Merge branch 'dev_carine' into 'master'

fix bug (index bam between star and htseq)

See merge request !2

src/RNAseq_cec.nf

@@ -26,6 +26,11 @@ include {
    star_mapping_fastq_out: "star_bam/"
 )
 
+include { index_bam
+  } from './nf_modules/samtools/main.nf' addParams(
+   htseq_out: "star_bam/"
+)
+
 include { htseq_count_with_gff
   } from './nf_modules/htseq/main.nf' addParams(
    htseq_out: "htseq_count/"
@@ -87,8 +92,11 @@ workflow {
       fastp.out.fastq,
   )
 
+  //// index bam
+  index_bam(star_mapping_fastq.out.bam)
+  
   htseq_count_with_gff(
-        star_mapping_fastq.out.bam,
+        index_bam.out.bam_idx,
         genome_gff3_file
         )