Fix strict syntax errors

lib/Utils.groovy

@@ -1,7 +1,7 @@
 import groovy.json.JsonSlurper
 
 
-class WorkflowScrnaseq {
+class Utils {
     // Retrieve the aligner-specific protocol based on the specified protocol.
     // Returns a map ["protocol": protocol, "extra_args": <extra args>, "whitelist": <path to whitelist>]
     // extra_args and whitelist are optional.

modules/local/parse_cellrangermulti_samplesheet.nf

@@ -5,7 +5,7 @@ process PARSE_CELLRANGERMULTI_SAMPLESHEET {
     //
 
     label 'process_low'
-    publishDir = [ enabled: false ]
+    publishDir enabled: false
 
     conda "conda-forge::python=3.9.5"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?

nextflow.config

@@ -228,7 +228,6 @@ profiles {
     test                 { includeConfig 'conf/test.config'                  }
     test_full            { includeConfig 'conf/test_full.config'             }
     test_cellrangermulti { includeConfig 'conf/test_cellranger_multi.config' }
-    test_multiome        { includeConfig 'conf/test_multiome.config'         }
 }
 
 // Load nf-core custom profiles from different institutions

subworkflows/local/align_cellrangermulti.nf

@@ -32,7 +32,7 @@ workflow CELLRANGER_MULTI_ALIGN {
         .map{ meta ->
             def meta_clone = meta.clone()
             def data_dict  = meta_clone.find{ it.key == "${meta_clone.feature_type}" }
-            fastqs = data_dict?.value
+            def fastqs = data_dict?.value
             meta_clone.remove( data_dict?.key )
             [ meta_clone, fastqs ]
         }
@@ -145,15 +145,14 @@ workflow CELLRANGER_MULTI_ALIGN {
             if ( params.gex_frna_probe_set && params.gex_reference_version ) {
                 def probeset_file = file(params.gex_frna_probe_set)
                 def probeset_reference = null
-                probeset_file.withReader { reader ->
-                    String line
-                    while ((line = reader.readLine()) != null) {
-                        if (line.startsWith("#reference_genome=")) {
-                            ref_split = line.split("=")
-                            if (ref_split.size() > 1) {
-                                probeset_reference = ref_split[1].trim()
-                            }
-                            break
+                def done = false
+                probeset_file.eachLine { line ->
+                    if (done)
+                        return
+                    if (line.startsWith("#reference_genome=")) {
+                        def ref_split = line.split("=")
+                        if (ref_split.size() > 1) {
+                            probeset_reference = ref_split[1].trim()
                         }
                     }
                 }
@@ -249,27 +248,27 @@ workflow CELLRANGER_MULTI_ALIGN {
 }
 
 def parse_demultiplexed_output_channels(in_ch, pattern) {
-    out_ch =
-    in_ch.map { meta, mtx_files ->
-        def desired_files = []
-        mtx_files.each{ if ( it.toString().contains("${pattern}") ) { desired_files.add( it ) } }
-        [ meta, desired_files ]
-    }                    // separate only desired files
-    .transpose()         // transpose for handling one meta/file pair at a time
-    .map { meta, mtx_files ->
-        def meta_clone = meta.clone()
-        meta_clone.input_type = pattern.contains('raw_') ? 'raw' : 'filtered' // add metadata for conversion workflow
-        if ( mtx_files.toString().contains("per_sample_outs") ) {
-            def demultiplexed_sample_id = mtx_files.toString().split('/per_sample_outs/')[1].split('/')[0]
-            if ( demultiplexed_sample_id.toString() == meta.id) {
-                return null
+    def out_ch = in_ch
+        .map { meta, mtx_files ->
+            def desired_files = []
+            mtx_files.each{ if ( it.toString().contains("${pattern}") ) { desired_files.add( it ) } }
+            [ meta, desired_files ]
+        }                    // separate only desired files
+        .transpose()         // transpose for handling one meta/file pair at a time
+        .map { meta, mtx_files ->
+            def meta_clone = meta.clone()
+            meta_clone.input_type = pattern.contains('raw_') ? 'raw' : 'filtered' // add metadata for conversion workflow
+            if ( mtx_files.toString().contains("per_sample_outs") ) {
+                def demultiplexed_sample_id = mtx_files.toString().split('/per_sample_outs/')[1].split('/')[0]
+                if ( demultiplexed_sample_id.toString() == meta.id) {
+                    return null
+                }
+                meta_clone.id = demultiplexed_sample_id.toString()
             }
-            meta_clone.id = demultiplexed_sample_id.toString()
-        }
-        [ meta_clone, mtx_files ]
-    }                    // check if output is from demultiplexed sample, if yes, correct meta.id for proper conversion naming
-    .filter{ it != null } // remove nulls from previous step
-    .groupTuple( by: 0 ) // group it back as one file collection per sample
+            [ meta_clone, mtx_files ]
+        }                    // check if output is from demultiplexed sample, if yes, correct meta.id for proper conversion naming
+        .filter{ it != null } // remove nulls from previous step
+        .groupTuple( by: 0 ) // group it back as one file collection per sample
 
     return out_ch
 }

subworkflows/local/kallisto_bustools.nf

@@ -5,8 +5,6 @@ include {KALLISTOBUSTOOLS_COUNT }             from '../../modules/nf-core/kallis
 include { GUNZIP }                      from '../../modules/nf-core/gunzip/main'
 include { KALLISTOBUSTOOLS_REF }        from '../../modules/nf-core/kallistobustools/ref/main'
 
-def multiqc_report    = []
-
 workflow KALLISTO_BUSTOOLS {
     take:
     genome_fasta

subworkflows/local/utils_nfcore_scrnaseq_pipeline/main.nf

@@ -235,7 +235,7 @@ def validateInputParameters() {
 // Validate cellranger_multi_barcodes samplesheet for uniqueness and conditional requirements
 //
 def validateCellrangerMultiBarcodes() {
-    cellranger_multi_barcodes = file(params.cellranger_multi_barcodes).splitCsv(header: true)
+    def cellranger_multi_barcodes = file(params.cellranger_multi_barcodes).splitCsv(header: true)
 
     // Get unique samples from input samplesheet for cross-validation
     def inputSamples = file(params.input).splitCsv(header: true).collect { it.sample }.toSet()