0' }"
input:
path multiqc_files, stageAs: "?/*"
@@ -25,9 +25,10 @@ process MULTIQC {
script:
def args = task.ext.args ?: ''
+ def prefix = task.ext.prefix ? "--filename ${task.ext.prefix}.html" : ''
def config = multiqc_config ? "--config $multiqc_config" : ''
def extra_config = extra_multiqc_config ? "--config $extra_multiqc_config" : ''
- def logo = multiqc_logo ? /--cl-config 'custom_logo: "${multiqc_logo}"'/ : ''
+ def logo = multiqc_logo ? "--cl-config 'custom_logo: \"${multiqc_logo}\"'" : ''
def replace = replace_names ? "--replace-names ${replace_names}" : ''
def samples = sample_names ? "--sample-names ${sample_names}" : ''
"""
@@ -35,6 +36,7 @@ process MULTIQC {
--force \\
$args \\
$config \\
+ $prefix \\
$extra_config \\
$logo \\
$replace \\
diff --git a/modules/nf-core/multiqc/tests/main.nf.test b/modules/nf-core/multiqc/tests/main.nf.test
index 6aa27f4..33316a7 100644
--- a/modules/nf-core/multiqc/tests/main.nf.test
+++ b/modules/nf-core/multiqc/tests/main.nf.test
@@ -8,6 +8,8 @@ nextflow_process {
tag "modules_nfcore"
tag "multiqc"
+ config "./nextflow.config"
+
test("sarscov2 single-end [fastqc]") {
when {
diff --git a/modules/nf-core/multiqc/tests/main.nf.test.snap b/modules/nf-core/multiqc/tests/main.nf.test.snap
index 45e95e5..83fa080 100644
--- a/modules/nf-core/multiqc/tests/main.nf.test.snap
+++ b/modules/nf-core/multiqc/tests/main.nf.test.snap
@@ -2,7 +2,7 @@
"multiqc_versions_single": {
"content": [
[
- "versions.yml:md5,87904cd321df21fac35d18f0fc01bb19"
+ "versions.yml:md5,6eb13f3b11bbcbfc98ad3166420ff760"
]
],
"meta": {
@@ -17,7 +17,7 @@
"multiqc_report.html",
"multiqc_data",
"multiqc_plots",
- "versions.yml:md5,87904cd321df21fac35d18f0fc01bb19"
+ "versions.yml:md5,6eb13f3b11bbcbfc98ad3166420ff760"
]
],
"meta": {
@@ -29,7 +29,7 @@
"multiqc_versions_config": {
"content": [
[
- "versions.yml:md5,87904cd321df21fac35d18f0fc01bb19"
+ "versions.yml:md5,6eb13f3b11bbcbfc98ad3166420ff760"
]
],
"meta": {
@@ -38,4 +38,4 @@
},
"timestamp": "2024-07-10T11:26:56.709849369"
}
-}
\ No newline at end of file
+}
diff --git a/modules/nf-core/multiqc/tests/nextflow.config b/modules/nf-core/multiqc/tests/nextflow.config
new file mode 100644
index 0000000..c537a6a
--- /dev/null
+++ b/modules/nf-core/multiqc/tests/nextflow.config
@@ -0,0 +1,5 @@
+process {
+ withName: 'MULTIQC' {
+ ext.prefix = null
+ }
+}
diff --git a/subworkflows/nf-core/utils_nextflow_pipeline/main.nf b/subworkflows/nf-core/utils_nextflow_pipeline/main.nf
index ac31f28..28e32b2 100644
--- a/subworkflows/nf-core/utils_nextflow_pipeline/main.nf
+++ b/subworkflows/nf-core/utils_nextflow_pipeline/main.nf
@@ -2,10 +2,6 @@
// Subworkflow with functionality that may be useful for any Nextflow pipeline
//
-import org.yaml.snakeyaml.Yaml
-import groovy.json.JsonOutput
-import nextflow.extension.FilesEx
-
/*
========================================================================================
SUBWORKFLOW DEFINITION
@@ -58,7 +54,7 @@ workflow UTILS_NEXTFLOW_PIPELINE {
// Generate version string
//
def getWorkflowVersion() {
- String version_string = ""
+ def version_string = "" as String
if (workflow.manifest.version) {
def prefix_v = workflow.manifest.version[0] != 'v' ? 'v' : ''
version_string += "${prefix_v}${workflow.manifest.version}"
@@ -79,10 +75,10 @@ def dumpParametersToJSON(outdir) {
def timestamp = new java.util.Date().format( 'yyyy-MM-dd_HH-mm-ss')
def filename = "params_${timestamp}.json"
def temp_pf = new File(workflow.launchDir.toString(), ".${filename}")
- def jsonStr = JsonOutput.toJson(params)
- temp_pf.text = JsonOutput.prettyPrint(jsonStr)
+ def jsonStr = groovy.json.JsonOutput.toJson(params)
+ temp_pf.text = groovy.json.JsonOutput.prettyPrint(jsonStr)
- FilesEx.copyTo(temp_pf.toPath(), "${outdir}/pipeline_info/params_${timestamp}.json")
+ nextflow.extension.FilesEx.copyTo(temp_pf.toPath(), "${outdir}/pipeline_info/params_${timestamp}.json")
temp_pf.delete()
}
@@ -90,7 +86,7 @@ def dumpParametersToJSON(outdir) {
// When running with -profile conda, warn if channels have not been set-up appropriately
//
def checkCondaChannels() {
- Yaml parser = new Yaml()
