update syntax

Author: rlancaster96

workflows/calling/tumor_only_svc.nf

@@ -1,9 +1,9 @@
 #!/usr/bin/env nextflow
 
 // Nextflow Pipeline Version
-params.release = "v0.2.4"
-params.releasedate = "11-25-2024"
-params.githublink = "https://github.com/ohsu-cedar-comp-hub/WGS-nextflow-workflow/releases/tag/v0.2.4"
+params.release = ""
+params.releasedate = ""
+params.githublink = "https://github.com/ohsu-cedar-comp-hub/WGS-nextflow-workflow/releases/tag/"
 
 // Import tools
 include { TUMORONLYGETPILEUPSUMMARIES } from '../../tools/gatk/get_pileup_summaries.nf'
@@ -33,15 +33,15 @@ workflow {
 
     // gatk getpileupsummaries
     TUMORONLYGETPILEUPSUMMARIES(tumor_ch, tumor_ch_bai, params.exac)
-    tumor_table = GETPILEUPSUMMARIES.out
+    tumor_table = TUMORONLYGETPILEUPSUMMARIES.out
 
     // gatk calculate contamination from pileup summaries
     TUMORONLYCALCULATECONTAMINATION(tumor_table)
-    contam_table = CALCULATECONTAMINATION.out.contamination.collect()
-    segment_table = CALCULATECONTAMINATION.out.segment.collect()
+    contam_table = TUMORONLYCALCULATECONTAMINATION.out.contamination.collect()
+    segment_table = TUMORONLYCALCULATECONTAMINATION.out.segment.collect()
 
     // Merge and prepare VCF
-    BGZIP(MUTECT2.out.vcf) // concatenation requires bgzip'd files 
+    BGZIP(TUMORONLYMUTECT2.out.vcf) // concatenation requires bgzip'd files 
     vcfs_ch = BGZIP.out.vcf.collect() // collect all bgzip vcf outputs into a channel
     split_vcf_index = BGZIP.out.index.collect() // collect all bgzip index outputs into a channel
     // concatenate, normalize, and sort the VCF
@@ -50,13 +50,13 @@ workflow {
     unfiltered_vcf_index = PREPAREVCF.out.index
 
     // Merge stats file
-    stats = MUTECT2.out.stats
+    stats = TUMORONLYMUTECT2.out.stats
     stats_ch = stats.collect()
     MERGESTATS(stats_ch, params.sample_id)
     filter_stats = MERGESTATS.out
 
     // Merge f1r2 read orientation files 
-    f1r2files = MUTECT2.out.f1r2
+    f1r2files = TUMORONLYMUTECT2.out.f1r2
     f1r2_ch = f1r2files.collect()
     LEARNORIENTATION(f1r2_ch, params.sample_id)
     orientationmodel = LEARNORIENTATION.out