From 8667704ae8d70af154c74d66911881f02257d37c Mon Sep 17 00:00:00 2001
From: aliarifki <aliarifki@outlook.fr>
Date: Thu, 22 Jun 2023 10:02:53 +0200
Subject: [PATCH] Ajout ded l'option barcode aux scripts R

---
 src/bolero.nf                               | 16 ++++++++++------
 src/nf_modules/junction_nanosplicer/main.nf |  4 ++--
 src/nf_modules/rna_count/main.nf            |  2 +-
 src/nf_modules/start_positions/main.nf      |  2 +-
 4 files changed, 14 insertions(+), 10 deletions(-)

diff --git a/src/bolero.nf b/src/bolero.nf
index cd2387a..52f67da 100755
--- a/src/bolero.nf
+++ b/src/bolero.nf
@@ -92,6 +92,8 @@ params.num_callers = 16
 params.chunks_per_runner = 512
 params.chunk_size = 1900
 params.config_file = ""
+params.kit_barcoding = "EXP-PBC001"
+
 
 /* Params out */
 
@@ -104,7 +106,6 @@ params.minimap2_genome_out = "05_minimap2/"
 params.start_position_counts_out = "06_start_positions/"
 params.nanosplicer_out = "07_nanosplicer/"
 params.rna_count_out = "08_RNA_count/"
-params.pycoQC_out = "pycoQC/"
 
 /*
  ****************************************************************
@@ -156,6 +157,7 @@ Channel
     .map(it -> [it.baseName, it])
     .set{barcodes}
 
+
 // Test pour barcoding process
 Channel
     .fromPath(params.pass)
@@ -169,16 +171,18 @@ Channel
 
 if(!params.skipBC) {
   /* Hardware configuration, if Nvidia CUDA compatible graphic card is installed, use guppy-gpu, else guppy-cpu (much slower)*/
-  include { barcoding } from "./nf_modules/ont-guppy/main.nf"
   if(params.gpu_mode) {
     include { basecall_fast5_gpu } from "./nf_modules/ont-guppy/main.nf"
+    include { barcoding_gpu } from "./nf_modules/ont-guppy/main.nf"
   }
   else {
     include { basecall_fast5_cpu } from "./nf_modules/ont-guppy/main.nf"
+    include { barcoding_cpu } from "./nf_modules/ont-guppy/main.nf"
   }
 }
 
-include { pycoqc } from "./nf_modules/pycoqc/main.nf"
+include { barcoding_cpu } from "./nf_modules/ont-guppy/main.nf"
+include { control_basecalling } from "./nf_modules/pycoqc/main.nf"
 include { concatenate } from "./nf_modules/seqkit/main.nf"
 include { cut_5pRACE } from "./nf_modules/cutadapt/main.nf"
 include { hbv_genome } from "./nf_modules/minimap2/main.nf"
@@ -201,7 +205,7 @@ include { rna_count } from "./nf_modules/rna_count/main.nf"
 
 workflow {
   pass.view()
-  barcoding(pass)
+  barcoding_cpu(pass)
   //######################## BASECALLING ########################
 
 /*
@@ -214,12 +218,12 @@ workflow {
     if(params.gpu_mode) {
       basecall_fast5_gpu(input)
       concatenate(basecall_fast5_gpu.out.pass)
-      pycoqc(basecall_fast5_gpu.sequencing_summary)
+      control_basecalling(basecall_fast5_gpu.sequencing_summary)
     }
     else {
       basecall_fast5_cpu(input)
       concatenate(basecall_fast5_cpu.out.pass)
-      pycoqc(basecall_fast5_cpu.sequencing_summary)
+      control_basecalling(basecall_fast5_cpu.sequencing_summary)
     }
   }
 
diff --git a/src/nf_modules/junction_nanosplicer/main.nf b/src/nf_modules/junction_nanosplicer/main.nf
index fb39139..a48c713 100644
--- a/src/nf_modules/junction_nanosplicer/main.nf
+++ b/src/nf_modules/junction_nanosplicer/main.nf
@@ -15,13 +15,13 @@ process junctions_nanosplicer{
     tuple val(barcode), path(csv)
 
   output:
-    path("${barcode}/JWR_check_parsed.csv")
+    path("${barcode}/${barcode}_JWR_check_parsed.csv")
     tuple val(barcode), path("${barcode}/${barcode}_identified_SPvariants.csv"), emit: identified_SPvariants
 
   script:
     """
     mkdir ${barcode}
     cd ${barcode}/
-    Rscript /Junctions_NanoSplicer.R -c ../${txt} -j ../${csv}
+    Rscript /Junctions_NanoSplicer.R -c ../${txt} -j ../${csv} -b ${barcode}
     """
 }
\ No newline at end of file
diff --git a/src/nf_modules/rna_count/main.nf b/src/nf_modules/rna_count/main.nf
index 06afba6..448f598 100644
--- a/src/nf_modules/rna_count/main.nf
+++ b/src/nf_modules/rna_count/main.nf
@@ -23,6 +23,6 @@ process rna_count{
     """
     mkdir ${barcode}
     cd ${barcode}/
-    Rscript /HBV_RNAs_count.R -s ../${spvariants} -c ../${classification}
+    Rscript /HBV_RNAs_count.R -s ../${spvariants} -c ../${classification} -b ${barcode}
     """
 }
diff --git a/src/nf_modules/start_positions/main.nf b/src/nf_modules/start_positions/main.nf
index 668d50a..4995870 100644
--- a/src/nf_modules/start_positions/main.nf
+++ b/src/nf_modules/start_positions/main.nf
@@ -22,7 +22,7 @@ process start_position_individuals{
     """
     mkdir ${barcode}
     cd ${barcode}/
-    Rscript /Start_positions.R -i ../${start_position_counts}
+    Rscript /Start_positions.R -i ../${start_position_counts} -b ${barcode}
     mv Rplots.pdf ${barcode}_Rplots.pdf
     """
 }
\ No newline at end of file
-- 
GitLab