refactor: Move primer3 to a subworkflow

main.nf

@@ -17,11 +17,8 @@ log.info paramsSummaryLog(workflow)
 // Create a new channel of metadata from a sample sheet passed to the pipeline through the --input parameter
 ch_input = Channel.fromList(samplesheetToList(params.input, "assets/schema_input.json"))
 
-include { seqkit_fetch_target } from "./modules/seqkit_fetch_target"
-include { primer3_conf } from "./modules/primer3_conf/"
-include { primer3_index } from "./modules/primer3_index/"
-include { primer3_calc } from "./modules/primer3_calc/"
-include { primer3_results2fasta } from "./modules/primer3_results2fasta/"
+
+include { PRIMER3 } from './subworkflows/primer3'
 
 workflow {
   // Read in bed file(s)
@@ -32,21 +29,3 @@ workflow {
     Channel.fromPath(params.fasta),
   )
 }
-workflow PRIMER3 {
-  take:
-  seq
-  ref
-
-  main:
-  seq.view()
-  seqkit_fetch_target(seq,ref)
-  target = seqkit_fetch_target.out.fasta
-
-  primer3_conf(target,ref)
-  primer3_index(ref)
-  primer3_calc(primer3_conf.out,primer3_index.out)
-  primer3_results2fasta(primer3_calc.out)
-
-  emit:
-  primer3_results2fasta.out
-}

subworkflows/primer3/main.nf

@@ -0,0 +1,24 @@
+include { seqkit_fetch_target } from "../../modules/seqkit_fetch_target"
+include { primer3_conf } from "../../modules/primer3_conf/"
+include { primer3_index } from "../../modules/primer3_index/"
+include { primer3_calc } from "../../modules/primer3_calc/"
+include { primer3_results2fasta } from "../../modules/primer3_results2fasta/"
+
+workflow PRIMER3 {
+  take:
+  seq // = Channel.of(params.targetseq)
+  ref // = Channel.fromPath(params.fasta)
+
+  main:
+  seq.view()
+  seqkit_fetch_target(seq,ref)
+  target = seqkit_fetch_target.out.fasta
+
+  primer3_conf(target,ref)
+  primer3_index(ref)
+  primer3_calc(primer3_conf.out,primer3_index.out)
+  primer3_results2fasta(primer3_calc.out)
+
+  emit:
+  primer3_results2fasta.out
+}