Channel -> channel in some subwfs

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()))
 }
 
 //

subworkflows/nf-core/vcf_annotate_ensemblvep_snpeff/main.nf

@@ -25,9 +25,9 @@ workflow VCF_ANNOTATE_ENSEMBLVEP_SNPEFF {
     val_sites_per_chunk         //   value: the amount of variants per scattered VCF
 
     main:
-    def ch_versions  = Channel.empty()
-    def ch_vep_input = Channel.empty()
-    def ch_scatter   = Channel.empty()
+    def ch_versions  = channel.empty()
+    def ch_vep_input = channel.empty()
+    def ch_scatter   = channel.empty()
 
     // Check if val_sites_per_chunk is set and scatter if it is
     if(val_sites_per_chunk) {
@@ -89,8 +89,8 @@ workflow VCF_ANNOTATE_ENSEMBLVEP_SNPEFF {
     }
 
     // Annotate with ensemblvep if it's part of the requested tools
-    def ch_vep_output   = Channel.empty()
-    def ch_vep_reports  = Channel.empty()
+    def ch_vep_output   = channel.empty()
+    def ch_vep_reports  = channel.empty()
     if("ensemblvep" in val_tools_to_use){
         ENSEMBLVEP_VEP(
             ch_vep_input,
@@ -110,10 +110,10 @@ workflow VCF_ANNOTATE_ENSEMBLVEP_SNPEFF {
     }
 
     // Annotate with snpeff if it's part of the requested tools
-    def ch_snpeff_output    = Channel.empty()
-    def ch_snpeff_reports   = Channel.empty()
-    def ch_snpeff_html      = Channel.empty()
-    def ch_snpeff_genes     = Channel.empty()
+    def ch_snpeff_output    = channel.empty()
+    def ch_snpeff_reports   = channel.empty()
+    def ch_snpeff_html      = channel.empty()
+    def ch_snpeff_genes     = channel.empty()
     if("snpeff" in val_tools_to_use){
         SNPEFF_SNPEFF(
             ch_vep_output,
@@ -137,7 +137,7 @@ workflow VCF_ANNOTATE_ENSEMBLVEP_SNPEFF {
     }
 
     // Gather the files back together if they were scattered
-    def ch_ready_vcfs = Channel.empty()
+    def ch_ready_vcfs = channel.empty()
     if(val_sites_per_chunk) {
         //
         // Concatenate the VCFs back together with bcftools concat

subworkflows/nf-core/vcf_annotate_snpeff/main.nf

@@ -12,7 +12,7 @@ workflow VCF_ANNOTATE_SNPEFF {
     ch_snpeff_cache // channel: [ path(cache) ] (optional)
 
     main:
-    ch_versions = Channel.empty()
+    ch_versions = channel.empty()
 
     SNPEFF_SNPEFF(ch_vcf, val_snpeff_db, ch_snpeff_cache)
     TABIX_BGZIPTABIX(SNPEFF_SNPEFF.out.vcf)