Fix: update for Nextflow v2 parser's strict syntax requirements

.github/workflows/build.yml

@@ -18,7 +18,7 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: ["3.11"]
+        python-version: ["3.13"]
 
     steps:
       - uses: actions/checkout@v3

conf/base.config

@@ -10,10 +10,11 @@
 
 process {
 
-    // TODO nf-core: Check the defaults for all processes
-    cpus   = { check_max( 1    * task.attempt, 'cpus'   ) }
-    memory = { check_max( 6.GB * task.attempt, 'memory' ) }
-    time   = { check_max( 4.h  * task.attempt, 'time'   ) }
+    resourceLimits = [
+        cpus: params.max_cpus,
+        memory: params.max_memory,
+        time: params.max_time
+    ]
 
     errorStrategy = { task.exitStatus in ((130..145) + 104) ? 'retry' : 'finish' }
     maxRetries    = 1
@@ -27,30 +28,30 @@ process {
     // TODO nf-core: Customise requirements for specific processes.
     // See https://www.nextflow.io/docs/latest/config.html#config-process-selectors
     withLabel:process_single {
-        cpus   = { check_max( 1                  , 'cpus'    ) }
-        memory = { check_max( 6.GB * task.attempt, 'memory'  ) }
-        time   = { check_max( 4.h  * task.attempt, 'time'    ) }
+        cpus   = { 1 }
+        memory = { 6.GB * task.attempt }
+        time   = { 4.h  * task.attempt }
     }
     withLabel:process_low {
-        cpus   = { check_max( 2     * task.attempt, 'cpus'    ) }
-        memory = { check_max( 12.GB * task.attempt, 'memory'  ) }
-        time   = { check_max( 4.h   * task.attempt, 'time'    ) }
+        cpus   = { 2     * task.attempt }
+        memory = { 12.GB * task.attempt }
+        time   = { 4.h   * task.attempt }
     }
     withLabel:process_medium {
-        cpus   = { check_max( 6     * task.attempt, 'cpus'    ) }
-        memory = { check_max( 36.GB * task.attempt, 'memory'  ) }
-        time   = { check_max( 8.h   * task.attempt, 'time'    ) }
+        cpus   = { 6     * task.attempt }
+        memory = { 36.GB * task.attempt }
+        time   = { 8.h   * task.attempt }
     }
     withLabel:process_high {
-        cpus   = { check_max( 12    * task.attempt, 'cpus'    ) }
-        memory = { check_max( 72.GB * task.attempt, 'memory'  ) }
-        time   = { check_max( 16.h  * task.attempt, 'time'    ) }
+        cpus   = { 12    * task.attempt }
+        memory = { 72.GB * task.attempt }
+        time   = { 16.h  * task.attempt }
     }
     withLabel:process_long {
-        time   = { check_max( 20.h  * task.attempt, 'time'    ) }
+        time   = { 20.h  * task.attempt }
     }
     withLabel:process_high_memory {
-        memory = { check_max( 200.GB * task.attempt, 'memory' ) }
+        memory = { 200.GB * task.attempt }
     }
     withLabel:error_ignore {
         errorStrategy = 'ignore'
@@ -66,8 +67,8 @@ process {
 
     // Custom CCBR resource requirements
     withLabel:process_higher {
-        cpus   = { check_max( 32    * task.attempt, 'cpus'    ) }
-        memory = { check_max( 72.GB * task.attempt, 'memory'  ) }
-        time   = { check_max( 16.h  * task.attempt, 'time'    ) }
+        cpus   = { 32    * task.attempt }
+        memory = { 72.GB * task.attempt }
+        time   = { 16.h  * task.attempt }
     }
 }

main.nf

@@ -7,33 +7,25 @@ include { BAGEL       } from './subworkflows/local/bagel.nf'
 // MODULES
 include { DRUGZ } from './modules/local/drugz.nf'
 
-workflow.onComplete {
-    if (!workflow.stubRun && !workflow.commandLine.contains('-preview')) {
-        def message = Utils.spooker(workflow)
-        if (message) {
-            println message
-        }
-    }
-}
-
 // Plugins
 include { validateParameters; paramsSummaryLog } from 'plugin/nf-schema'
 
 workflow LOG {
-    log.info """\
-            CRISPIN 🍪 $workflow.manifest.version
-            ===================================
-            cmd line     : $workflow.commandLine
-            start time   : $workflow.start
-            launchDir    : $workflow.launchDir
-            input        : ${params.input}
-            """
-            .stripIndent()
+  log.info """\
+          CRISPIN 🍪 $workflow.manifest.version
+          ===================================
+          cmd line     : $workflow.commandLine
+          start time   : $workflow.start
+          launchDir    : $workflow.launchDir
+          input        : ${params.input}
+          """
+          .stripIndent()
 
