Add strict syntax support

modules.json

@@ -123,12 +123,12 @@
                     },
                     "utils_nfcore_pipeline": {
                         "branch": "master",
-                        "git_sha": "271e7fc14eb1320364416d996fb077421f3faed2",
+                        "git_sha": "f0b535b3ae20080f8db03dd5388876ad1ec29d70",
                         "installed_by": ["subworkflows"]
                     },
                     "utils_nfschema_plugin": {
                         "branch": "master",
-                        "git_sha": "4b406a74dc0449c0401ed87d5bfff4252fd277fd",
+                        "git_sha": "fdc08b8b1ae74f56686ce21f7ea11ad11990ce57",
                         "installed_by": ["subworkflows"]
                     }
                 }

modules/local/create_anndata_mudata/main.nf

@@ -31,7 +31,7 @@ process CREATE_ANNDATA_MUDATA {
     template 'create_anndata_mudata.py'
 
     stub:
-    def prefix = task.ext.prefix ?: "${meta.id}"
+    prefix = task.ext.prefix ?: "${meta.id}"
     """
     touch ${prefix}_genetic.h5ad
     touch ${prefix}_hashing.h5ad

modules/local/extract_hashes/main.nf

@@ -30,7 +30,7 @@ process EXTRACT_HASHES {
     """
 
     stub:
-    def prefix = task.ext.prefix ?: "${meta.id}"
+    prefix = task.ext.prefix ?: "${meta.id}"
 
     """
     touch ${prefix}_hashes.txt

modules/local/gene_summary/main.nf

@@ -31,7 +31,7 @@ process GENE_SUMMARY {
     template 'gene_summary.py'
 
     stub:
-    def prefix = task.ext.prefix ?: "${meta.id}"
+    prefix = task.ext.prefix ?: "${meta.id}"
     """
     touch ${prefix}_genetic_summary_assignment.csv
     touch ${prefix}_genetic_summary_classification.csv

modules/local/hash_summary/main.nf

@@ -36,7 +36,7 @@ process HASH_SUMMARY {
     template 'hash_summary.py'
 
     stub:
-    def prefix = task.ext.prefix ?: "${meta.id}"
+    prefix = task.ext.prefix ?: "${meta.id}"
     """
     touch ${prefix}_hashing_summary_assignment.csv
     touch ${prefix}_hashing_summary_classification.csv

modules/local/htodemux_visualization/main.nf

@@ -56,7 +56,7 @@ process HTODEMUX_VISUALIZATION {
     template 'htodemux_visualization.R'
 
     stub:
-    def prefix = task.ext.prefix ?: "${meta.id}"
+    prefix = task.ext.prefix ?: "${meta.id}"
     """
     touch ${prefix}_ridge_htodemux.jpeg
     touch ${prefix}_featureScatter_htodemux.jpeg

modules/local/preprocessing_for_htodemux_multiseq/main.nf

@@ -35,7 +35,7 @@ process PREPROCESSING_FOR_HTODEMUX_MULTISEQ {
     template 'pre_processing.R'
 
     stub:
-    def prefix = task.ext.prefix ?: "${meta.id}"
+    prefix = task.ext.prefix ?: "${meta.id}"
     """
     touch ${prefix}_preprocessed.rds
     touch ${prefix}_params_preprocessing.csv

subworkflows/local/genetic_demultiplexing/main.nf

@@ -131,7 +131,7 @@ workflow GENETIC_DEMULTIPLEXING {
         .join(ch_demuxlet, remainder: true)
         .join(ch_freemuxlet, remainder: true)
         .join(ch_souporcell, remainder: true)
-        .map { tuple -> tuple.collect { it == null ? [] : it } }
+        .map { tuple -> tuple.collect { val -> val == null ? [] : val } }
 
     GENE_SUMMARY(ch_summary)
 

subworkflows/local/hash_demultiplexing/main.nf

@@ -48,16 +48,6 @@ workflow HASH_DEMULTIPLEXING {
                 PREPROCESSING_FOR_HTODEMUX_MULTISEQ.out.seurat_object.map { meta, seurat_object -> [meta, seurat_object, "HTO"] }
             )
 
-            ch_assignments = HTODEMUX.out.assignment
-                .map { meta, assignment ->
-                    [meta, [result: assignment, method: 'htodemux_assignment']]
-                }
-
-            ch_classifications = HTODEMUX.out.classification
-                .map { meta, classification ->
-                    [meta, [result: classification, method: 'htodemux_classification']]
-                }
-
             ch_htodemux_assignments = ch_htodemux_assignments.mix(HTODEMUX.out.assignment)
             ch_htodemux_classifications = ch_htodemux_classifications.mix(HTODEMUX.out.classification)
 
@@ -112,7 +102,7 @@ workflow HASH_DEMULTIPLEXING {
                     meta,
                     hto,
                     params.gmmdemux_hto_names ? params.gmmdemux_hto_names : meta.hto_names,
-                    params.gmmdemux_estimated_n_cells ? gmmdemux_estimated_n_cells : [],
+                    params.gmmdemux_estimated_n_cells ? params.gmmdemux_estimated_n_cells : [],
                 ]
             }
 
@@ -159,7 +149,7 @@ workflow HASH_DEMULTIPLEXING {
         ch_versions = ch_versions.mix(HASHSOLO.out.versions)
     }
 
-    ch_summary = ch_samplesheet.map { meta, rna, hto -> [meta,hto] }
+    ch_summary = ch_samplesheet.map { meta, _rna, hto -> [meta,hto] }
         .join(ch_htodemux_assignments, remainder: true)
         .join(ch_htodemux_classifications, remainder: true)
         .join(ch_multiseq, remainder: true)
@@ -170,7 +160,7 @@ workflow HASH_DEMULTIPLEXING {
         .join(ch_hasheddrops_results, remainder: true)
         .join(ch_hasheddrops_id_to_hash, remainder: true)
         .join(ch_hashsolo, remainder: true)
-        .map { tuple -> tuple.collect { it == null ? [] : it } }
+        .map { tuple -> tuple.collect { val -> val == null ? [] : val } }
     // Empty inputs solved as recommended here:
     // https://nf-co.re/docs/guidelines/components/modules#optional-inputs
 

subworkflows/local/utils_nfcore_hadge_pipeline/main.nf

@@ -14,7 +14,6 @@ include { samplesheetToList         } from 'plugin/nf-schema'
 include { paramsHelp                } from 'plugin/nf-schema'
 include { completionEmail           } from '../../nf-core/utils_nfcore_pipeline'
 include { completionSummary         } 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 { UTILS_NEXTFLOW_PIPELINE   } from '../../nf-core/utils_nextflow_pipeline'
 
@@ -28,10 +27,10 @@ workflow PIPELINE_INITIALISATION {
     take:
     version           // boolean: Display version and exit
     validate_params   // boolean: Boolean whether to validate parameters against the schema at runtime
-    monochrome_logs   // boolean: Do not use coloured log outputs
+    _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
+    _input            //  string: Path to input samplesheet
     help              // boolean: Display help message and exit
     help_full         // boolean: Show the full help message
     show_hidden       // boolean: Show hidden parameters in the help message
@@ -148,9 +147,6 @@ workflow PIPELINE_COMPLETION {
         }
 
         completionSummary(monochrome_logs)
-        if (hook_url) {
-            imNotification(summary_params, hook_url)
-        }
     }
 
     workflow.onError {
@@ -214,8 +210,8 @@ def validateInputParameters() {
 //
 
 def validateHtoNames(Map meta){
-    if(meta.hto_names.split(",").any { it.contains('_') }){
-        def bad = meta.hto_names.split(",").findAll { it.contains('_') }.join(', ')
+    if(meta.hto_names.split(",").any { name -> name.contains('_') }){
+        def bad = meta.hto_names.split(",").findAll { name -> name.contains('_') }.join(', ')
         throw new IllegalArgumentException(
             "Running hadge with the methods htodemux or multiseq does not allow to use underscores ('_') in HTO names. Both tools require a SeuratObject as input, which will replace '_' with '-' leading to ambiguous or misleading assignment summaries. Please remove underscores ('_') from: ${bad}"
         )

workflows/hadge.nf

@@ -81,7 +81,7 @@ workflow HADGE {
                         }
 
     // create channels for deconvolution tools
-    ch_genetic = ch_preprocessed.map { meta, rna, _hto, bam, barcodes, vcf -> [meta, bam, barcodes, vcf] }
+    ch_genetic = ch_preprocessed.map { meta, _rna, _hto, bam, barcodes, vcf -> [meta, bam, barcodes, vcf] }
     ch_hashing = ch_preprocessed.map { meta, rna, hto, _bam, _barcodes, _vcf -> [meta, rna, hto] }
     ch_create_anndata_mudata = ch_preprocessed.map { meta, rna, hto, _bam, _barcodes, _vcf -> [meta, rna, hto] }
 
@@ -191,7 +191,7 @@ workflow HADGE {
         CREATE_ANNDATA_MUDATA(
             ch_create_anndata_mudata.map { tuple ->
                 // hto can be null in genetic mode
-                if (params.mode == 'genetic'){ tuple.collect { it == null ? [] : it } }
+                if (params.mode == 'genetic'){ tuple.collect { val -> val == null ? [] : val } }
                 else{ tuple }
             }
         )