+ def parser = new org.yaml.snakeyaml.Yaml()
def channels = []
try {
def config = parser.load("conda config --show channels".execute().text)
@@ -102,14 +98,16 @@ def checkCondaChannels() {
// 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 required_channels_in_order = ['conda-forge', 'bioconda']
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]))
+
+ required_channels_in_order.eachWithIndex { channel, index ->
+ if (index < required_channels_in_order.size() - 1) {
+ channel_priority_violation |= !(channels.indexOf(channel) < channels.indexOf(required_channels_in_order[index+1]))
+ }
}
if (channels_missing | channel_priority_violation) {
diff --git a/subworkflows/nf-core/utils_nextflow_pipeline/tests/nextflow.config b/subworkflows/nf-core/utils_nextflow_pipeline/tests/nextflow.config
index d0a926b..a09572e 100644
--- a/subworkflows/nf-core/utils_nextflow_pipeline/tests/nextflow.config
+++ b/subworkflows/nf-core/utils_nextflow_pipeline/tests/nextflow.config
@@ -3,7 +3,7 @@ manifest {
author = """nf-core"""
homePage = 'https://127.0.0.1'
description = """Dummy pipeline"""
- nextflowVersion = '!>=23.04.0'
+ nextflowVersion = '!>=23.04.0'
version = '9.9.9'
doi = 'https://doi.org/10.5281/zenodo.5070524'
}
diff --git a/subworkflows/nf-core/utils_nfcore_pipeline/main.nf b/subworkflows/nf-core/utils_nfcore_pipeline/main.nf
index 14558c3..cbd8495 100644
--- a/subworkflows/nf-core/utils_nfcore_pipeline/main.nf
+++ b/subworkflows/nf-core/utils_nfcore_pipeline/main.nf
@@ -2,9 +2,6 @@
// Subworkflow with utility functions specific to the nf-core pipeline template
//
-import org.yaml.snakeyaml.Yaml
-import nextflow.extension.FilesEx
-
/*
========================================================================================
SUBWORKFLOW DEFINITION
@@ -34,7 +31,7 @@ workflow UTILS_NFCORE_PIPELINE {
// Warn if a -profile or Nextflow config has not been provided to run the pipeline
//
def checkConfigProvided() {
- valid_config = true
+ def valid_config = true as Boolean
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" +
@@ -66,11 +63,13 @@ def checkProfileProvided(nextflow_cli_args) {
//
def workflowCitation() {
def temp_doi_ref = ""
- String[] manifest_doi = workflow.manifest.doi.tokenize(",")
+ def manifest_doi = workflow.manifest.doi.tokenize(",")
// Using a loop to handle multiple DOIs
// Removing `https://doi.org/` to handle pipelines using DOIs vs DOI resolvers
// Removing ` ` since the manifest.doi is a string and not a proper list
- for (String doi_ref: manifest_doi) temp_doi_ref += " https://doi.org/${doi_ref.replace('https://doi.org/', '').replace(' ', '')}\n"
+ manifest_doi.each { doi_ref ->
+ temp_doi_ref += " https://doi.org/${doi_ref.replace('https://doi.org/', '').replace(' ', '')}\n"
+ }
return "If you use ${workflow.manifest.name} for your analysis please cite:\n\n" +
"* The pipeline\n" +
temp_doi_ref + "\n" +
@@ -84,7 +83,7 @@ def workflowCitation() {
// Generate workflow version string
//
def getWorkflowVersion() {
- String version_string = ""
+ def version_string = "" as String
if (workflow.manifest.version) {
def prefix_v = workflow.manifest.version[0] != 'v' ? 'v' : ''
version_string += "${prefix_v}${workflow.manifest.version}"
@@ -102,8 +101,8 @@ def getWorkflowVersion() {
// Get software versions for pipeline
//
def processVersionsFromYAML(yaml_file) {
- Yaml yaml = new Yaml()
- versions = yaml.load(yaml_file).collectEntries { k, v -> [ k.tokenize(':')[-1], v ] }
+ def yaml = new org.yaml.snakeyaml.Yaml()
+ def versions = yaml.load(yaml_file).collectEntries { k, v -> [ k.tokenize(':')[-1], v ] }
return yaml.dumpAsMap(versions).trim()
}
@@ -124,7 +123,7 @@ def workflowVersionToYAML() {
def softwareVersionsToYAML(ch_versions) {
return ch_versions
.unique()
- .map { processVersionsFromYAML(it) }
+ .map { version -> processVersionsFromYAML(version) }
.unique()
.mix(Channel.of(workflowVersionToYAML()))
}
@@ -134,19 +133,19 @@ def softwareVersionsToYAML(ch_versions) {
//
def paramsSummaryMultiqc(summary_params) {
def summary_section = ''
- for (group in summary_params.keySet()) {
+ summary_params.keySet().each { group ->
