change gff fro gtf

src/RNAseq_cec.nf

@@ -3,7 +3,8 @@ nextflow.enable.dsl=2
 log.info "fastq files: ${params.fastq}"
 log.info "fasta cds file: ${params.cds_fasta}"
 log.info "fasta genomic file: ${params.genomic_fasta}"
-log.info "fasta gff3 file: ${params.genomic_gff3}"
+log.info "fasta gtf file: ${params.genomic_gtf}"
+
 
 include { fastp } from './nf_modules/fastp/main.nf' addParams(fastp_out: "fastQC/")
 include {
@@ -20,7 +21,7 @@ include {
 )
 
 include {
-    index_with_gff as star_index_with_gff;
+    index_with_gtf as star_index_with_gtf;
     mapping_fastq as star_mapping_fastq
  }  from './nf_modules/star/main.nf' addParams(
    star_mapping_fastq_out: "star_bam/"
@@ -31,7 +32,7 @@ include { index_bam
    htseq_out: "star_bam/"
 )
 
-include { htseq_count_with_gff
+include { htseq_count as htseq_count_with_gtf
   } from './nf_modules/htseq/main.nf' addParams(
    htseq_out: "htseq_count/"
 )
@@ -61,10 +62,10 @@ channel
   .set { genomic_fasta_file }
 
 channel
-  .fromPath( params.genomic_gff3 )
-  .ifEmpty { error "Cannot find any gff3 files matching: ${params.genomic_gff3}" }
+  .fromPath( params.genomic_gtf )
+  .ifEmpty { error "Cannot find any gtf files matching: ${params.genomic_gtf}" }
   .map { it -> [it.simpleName, it]}
-  .set { genome_gff3_file }
+  .set { genome_gtf_file }
 
 workflow {
   //trim data
@@ -82,7 +83,7 @@ workflow {
   //star mapping
 
   //// star index
-  star_index_with_gff(genomic_fasta_file,genome_gff3_file)
+  star_index_with_gtf(genomic_fasta_file,genome_gtf_file)
   star_index = star_index_with_gff.out
 
   ////star mapping
@@ -95,9 +96,9 @@ workflow {
   //// index bam
   index_bam(star_mapping_fastq.out.bam)
   
-  htseq_count_with_gff(
+  htseq_count_with_gtf(
         index_bam.out.bam_idx,
-        genome_gff3_file
+        genome_gtf_file
         )
   
   //report multiqc