Correction de bugs

Author:    aliarifki <aliarifki@outlook.fr>

interactive rebase in progress; onto 82915ae6
Last commands done (14 commands done):
   pick deae9a4b Correction des erreurs du script R
   pick 6f3ae8d6 Correction de bugs
Next commands to do (2 remaining commands):
   pick 329af6e1 Suppression du paramètre  options
   pick 2c3f0561 Suppression du channel pass en mode gpu
You are currently rebasing branch 'Alia' on '82915ae6'.

Changes to be committed:
	modified:   src/bolero.nf
	modified:   src/nf_modules/junction_nanosplicer/main.nf
	modified:   src/nf_modules/ont-guppy/main.nf
	modified:   src/nf_modules/pycoqc/main.nf
	modified:   src/nf_modules/rna_count/main.nf
	modified:   src/nf_modules/seqkit/main.nf

src/bolero.nf

@@ -160,9 +160,11 @@ Channel
 
 // Test pour barcoding process
 Channel
-    .fromPath(params.pass)
+    .fromPath('/home/alia/pipelines/bolero/results/01_Basecalling/pass/', type: 'dir')
     .set{pass}
-
+Channel
+    .fromPath('/home/alia/pipelines/bolero/results/01_Basecalling/sequencing_summary.txt')
+    .set{ss}
 /*
  ****************************************************************
                           Imports
@@ -196,7 +198,11 @@ 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"
+<<<<<<< HEAD
 >>>>>>> 8667704 (Ajout ded l'option barcode aux scripts R)
+=======
+include { control_bam } from "./nf_modules/pycoqc/main.nf"
+>>>>>>> 6f3ae8d (Correction de bugs)
 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"
@@ -232,23 +238,33 @@ 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(pass)  
-      barcoding_gpu.out.barcodes
-        .flatten()
-        .map{it -> [it.name, it]}
-        .set{tuples_barcode}
-      concatenate(tuples_barcode)
+      basecall_fast5_gpu(input)
+      if(params.kit_barcoding != ""){
+        barcoding_gpu(pass)  
+        barcoding_gpu.out.barcodes
+          .flatten()
+          .map{it -> [it.name, it]}
+          .set{tuples_barcode}
+        concatenate(tuples_barcode)
+      }
+      else{
+        concatenate(pass)
+      }
       //control_basecalling(basecall_fast5_gpu.out.sequencing_summary)
     }
     else {
-      //basecall_fast5_cpu(input)
-      barcoding_cpu(pass)  
-      barcoding_cpu.out.barcodes
-        .flatten()
-        .map{it -> [it.name, it]}
-        .set{tuples_barcode}
-      concatenate(tuples_barcode)
+      basecall_fast5_cpu(input)
+      if(params.kit_barcoding != ""){
+        barcoding_cpu(pass)  
+        barcoding_cpu.out.barcodes
+          .flatten()
+          .map{it -> [it.name, it]}
+          .set{tuples_barcode}
+        concatenate(tuples_barcode)
+      }
+      else{
+        concatenate(pass)
+      }
       //control_basecalling(basecall_fast5_cpu.out.sequencing_summary)
     }
   }
@@ -267,9 +283,16 @@ workflow {
   //########################## MAPPING ##########################
 
   hbv_genome(cut_5pRACE.out.fastq_cutadapt, genome.collect())
-
   sort_index_bam(hbv_genome.out.bam)
 
+  sort_index_bam.out.indexed_bam
+    .flatten()
+    .filter(~/.*bam$/)
+    .collect()
+    .set{bam_path}
+
+  //control_bam(ss, bam_path)
+
   //###################### START POSITIONS #######################
 
   start_position_counts(sort_index_bam.out.indexed_bam)

src/nf_modules/junction_nanosplicer/main.nf

@@ -11,8 +11,7 @@ process junctions_nanosplicer{
   }
 
   input:
-    tuple val(barcode), path(txt)
-    tuple val(barcode), path(csv)
+    tuple val(barcode), path(txt), path(csv)
 
   output:
     path("${barcode}/${barcode}_JWR_check_parsed.csv")

src/nf_modules/ont-guppy/main.nf

@@ -27,7 +27,7 @@ process basecall_fast5_gpu {
       errorKit "WARNING ! No kit type given..."
       errorKit.view()
   }
-/*
+
   if (params.config_file != "") {
     options = "-c /opt/ont/guppy/data/${params.config_file}"
   }
@@ -35,7 +35,7 @@ process basecall_fast5_gpu {
     options = "--flowcell ${params.flowcell} \
 --kit ${params.kit} "
   }
-*/
+
   input:
     path(fast5_folder)
 
