feat: Use getfasta to create fastas

main.nf

@@ -4,8 +4,8 @@ include { validateParameters; paramsHelp; paramsSummaryLog; samplesheetToList }
 
 // Print help message, supply typical command line usage for the pipeline
 if (params.help) {
-   log.info paramsHelp("nextflow run my_pipeline --input input_file.csv")
-   exit 0
+    log.info paramsHelp("nextflow run my_pipeline --input input_file.csv")
+    exit 0
 }
 
 // Validate input parameters
@@ -18,14 +18,22 @@ log.info paramsSummaryLog(workflow)
 ch_input = Channel.fromList(samplesheetToList(params.input, "assets/schema_input.json"))
 
 
+include { BEDTOOLS_GETFASTA } from './modules/nf-core/bedtools/getfasta'
+
 include { PRIMER3 } from './subworkflows/primer3'
 
 workflow {
-  // Read in bed file(s)
-  // Pull raw sequences in the bed files from the reference genome
-  // Run primer3 on the sequences
-  PRIMER3 (
-    Channel.of(params.targetseq),
-    Channel.fromPath(params.fasta),
-  )
+    // Pull raw sequences in the bed files from the reference genome
+    sequences = BEDTOOLS_GETFASTA (
+        ch_input,
+        params.fasta
+    ).fasta
+        .splitFasta( record: [id: true, seqString: true] )
+        .dump()
+
+    // Run primer3 on the sequences
+    PRIMER3 (
+        sequences,
+        Channel.fromPath(params.fasta),
+    )
 }

modules/seqkit_fetch_target/main.nf

@@ -2,7 +2,7 @@ process seqkit_fetch_target {
     conda "seqkit"
 
     input:
-    val seq
+    tuple val(id), val(seq)
     path fasta
 
     output:
@@ -11,20 +11,20 @@ process seqkit_fetch_target {
 
     shell:
     '''
-    echo ">seq
+    echo ">!{id}
     !{seq}
     " > seq.fa
 
-    seqkit locate -i --gtf -p "!{seq}" !{fasta} > !{seq}_target.gtf
+    seqkit locate -i --gtf -p "!{seq}" !{fasta} > !{id}_target.gtf
 
-    seqkit subseq --gtf !{seq}_target.gtf -u 50000 -d 50000 !{fasta} > !{seq}_target.fa
+    seqkit subseq --gtf !{seq}_target.gtf -u 50000 -d 50000 !{fasta} > !{id}_target.fa
 
-    if [[ ! -s !{seq}_target.gtf ]]
+    if [[ ! -s !{id}_target.gtf ]]
     then
     exit 7
     fi
 
-    seqkit stat !{seq}_target.gtf
-    seqkit stat !{seq}_target.fa
+    seqkit stat !{id}_target.gtf
+    seqkit stat !{id}_target.fa
     '''
 }

subworkflows/primer3/main.nf

@@ -6,11 +6,10 @@ include { primer3_results2fasta } from "../../modules/primer3_results2fasta/"
 
 workflow PRIMER3 {
   take:
-  seq // = Channel.of(params.targetseq)
-  ref // = Channel.fromPath(params.fasta)
+  seq // [id, sequence]
+  ref // fasta
 
   main:
-  seq.view()
   seqkit_fetch_target(seq,ref)
   target = seqkit_fetch_target.out.fasta