-    log.info paramsSummaryLog(workflow)
+  log.info paramsSummaryLog(workflow)
 }
 
 workflow {
+    main:
     LOG()
     validateParameters()
     INPUT_CHECK(file(params.input))
@@ -67,4 +59,12 @@ workflow {
     if (params.bagel_run) {
         BAGEL(ch_count, control)
     }
+
+    onComplete:
+    if (!workflow.stubRun && !workflow.commandLine.contains('-preview')) {
+        def message = Utils.spooker(workflow)
+        if (message) {
+            println message
+        }
+    }
 }

nextflow.config

@@ -4,6 +4,7 @@ params {
     input = null
     library = null
     outdir = 'results'
+    tracedir = "${params.outdir}/pipeline_info"
     exp_name = 'crispin'
 
     count_table   = null
@@ -54,7 +55,7 @@ profiles {
     singularity {
         singularity.enabled = true
         singularity.autoMounts = true
-        singularity.cacheDir = "/data/$USER/.singularity" // TODO this may be a different default on other (non biowulf) platforms
+        singularity.cacheDir = '/data/$USER/.singularity' // TODO this may be a different default on other (non biowulf) platforms
         envWhitelist='https_proxy,http_proxy,ftp_proxy,DISPLAY,SLURM_JOBID,SINGULARITY_BINDPATH'
     }
     biowulf {
@@ -94,76 +95,40 @@ env {
 // Capture exit codes from upstream processes when piping
 process.shell = ['/bin/bash', '-euo', 'pipefail']
 
-def trace_timestamp = new java.util.Date().format('yyyy-MM-dd_HH-mm-ss')
 timeline {
     enabled = true
-    file    = "${params.outdir}/pipeline_info/execution_timeline_${trace_timestamp}.html"
+    file    = { "${params.tracedir}/execution_timeline_${new java.util.Date().format('yyyy-MM-dd_HH-mm-ss')}.html" }()
 }
 report {
     enabled = true
-    file    = "${params.outdir}/pipeline_info/execution_report_${trace_timestamp}.html"
+    file    = { "${params.tracedir}/execution_report_${new java.util.Date().format('yyyy-MM-dd_HH-mm-ss')}.html" }()
 }
 trace {
     enabled = true
-    file    = "${params.outdir}/pipeline_info/execution_trace_${trace_timestamp}.txt"
+    file    = { "${params.tracedir}/execution_trace_${new java.util.Date().format('yyyy-MM-dd_HH-mm-ss')}.txt" }()
 }
 dag {
     enabled = true
-    file    = "${params.outdir}/pipeline_info/pipeline_dag_${trace_timestamp}.png"
+    file    = { "${params.tracedir}/pipeline_dag_${new java.util.Date().format('yyyy-MM-dd_HH-mm-ss')}.png" }()
 }
 
 includeConfig 'conf/modules.config'
 
 plugins {
-    id 'nf-schema@2.2.1'
+    id 'nf-schema@2.7.2'
 }
 validation {
     help {
         enabled = true
     }
 }
 
-String pipeline_version = new File("${projectDir}/VERSION").text
-
 manifest {
     name = "CCBR/CRISPIN"
     author = "CCR Collaborative Bioinformatics Resource"
     homePage = "https://github.com/CCBR/CRISPIN"
     description = "CRISPR screen pipeline"
     mainScript = "main.nf"
     defaultBranch = "main"
-    version = "${pipeline_version}"
-}
-
-// Function to ensure that resource requirements don't go beyond
-// a maximum limit
-def check_max(obj, type) {
-    if (type == 'memory') {
-        try {
-            if (obj.compareTo(params.max_memory as nextflow.util.MemoryUnit) == 1)
-                return params.max_memory as nextflow.util.MemoryUnit
-            else
-                return obj
-        } catch (all) {
-            println "   ### ERROR ###   Max memory '${params.max_memory}' is not valid! Using default value: $obj"
-            return obj
-        }
-    } else if (type == 'time') {
-        try {
-            if (obj.compareTo(params.max_time as nextflow.util.Duration) == 1)
-                return params.max_time as nextflow.util.Duration
-            else
-                return obj
-        } catch (all) {
-            println "   ### ERROR ###   Max time '${params.max_time}' is not valid! Using default value: $obj"
-            return obj
-        }
-    } else if (type == 'cpus') {
-        try {
-            return Math.min( obj, params.max_cpus as int )
-        } catch (all) {
-            println "   ### ERROR ###   Max cpus '${params.max_cpus}' is not valid! Using default value: $obj"
-            return obj
-        }
-    }
+    version = { -> new File("${projectDir}/VERSION").text.trim() }()
 }