Review suggestions

Author: ramprasadn

subworkflows/local/annotate_genome_snvs/main.nf

@@ -101,9 +101,10 @@ workflow ANNOTATE_GENOME_SNVS {
             .join(VCFANNO.out.tbi, failOnMismatch:true, failOnDuplicate:true)
             .set { ch_bcftools_view_in }
 
+        // filter on frequencies
         BCFTOOLS_VIEW(
             ch_bcftools_view_in,
-            [], [], [])  // filter on frequencies
+            [], [], [])
 
         // Annotating with CADD
         if (!val_cadd_resources.equals(null)) {

subworkflows/local/annotate_mt_snvs/main.nf

@@ -36,8 +36,6 @@ workflow ANNOTATE_MT_SNVS {
 
         VCFANNO_MT(ch_in_vcfanno, ch_vcfanno_toml, ch_vcfanno_lua, ch_vcfanno_resources)
 
-        ch_vcfanno_vcf = VCFANNO_MT.out.vcf
-
         // Annotating with CADD
         if (!val_cadd_resources.equals(null)) {
             ANNOTATE_CADD (
@@ -52,7 +50,7 @@ workflow ANNOTATE_MT_SNVS {
             ch_cadd_vcf = channel.empty()
         }
 
-        ch_vcfanno_vcf
+        VCFANNO_MT.out.vcf
             .join(ch_cadd_vcf, remainder: true)
             .branch { meta, vcfanno, cadd  ->
                 vcfanno: cadd.equals(null)

subworkflows/local/call_sv_MT/main.nf

@@ -1,5 +1,6 @@
 //
-// Call SV MT
+// Calls SV MT, concatenates FASTQs per sample, then runs MitoSalt and SaltShaker.
+// Also detects the number of discordant pairs using the mitodel script.
 //
 
 include { MT_DELETION   } from '../../../modules/local/mt_deletion_script'
@@ -43,10 +44,10 @@ workflow CALL_SV_MT {
 
             ch_reads
                 .map { meta, reads ->
-                        def groupKey = meta.sample
-                        return [groupKey, meta, reads]
+                        def sample_group_key = meta.sample
+                        return [sample_group_key, meta, reads]
                 }
-                .groupTuple(by: 0)
+                .groupTuple()
                 .map { sample_id, meta_list, reads_list ->
                     def combined_meta = meta_list[0].clone()
                     combined_meta.id = sample_id