@@ -60,8 +60,7 @@ guppy_basecaller --compress_fastq \
    --gpu_runners_per_device ${params.gpu_runners_per_device} \
    --num_callers ${params.num_callers} \
    --chunks_per_runner ${params.chunks_per_runner} \
-   --flowcell ${params.flowcell} \
-   --kit ${params.kit} 
+   ${options}
 """
 }
 
@@ -84,6 +83,14 @@ process basecall_fast5_cpu {
       errorKit.view()
   }
 
+  if (params.config_file != "") {
+    options = "-c /opt/ont/guppy/data/${params.config_file}"
+  }
+  else {
+    options = "--flowcell ${params.flowcell} \
+--kit ${params.kit} "
+  }
+
   input:
     val(fast5_folder)
 
@@ -95,16 +102,20 @@ process basecall_fast5_cpu {
 
   script:
 """
-echo "Start basecalling using CPUs."
-find ${fast5_folder} -type f -name "*.fast5" > allfast5files.txt
+echo "Start basecalling using G=CPUs."
+# guppy_basecaller --print_workflows
+path=\$(readlink -f ${fast5_folder})
+find \${path} -type f -name "*.fast5" > allfast5files.txt
 guppy_basecaller --compress_fastq \
    -i / \
    --input_file_list allfast5files.txt \
    -s . \
-   --cpu_threads_per_caller ${params.cpu_threads_per_caller} \
+   -x "cuda:all" \
+   --min_qscore ${params.min_qscore} \
+   --cpu_runners_per_device ${params.cpu_runners_per_device} \
    --num_callers ${params.num_callers} \
-   --flowcell ${params.flowcell} \
-   --kit ${params.kit}
+   --chunks_per_runner ${params.chunks_per_runner} \
+   ${options}
 """
 }
 <<<<<<< HEAD
@@ -114,7 +125,7 @@ params.kit_barcoding = "EXP-PBC001"
 process barcoding_gpu {
   container = "${container_url}"
   label "gpus"
-  tag "$fast5_folder"
+  tag "$pass_path"
   if (params.barcoding_out != "") {
     publishDir "results/${params.barcoding_out}", mode: 'copy'
   }
@@ -142,7 +153,7 @@ guppy_barcoder \
 process barcoding_cpu {
   container = "${container_url}"
   label "big_mem_multi_cpus"
-  tag "$fast5_folder"
+  tag "$pass_path"
   if (params.barcoding_out != "") {
     publishDir "results/${params.barcoding_out}", mode: 'copy'
   }

src/nf_modules/pycoqc/main.nf

@@ -36,7 +36,8 @@ process control_bam {
   path("*.txt")
 
   """
-  find results/${params.minimap2_genome_out} -type f -name "*sorted.bam" > allbamfiles.txt
-  #pycoQC -f ${txt} -a ${path_bam} -o Control_mapping.html
+  mkdir bam/
+  mv ${path_bam} bam/
+  pycoQC -f ${txt} -a bam/ -o Control_mapping.html
   """
 }
\ No newline at end of file

src/nf_modules/rna_count/main.nf

@@ -11,8 +11,7 @@ process rna_count{
   }
 
   input:
-    tuple val(barcode), path(spvariants)
-    tuple val(barcode), path(classification)
+    tuple val(barcode), path(spvariants), path(classification)
 
   output:
     path("${barcode}/*.csv")

src/nf_modules/seqkit/main.nf

@@ -87,4 +87,24 @@ process concatenate {
     seqkit scat -j ${task.cpus} -f \${path} --gz-only > ${barcode}_merged.fastq
     gzip ${barcode}_merged.fastq
     """
+}
+
+process concatenate_BC {
+  container = "${container_url}"
+  label "big_mem_multi_cpus"
+  tag "${barcode}"
+  if (params.fastq_out != "") {
+    publishDir "results/${params.fastq_out}", mode: 'copy'
+  }
+
+  input:
+    path(path)
+
+  output:
+    path("test.txt")
+
+  script:
+    """
+    echo ${path} \$(readlink -f ${path}) > test.txt
+    """
 }
\ No newline at end of file