refactor: Split after seqkit

Just no reason to split it sooner

main.nf

@@ -23,17 +23,16 @@ include { BEDTOOLS_GETFASTA } from './modules/nf-core/bedtools/getfasta'
 include { PRIMER3 } from './subworkflows/primer3'
 
 workflow {
+    ch_fasta = channel.fromPath(params.fasta)
     // Pull raw sequences in the bed files from the reference genome
-    sequences = BEDTOOLS_GETFASTA (
+    BEDTOOLS_GETFASTA (
         ch_input,
-        params.fasta
-    ).fasta
-        .splitFasta(file: true)
-        .dump()
+        ch_fasta.first()
+    )
 
     // Run primer3 on the sequences
     PRIMER3 (
-        sequences,
-        Channel.fromPath(params.fasta),
+        BEDTOOLS_GETFASTA.out.fasta,
+        ch_fasta.first(),
     )
 }

modules/seqkit_fetch_target/main.nf

@@ -7,22 +7,22 @@ process seqkit_fetch_target {
     path fasta
 
     output:
-    path "${seq}_target.fa" , emit:fasta
-    path "${seq}_target.gtf" , emit:gtf
+    path "*_targets.fa" , emit:fasta
+    path "*_targets.gtf" , emit:gtf
 
     shell:
     def prefix = task.ext.prefix ?: "${meta.id}"
     '''
-    cat !{fasta} | seqkit locate -i --gtf -f !{seq_fasta} > !{meta.id}_target.gtf
+    cat !{fasta} | seqkit locate -i --gtf -f !{seq_fasta} > !{meta.id}_targets.gtf
 
-    seqkit subseq --gtf !{meta.id}_target.gtf -u 50000 -d 50000 !{fasta} > !{meta.id}_target.fa
+    seqkit subseq --gtf !{meta.id}_targets.gtf -u 50000 -d 50000 !{fasta} > !{meta.id}_targets.fa
 
-    if [[ ! -s !{meta.id}_target.gtf ]]
+    if [[ ! -s !{meta.id}_targets.gtf ]]
     then
     exit 7
     fi
 
-    seqkit stat !{meta.id}_target.gtf
-    seqkit stat !{meta.id}_target.fa
+    seqkit stat !{meta.id}_targets.gtf
+    seqkit stat !{meta.id}_targets.fa
     '''
 }

subworkflows/primer3/main.nf

@@ -6,12 +6,14 @@ include { primer3_results2fasta } from "../../modules/primer3_results2fasta/"
 
 workflow PRIMER3 {
   take:
-  seq_fasta // [id, sequence]
+  seq_fasta // [meta, fasta]
   ref // fasta
 
   main:
   seqkit_fetch_target(seq_fasta,ref)
   target = seqkit_fetch_target.out.fasta
+        .splitFasta(file: true)
+
 
   primer3_conf(target,ref)
   primer3_index(ref)