From 33755d9ab2f4d3a9cfc14f0fce5cb105ffd2cfe7 Mon Sep 17 00:00:00 2001
From: Victor Le Bars <vlebars@genossh.genouest.org>
Date: Wed, 10 Jan 2024 10:02:12 +0100
Subject: [PATCH] add stranded option for bambu in param

---
 bin/run_bambu.R        | 9 ++++++++-
 modules/bambu/bambu.nf | 1 +
 nextflow.config        | 1 +
 3 files changed, 10 insertions(+), 1 deletion(-)

diff --git a/bin/run_bambu.R b/bin/run_bambu.R
index e68d601..aa5a973 100755
--- a/bin/run_bambu.R
+++ b/bin/run_bambu.R
@@ -14,7 +14,13 @@ genomeseq      <- strsplit(grep('--fasta*', args, value = TRUE), split = '=')[[1
 genomeSequence <- Rsamtools::FaFile(genomeseq)
 Rsamtools::indexFa(genomeseq)
 annot_gtf      <- strsplit(grep('--annotation*', args, value = TRUE), split = '=')[[1]][[2]]
-readlist       <- args[5:length(args)]
+bambu_strand   <- strsplit(grep('--bambu_strand*', args, value = TRUE), split = '=')[[1]][[2]]
+if (bambu_strand=="true"){
+  bambu_strand=TRUE
+} else {
+  bambu_strand=FALSE
+}
+readlist       <- args[6:length(args)]
 
 print("BAMs:")
 readlist
@@ -30,6 +36,7 @@ se     <- bambu(
   ncore = ncore,
   verbose = TRUE,
   NDR = 1,
+  stranded = bambu_strand,
   opt.discovery = list(min.txScore.singleExon = 0)
 )
 
diff --git a/modules/bambu/bambu.nf b/modules/bambu/bambu.nf
index 4195a77..e359872 100755
--- a/modules/bambu/bambu.nf
+++ b/modules/bambu/bambu.nf
@@ -25,6 +25,7 @@ process BAMBU {
     --ncore=${params.maxCpu} \
     --annotation=${ref} \
     --fasta=${fa} \
+    --bambu_strand=${params.bambu_strand} \
     *.bam
 
   sed -i 's/*/./g' extended_annotations.gtf
diff --git a/nextflow.config b/nextflow.config
index fa22833..e9fa7fe 100755
--- a/nextflow.config
+++ b/nextflow.config
@@ -11,6 +11,7 @@ params {
   operation         = "intersection"
   tfkmers_model     = null
   tfkmers_tokenizer = null
+  bambu_strand      = true
 }
 
 process {