refactor: lowercase channel factory across subworkflows + workflows

subworkflows/local/call.nf

@@ -38,13 +38,13 @@ workflow CALL {
         .set { ch_collected_faa }   // Set the resulting list to ch_collected_faa
 
     // Collect all individual fasta to pass to quast
-    Channel.empty()
+    channel.empty()
         .mix( ch_called_genes  )
         .collect()
         .set { ch_collected_fna }
 
     // Collect all individual fasta to pass to quast
-    Channel.empty()
+    channel.empty()
         .mix( ch_filtered_fasta, ch_gene_gff  )
         .collect()
         .set { ch_collected_fasta }

subworkflows/local/collect_rna.nf

@@ -33,7 +33,7 @@ workflow COLLECT_RNA {
     // If we didn't run call
     if (!call) {
         if (params.rrnas) {
-            Channel.fromPath("${params.rrnas}/*.tsv", checkIfExists: true)
+            channel.fromPath("${params.rrnas}/*.tsv", checkIfExists: true)
                 .ifEmpty { exit 1, "Cannot find individual rRNA files generated with barrnap at: ${params.rrnas}\nNB: Path needs to follow pattern: path/to/directory" }
                 .collect()
                 .set { ch_collected_rRNAs }
@@ -43,7 +43,7 @@ workflow COLLECT_RNA {
             log.warn("No rRNA files provided, skipping rRNA steps.")
         }
         if (params.trnas) {
-            Channel.fromPath("${params.trnas}/*.tsv", checkIfExists: true)
+            channel.fromPath("${params.trnas}/*.tsv", checkIfExists: true)
                 .ifEmpty { exit 1, "Cannot find individual tRNA files generated with tRNAscan-SE. Cannot find any files at: ${params.trnas}\nNB: Path needs to follow pattern: path/to/directory" }
                 .collect()
                 .set { ch_collected_tRNAs }
@@ -57,14 +57,14 @@ workflow COLLECT_RNA {
         TRNA_SCAN( ch_fasta )
         ch_trna_scan = TRNA_SCAN.out.trna_scan_out
         // Collect all input_fasta formatted tRNA files
-        Channel.empty()
+        channel.empty()
             .mix( ch_trna_scan )
             .collect()
             .set { ch_collected_tRNAs }
         // Run barrnap on each fasta to identify rRNAs
         RRNA_SCAN( ch_fasta )
         ch_rrna_scan = RRNA_SCAN.out.rrna_scan_out
-        Channel.empty()
+        channel.empty()
             .mix( ch_rrna_scan )
             .collect()
             .set { ch_collected_rRNAs }

subworkflows/local/db_search.nf

@@ -402,29 +402,29 @@ workflow DB_CHANNEL_SETUP {
     main:
 
     index_mmseqs = false
-    ch_kegg_db = Channel.empty()
-    ch_kofam_db = Channel.empty()
-    ch_dbcan_db = Channel.empty()
-    ch_camper_hmm_db = Channel.empty()
-    ch_camper_mmseqs_db = Channel.empty()
-    ch_camper_mmseqs_list = Channel.empty()
-    ch_merops_db = Channel.empty()
-    ch_pfam_mmseqs_db = Channel.empty()
-    ch_heme_db = Channel.empty()
-    ch_sulfur_db = Channel.empty()
-    ch_uniref_db = Channel.empty()
-    ch_metals_db = Channel.empty()
-    ch_antismash_db = Channel.empty()
-    ch_card_db = Channel.empty()
-    ch_tcdb_db = Channel.empty()
-    ch_dram_db = Channel.empty()
-    ch_methyl_db = Channel.empty()
-    ch_fegenie_db = Channel.empty()
-    ch_canthyd_hmm_db = Channel.empty()
-    ch_canthyd_mmseqs_db = Channel.empty()
-    ch_canthyd_mmseqs_list = Channel.empty()
-    ch_vogdb_db = Channel.empty()
-    ch_viral_db = Channel.empty()
+    ch_kegg_db = channel.empty()
+    ch_kofam_db = channel.empty()
+    ch_dbcan_db = channel.empty()
+    ch_camper_hmm_db = channel.empty()
+    ch_camper_mmseqs_db = channel.empty()
+    ch_camper_mmseqs_list = channel.empty()
+    ch_merops_db = channel.empty()
+    ch_pfam_mmseqs_db = channel.empty()
+    ch_heme_db = channel.empty()
+    ch_sulfur_db = channel.empty()
+    ch_uniref_db = channel.empty()
+    ch_metals_db = channel.empty()
+    ch_antismash_db = channel.empty()
+    ch_card_db = channel.empty()
+    ch_tcdb_db = channel.empty()
+    ch_dram_db = channel.empty()
+    ch_methyl_db = channel.empty()
+    ch_fegenie_db = channel.empty()
+    ch_canthyd_hmm_db = channel.empty()
+    ch_canthyd_mmseqs_db = channel.empty()
+    ch_canthyd_mmseqs_list = channel.empty()
+    ch_vogdb_db = channel.empty()
+    ch_viral_db = channel.empty()
 
     if (use_kegg) {
         ch_kegg_db = file(params.kegg_db).exists() ? file(params.kegg_db) : error("Error: If using --annotate, you must supply prebuilt databases. KEGG database file not found at ${params.kegg_db}")

subworkflows/local/merge.nf

@@ -31,10 +31,10 @@ workflow MERGE {
     }
 
     // Create a channel with the paths to the .tsv files
-    Channel
+    channel
         .from(tsv_files.collect { annotations_dir.toString() + '/' + it })
         .set { ch_merge_annotations }
-    Channel.empty()
+    channel.empty()
         .mix( ch_merge_annotations )
         .collect()
         .set { ch_merge_annotations_collected }

subworkflows/local/qc.nf

@@ -49,15 +49,15 @@ workflow QC {
 
     if( params.generate_gff || params.generate_gbk ){
         if (!call) {
-            ch_called_genes = Channel
+            ch_called_genes = channel
                 .fromPath(file(params.input_genes) / params.genes_fna_fmt, checkIfExists: true)
                 .ifEmpty { exit 1, "If you specify --generate_gff or --generate_gbk without --call, you must provide a fasta file of called genes using --input_genes and --genes_fna_fmt,. Cannot find any called gene fasta files matching: ${params.input_genes} and ${params.genes_fna_fmt}\nNB: Path needs to follow pattern: path/to/directory/" }
                 .map {
                     input_fastaName = it.getBaseName()
                     tuple(input_fastaName, it)
                 }
             // Collect all individual fasta to pass to quast
-            Channel.empty()
+            channel.empty()
                 .mix( ch_called_genes  )
                 .collect()
                 .set { ch_collected_fna }

subworkflows/local/utils_nfcore_dram_pipeline/main.nf

@@ -41,7 +41,7 @@ workflow PIPELINE_INITIALISATION {
 
     main:
 
-    ch_versions = Channel.empty()
+    ch_versions = channel.empty()
 
     //
     // Print version and exit if required and dump pipeline parameters to JSON file

subworkflows/nf-core/utils_nfcore_pipeline/main.nf

@@ -98,7 +98,7 @@ def workflowVersionToYAML() {
 // Get channel of software versions used in pipeline in YAML format
 //
 def softwareVersionsToYAML(ch_versions) {
-    return ch_versions.unique().map { version -> processVersionsFromYAML(version) }.unique().mix(Channel.of(workflowVersionToYAML()))
+    return ch_versions.unique().map { version -> processVersionsFromYAML(version) }.unique().mix(channel.of(workflowVersionToYAML()))
 }
 
 //

workflows/dram.nf

@@ -36,9 +36,9 @@ workflow DRAM {
     // Setup
     //
 
-    ch_versions = Channel.empty()
-    ch_multiqc_files = Channel.empty()
-    ch_fasta = Channel.empty()
+    ch_versions = channel.empty()
+    ch_multiqc_files = channel.empty()
+    ch_fasta = channel.empty()
 
     default_sheet = file(params.distill_dummy_sheet)
     distill_flag = (params.summarize || params.distill_topic != "" || params.distill_ecosystem != "" || params.distill_custom != "" || params.sum_ecos != "")
@@ -59,7 +59,7 @@ workflow DRAM {
     }
 
     if (params.input_fasta && (params.rename || call)) {
-        ch_fasta = Channel
+        ch_fasta = channel
             .fromPath(file(params.input_fasta) / params.fasta_fmt, checkIfExists: true)
                 .ifEmpty { exit 1, "Cannot find any fasta files matching: ${params.input_fasta}\nNB: Path needs to follow pattern: path/to/directory/" }
 
@@ -264,7 +264,7 @@ workflow DRAM {
                 ch_final_annots = ADD_ANNOTATIONS.out.combined_annots_out
             }
         } else if (params.annotations) {
-            ch_final_annots = Channel
+            ch_final_annots = channel
                 .fromPath(params.annotations, checkIfExists: true)
                 .ifEmpty { exit 1, "Parameter annotations problem: Cannot find any called gene files matching: ${params.annotations}\nNB: Path needs to follow pattern: path/to/directory/" }
         } else {
@@ -309,24 +309,24 @@ workflow DRAM {
     //
     // MODULE: MultiQC
     //
-    ch_multiqc_config        = Channel.fromPath(
+    ch_multiqc_config        = channel.fromPath(
         "$projectDir/assets/multiqc_config.yml", checkIfExists: true)
     ch_multiqc_custom_config = params.multiqc_config ?
-        Channel.fromPath(params.multiqc_config, checkIfExists: true) :
-        Channel.empty()
+        channel.fromPath(params.multiqc_config, checkIfExists: true) :
+        channel.empty()
     ch_multiqc_logo          = params.multiqc_logo ?
-        Channel.fromPath(params.multiqc_logo, checkIfExists: true) :
-        Channel.empty()
+        channel.fromPath(params.multiqc_logo, checkIfExists: true) :
+        channel.empty()
 
     summary_params      = paramsSummaryMap(
         workflow, parameters_schema: "nextflow_schema.json")
-    ch_workflow_summary = Channel.value(paramsSummaryMultiqc(summary_params))
+    ch_workflow_summary = channel.value(paramsSummaryMultiqc(summary_params))
     ch_multiqc_files = ch_multiqc_files.mix(
         ch_workflow_summary.collectFile(name: 'workflow_summary_mqc.yaml'))
     ch_multiqc_custom_methods_description = params.multiqc_methods_description ?
         file(params.multiqc_methods_description, checkIfExists: true) :
         file("$projectDir/assets/methods_description_template.yml", checkIfExists: true)
-    ch_methods_description                = Channel.value(
+    ch_methods_description                = channel.value(
         methodsDescriptionText(ch_multiqc_custom_methods_description))
 
     ch_multiqc_files = ch_multiqc_files.mix(ch_collated_versions)