Update Bambu version

-Update from version 3.0.8 to 3.4.1 (latest bioconductor release).

main.nf

@@ -38,7 +38,7 @@ include { logHeader           } from './modules/header.nf'
 log.info logHeader(params)
 
 if (params.tx_discovery == "bambu"){
-  log.warn """You are using Bambu as the transcript discovery tool. Please note that Bambu takes into account strandedness by default.
+  log.warn """You are using Bambu as the transcript discovery tool. Please note that Bambu takes by default strandedness into account.
   Bambu using strandedness: ${params.bambu_strand}. Please verifiy that it corresponds to your sequencing protocol.
   You can change strandedness mode using the --bambu_strand parameter (options: true or false).
   """

modules/bambu/bambu.nf

@@ -1,8 +1,8 @@
 process BAMBU {
   conda (params.enable_conda ? "bioconda::bioconductor-bambu=3.0.8" : null)
   container "${ workflow.containerEngine == 'singularity' ? 
-                'https://depot.galaxyproject.org/singularity/bioconductor-bambu:3.0.8--r42hc247a5b_0' :
-                'quay.io/biocontainers/bioconductor-bambu:3.0.8--r42hc247a5b_0' }"
+                'https://depot.galaxyproject.org/singularity/bioconductor-bambu:3.4.0--r43hf17093f_1' :
+                'quay.io/biocontainers/bioconductor-bambu:3.4.0--r43hf17093f_1 ' }"
   publishDir "$params.outdir/bambu", mode: 'copy'
   cpus params.maxCpu
   memory params.maxMemory
@@ -58,4 +58,4 @@ process BAMBU {
     rm valid_transcripts.txt
   fi
   '''
-}
+}

modules/stringtie/stringtie_merge_counts.nf

@@ -1,7 +1,7 @@
 process MERGE_COUNTS {
   publishDir "$params.outdir/stringtie2", mode: 'copy', pattern: '*.txt'
   if (params.filter == false){
-    publishDir "$params.outdir/final", mode: 'copy', pattern: 'counts_transcript.txt', saveAs: {filename -> 'counts_transcript.full.gtf'}
+    publishDir "$params.outdir/final", mode: 'copy', pattern: 'counts_transcript.txt', saveAs: {filename -> 'counts_transcript.full.txt'}
   }
 
   input: