From b9928b0e797ade4b3e5ef260094589054bd71325 Mon Sep 17 00:00:00 2001
From: aliarifki <aliarifki@outlook.fr>
Date: Fri, 23 Jun 2023 16:22:44 +0200
Subject: [PATCH] Transformation des fichiers de sortie de barcoding en tuple
 pour concatenate
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Author:    aliarifki <aliarifki@outlook.fr>

interactive rebase in progress; onto 82915ae
Last commands done (12 commands done):
   pick 87fcb74 Erreur de parenthèse
   pick bd1fefe Transformation des fichiers de sortie de barcoding en tuple pour concatenate
Next commands to do (4 remaining commands):
   pick deae9a4 Correction des erreurs du script R
   pick 6f3ae8d Correction de bugs
You are currently rebasing branch 'Alia' on '82915ae'.

Changes to be committed:
	modified:   src/bolero.nf
	modified:   src/nf_modules/ont-guppy/main.nf
	modified:   src/nf_modules/pycoqc/main.nf
---
 src/bolero.nf                    | 37 +++++++++++++++++++++-----------
 src/nf_modules/ont-guppy/main.nf |  9 ++++++--
 src/nf_modules/pycoqc/main.nf    |  6 ++++--
 3 files changed, 35 insertions(+), 17 deletions(-)

diff --git a/src/bolero.nf b/src/bolero.nf
index a469a8d..76d6368 100755
--- a/src/bolero.nf
+++ b/src/bolero.nf
@@ -97,7 +97,7 @@ params.kit_barcoding = "EXP-PBC001"
 
 /* Params out */
 
-params.basecalling_out = "01_Basecalling/"
+params.basecalling_out = "01_basecalling/"
 params.barcoding_out = "02_barcoding/"
 params.fastq_out = "03_fastq/"
 params.seqkit_grep_out = "03_fastq/"
@@ -157,12 +157,12 @@ Channel
     .map(it -> [it.baseName, it])
     .set{barcodes}
 
-/*
+
 // Test pour barcoding process
 Channel
     .fromPath(params.pass)
     .set{pass}
-*/
+
 /*
  ****************************************************************
                           Imports
@@ -184,6 +184,7 @@ if(!params.skipBC) {
 <<<<<<< HEAD
 <<<<<<< HEAD
 <<<<<<< HEAD
+<<<<<<< HEAD
 // include { barecode } from "./nf_modules/barecode/main.nf" 
 =======
 >>>>>>> c281bb3789a8d844085e21f749580c29d43b35d6
@@ -192,6 +193,8 @@ include { pycoqc } from "./nf_modules/pycoqc/main.nf"
 >>>>>>> 9ef97be (Contrôle qualité et basecalling en mode gpu)
 =======
 include { barcoding_cpu } from "./nf_modules/ont-guppy/main.nf"
+=======
+>>>>>>> bd1fefe (Transformation des fichiers de sortie de barcoding en tuple pour concatenate)
 include { control_basecalling } from "./nf_modules/pycoqc/main.nf"
 >>>>>>> 8667704 (Ajout ded l'option barcode aux scripts R)
 include { concatenate } from "./nf_modules/seqkit/main.nf"
@@ -229,21 +232,29 @@ workflow {
   //il reste à adapter ça
   else { // we take fast5 files as input and proceed to basecalling with guppy
     if(params.gpu_mode) {
-      basecall_fast5_gpu(input)
-      barcoding_gpu(basecall_fast5_gpu.out.pass)
-      //concatenate(basecall_fast5_gpu.out.pass)
-      control_basecalling(basecall_fast5_gpu.out.sequencing_summary)
+      //basecall_fast5_gpu(input)
+      barcoding_gpu(pass)  
+      barcoding_gpu.out.barcodes
+        .flatten()
+        .map{it -> [it.name, it]}
+        .set{tuples_barcode}
+      concatenate(tuples_barcode)
+      //control_basecalling(basecall_fast5_gpu.out.sequencing_summary)
     }
     else {
-      basecall_fast5_cpu(input)
-      barcoding_cpu(basecall_fast5_cpu.out.pass)
-      //concatenate(basecall_fast5_cpu.out.pass)
-      control_basecalling(basecall_fast5_cpu.out.sequencing_summary)
+      //basecall_fast5_cpu(input)
+      barcoding_cpu(pass)  
+      barcoding_cpu.out.barcodes
+        .flatten()
+        .map{it -> [it.name, it]}
+        .set{tuples_barcode}
+      concatenate(tuples_barcode)
+      //control_basecalling(basecall_fast5_cpu.out.sequencing_summary)
     }
   }
 
 
-/*
+
   //####################### PREPROCESSING #######################
     
 
@@ -272,5 +283,5 @@ workflow {
   //#################### VARIANTS D'EPISSAGE ####################
 
   rna_count(junctions_nanosplicer.out.identified_SPvariants, start_position_individuals.out.classification_of_reads)
-*/
+
 }
diff --git a/src/nf_modules/ont-guppy/main.nf b/src/nf_modules/ont-guppy/main.nf
index 8e3fe77..f00c006 100644
--- a/src/nf_modules/ont-guppy/main.nf
+++ b/src/nf_modules/ont-guppy/main.nf
@@ -123,7 +123,7 @@ process barcoding_gpu {
     path(pass_path)
   
   output:
-    path("*")
+    path("barcode*"), emit: barcodes
   
   script:
 """
@@ -151,10 +151,11 @@ process barcoding_cpu {
     path(pass_path)
   
   output:
-    path("*")
+    path("barcode*"), emit: barcodes
   
   script:
 """
+mkdir barcoding/
 guppy_barcoder \
   --input_path ${pass_path} \
   --save_path . \
@@ -166,4 +167,8 @@ guppy_barcoder \
   --compress_fastq
 """
 }
+<<<<<<< HEAD
 >>>>>>> 622494c (Ajout du process barcoding)
+=======
+
+>>>>>>> bd1fefe (Transformation des fichiers de sortie de barcoding en tuple pour concatenate)
diff --git a/src/nf_modules/pycoqc/main.nf b/src/nf_modules/pycoqc/main.nf
index 4b70e83..1503479 100644
--- a/src/nf_modules/pycoqc/main.nf
+++ b/src/nf_modules/pycoqc/main.nf
@@ -30,11 +30,13 @@ process control_bam {
 
   input:
   path(txt)
+  path(path_bam)
 
   output:
-  path("*.html")
+  path("*.txt")
 
   """
-  pycoQC -f ${txt} -o Control_mapping.html)
+  find results/${params.minimap2_genome_out} -type f -name "*sorted.bam" > allbamfiles.txt
+  #pycoQC -f ${txt} -a ${path_bam} -o Control_mapping.html
   """
 }
\ No newline at end of file
-- 
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