def group_params = summary_params.get(group) // This gets the parameters of that particular group
if (group_params) {
summary_section += " $group
\n"
summary_section += " \n"
- for (param in group_params.keySet()) {
+ group_params.keySet().sort().each { param ->
summary_section += " - $param
- ${group_params.get(param) ?: 'N/A'}
\n"
}
summary_section += "
\n"
}
}
- String yaml_file_text = "id: '${workflow.manifest.name.replace('/','-')}-summary'\n"
+ def yaml_file_text = "id: '${workflow.manifest.name.replace('/','-')}-summary'\n" as String
yaml_file_text += "description: ' - this information is collected when the pipeline is started.'\n"
yaml_file_text += "section_name: '${workflow.manifest.name} Workflow Summary'\n"
yaml_file_text += "section_href: 'https://github.com/${workflow.manifest.name}'\n"
@@ -161,7 +160,7 @@ def paramsSummaryMultiqc(summary_params) {
// nf-core logo
//
def nfCoreLogo(monochrome_logs=true) {
- Map colors = logColours(monochrome_logs)
+ def colors = logColours(monochrome_logs) as Map
String.format(
"""\n
${dashedLine(monochrome_logs)}
@@ -180,7 +179,7 @@ def nfCoreLogo(monochrome_logs=true) {
// Return dashed line
//
def dashedLine(monochrome_logs=true) {
- Map colors = logColours(monochrome_logs)
+ def colors = logColours(monochrome_logs) as Map
return "-${colors.dim}----------------------------------------------------${colors.reset}-"
}
@@ -188,7 +187,7 @@ def dashedLine(monochrome_logs=true) {
// ANSII colours used for terminal logging
//
def logColours(monochrome_logs=true) {
- Map colorcodes = [:]
+ def colorcodes = [:] as Map
// Reset / Meta
colorcodes['reset'] = monochrome_logs ? '' : "\033[0m"
@@ -287,7 +286,7 @@ def completionEmail(summary_params, email, email_on_fail, plaintext_email, outdi
}
def summary = [:]
- for (group in summary_params.keySet()) {
+ summary_params.keySet().sort().each { group ->
summary << summary_params[group]
}
@@ -344,10 +343,10 @@ def completionEmail(summary_params, email, email_on_fail, plaintext_email, outdi
def sendmail_html = sendmail_template.toString()
// Send the HTML e-mail
- Map colors = logColours(monochrome_logs)
+ def colors = logColours(monochrome_logs) as Map
if (email_address) {
try {
- if (plaintext_email) { throw GroovyException('Send plaintext e-mail, not HTML') }
+ if (plaintext_email) { throw new org.codehaus.groovy.GroovyException('Send plaintext e-mail, not HTML') }
// Try to send HTML e-mail using sendmail
def sendmail_tf = new File(workflow.launchDir.toString(), ".sendmail_tmp.html")
sendmail_tf.withWriter { w -> w << sendmail_html }
@@ -364,13 +363,13 @@ def completionEmail(summary_params, email, email_on_fail, plaintext_email, outdi
// Write summary e-mail HTML to a file
def output_hf = new File(workflow.launchDir.toString(), ".pipeline_report.html")
output_hf.withWriter { w -> w << email_html }
- FilesEx.copyTo(output_hf.toPath(), "${outdir}/pipeline_info/pipeline_report.html");
+ nextflow.extension.FilesEx.copyTo(output_hf.toPath(), "${outdir}/pipeline_info/pipeline_report.html");
output_hf.delete()
// Write summary e-mail TXT to a file
def output_tf = new File(workflow.launchDir.toString(), ".pipeline_report.txt")
output_tf.withWriter { w -> w << email_txt }
- FilesEx.copyTo(output_tf.toPath(), "${outdir}/pipeline_info/pipeline_report.txt");
+ nextflow.extension.FilesEx.copyTo(output_tf.toPath(), "${outdir}/pipeline_info/pipeline_report.txt");
output_tf.delete()
}
@@ -378,7 +377,7 @@ def completionEmail(summary_params, email, email_on_fail, plaintext_email, outdi
// Print pipeline summary on completion
//
def completionSummary(monochrome_logs=true) {
- Map colors = logColours(monochrome_logs)
+ def colors = logColours(monochrome_logs) as Map
if (workflow.success) {
if (workflow.stats.ignoredCount == 0) {
log.info "-${colors.purple}[$workflow.manifest.name]${colors.green} Pipeline completed successfully${colors.reset}-"
@@ -395,7 +394,7 @@ def completionSummary(monochrome_logs=true) {
//
def imNotification(summary_params, hook_url) {
def summary = [:]
- for (group in summary_params.keySet()) {
+ summary_params.keySet().sort().each { group ->
summary << summary_params[group]
}