emaze: change imput from gtf to fasta to compute transcript length

src/nf_modules/emase-zero/main.nf

@@ -3,6 +3,7 @@ container_url = "lbmc/emase-zero:${version}"
 
 include { tr2g } from "./../kb/main.nf"
 include { bam2ec } from "./../alntools/main.nf"
+include { fasta_to_transcripts_lengths } from "./../bioawk/main.nf"
 
 
 params.count = "-m 2"
@@ -10,7 +11,7 @@ params.count_out = ""
 workflow count {
   take:
     bam_idx
-    gtf
+    fasta
     transcript_to_gene
 
   main:
@@ -18,7 +19,8 @@ workflow count {
       .ifEmpty(["NO T2G", ""])
       .set{ transcript_to_gene_optional }
     tr2g(gtf, transcript_to_gene_optional)
-    bam2ec(bam_idx, gtf)
+    fasta_to_transcripts_lengths(fasta)
+    bam2ec(bam_idx, fasta_to_transcripts_lengths.out.tsv.collect())
     emase(bam2ec.out.bin, bam2ec.out.tsv, tr2g.out.t2g)
 
   emit: