Merge branch 'Alia' into 'master'

Alia

See merge request testoni-lab/bolero!7

src/bolero.nf

@@ -92,7 +92,8 @@ params.num_callers = 16
 params.chunks_per_runner = 512
 params.chunk_size = 1900
 params.config_file = ""
-params.kit_barcoding = "EXP-PBC001"
+params.kit_barcoding = ""
+//"EXP-PBC001"
 
 
 /* Params out */
@@ -106,6 +107,7 @@ 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.rna_qc_out = "09_quality_control/"
 
 /*
  ****************************************************************
@@ -115,6 +117,7 @@ params.rna_count_out = "08_RNA_count/"
 
 log.info "fast5/q folder : ${params.input}"
 log.info "5'RACE adapter sequence : ${params.adapt}"
+log.info "Gene specific primer : ${params.gsp}"
 if(!params.skipBC) log.info "Guppy basecalling calculation using GPU mode : ${params.gpu_mode}."
 log.info "Genome file : ${params.genome}"
 log.info "Genome annotation file : ${params.gtf}"
@@ -201,7 +204,6 @@ include { jwr_checker } from "./nf_modules/nanosplicer/main.nf"
 include { junctions_nanosplicer } from "./nf_modules/junction_nanosplicer/main.nf"
 include { rna_count } from "./nf_modules/rna_count/main.nf"
 
-
 /*
  ****************************************************************
                           Workflow
@@ -233,12 +235,16 @@ workflow {
         concatenate(tuples_barcode)
       }
       else{
-        concatenate(basecall_fast5_gpu.out.pass)
+        basecall_fast5_gpu.out.pass
+          .map{it -> ["Sample", it]}
+          .set{tuple_sample}
+        concatenate(tuple_sample)
       }
       control_basecalling(basecall_fast5_gpu.out.sequencing_summary)
+
     }
     else {
-      basecall_fast5_cpu(input)
+      //basecall_fast5_cpu(input)
       if(params.kit_barcoding != ""){
         barcoding_cpu(pass)  
         barcoding_cpu.out.barcodes
@@ -248,16 +254,19 @@ workflow {
         concatenate(tuples_barcode)
       }
       else{
-        concatenate(pass)
+        pass
+          .map{it -> ["Sample", it]}
+          .set{tuple_sample}
+        concatenate(tuple_sample)
       }
-      //control_basecalling(basecall_fast5_cpu.out.sequencing_summary)
+      control_basecalling(ss)
     }
   }
 
 
 
   //####################### PREPROCESSING #######################
-    
+  
 
   //Filtration (seqkit_grep looks for the 5'RACE and the gsp patterns in the reads to keep only mature ARNs)
   seqkit_grep(concatenate.out.merged_fastq, params.adapt, params.gsp)
@@ -269,14 +278,8 @@ workflow {
 
   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)
+  //il faut ajouter une boucle if pour le mode cpu/gpu
+  control_bam(basecall_fast5_gpu.out.sequencing_summary.collect(), sort_index_bam.out.indexed_bam)
 
   //###################### START POSITIONS #######################
 

src/nextflow.config

@@ -146,7 +146,7 @@ profiles {
     singularity.runOptions = "--bind /data,/home"
     process {
       errorStrategy = 'finish'
-      memory = '256GB'
+      memory = '32GB'
       withLabel: big_mem_mono_cpus {
         cpus = 1
       }

src/nf_modules/minimap2/main.nf

@@ -85,7 +85,7 @@ process hbv_transcriptome {
   """
 }
 
-params.mapping_hbv_genome = "-ax splice --secondary=no -G 1650 -u n --eqx"
+params.mapping_hbv_genome = "-ax splice --secondary=no -u n --splice-flank=no --eqx"
 process hbv_genome {
   container = "${container_url}"
   label "big_mem_multi_cpus"

src/nf_modules/ont-guppy/main.nf

@@ -119,8 +119,6 @@ guppy_basecaller --compress_fastq \
    ${options}
 """
 }
-<<<<<<< HEAD
-=======
 
 params.kit_barcoding = "EXP-PBC001"
 process barcoding_gpu {
@@ -178,9 +176,4 @@ guppy_barcoder \
   --trim_adapters \
   --compress_fastq
 """
-}
-<<<<<<< HEAD
->>>>>>> 622494c (Ajout du process barcoding)
-=======
-
->>>>>>> bd1fefe (Transformation des fichiers de sortie de barcoding en tuple pour concatenate)
+}
\ No newline at end of file

src/nf_modules/pycoqc/main.nf

 version = "2.5.2"
 container_url = "xgrand/pycoqc:${version}"
 
+params.rna_qc_out = ""
 process control_basecalling {
   container = "${container_url}"
   label "small_mem_mono_cpus"
   
-  if (params.basecalling_out != "") {
-    publishDir "results/${params.basecalling_out}", mode: 'copy'
+  if (params.rna_qc_out != "") {
+    publishDir "results/${params.rna_qc_out}QC_basecalling/", mode: 'copy'
   }
 
   input:
@@ -16,7 +17,7 @@ process control_basecalling {
   path("*.html")
 
   """
-  pycoQC -f ${txt} -o Control_basecalling.html
+  pycoQC -f ${txt} -o QC_basecalling.html
   """
 }
 
@@ -24,20 +25,18 @@ process control_bam {
   container = "${container_url}"
   label "small_mem_mono_cpus"
   
-  if (params.basecalling_out != "") {
-    publishDir "results/${params.basecalling_out}", mode: 'copy'
+  if (params.rna_qc_out != "") {
+    publishDir "results/${params.rna_qc_out}QC_mapping/", mode: 'copy'
   }
 
   input:
   path(txt)
-  path(path_bam)
+  tuple val(barcode), path(bam), path(bai)
 
   output:
-  path("*.txt")
+  path("*.html")
 
   """
-  mkdir bam/
-  mv ${path_bam} bam/
-  pycoQC -f ${txt} -a bam/ -o Control_mapping.html
+  pycoQC -f ${txt} -a ${bam} -o ${barcode}_QC_mapping.html
   """
 }
\ No newline at end of file

src/nf_modules/samtools/main.nf

@@ -24,6 +24,7 @@ samtools sort -@ ${task.cpus} ${bam} -O BAM -o ${bam.simpleName}_sorted.bam
 
 params.start_position_counts_out = ""
 process start_position_counts {
+    container = "${container_url}"
     tag "${barcode}"
     label "big_mem_multi_cpus"
     publishDir "results/${params.start_position_counts_out}", mode: 'copy'
@@ -37,10 +38,9 @@ process start_position_counts {
     script:
 """
 mkdir ${barcode}
-cd ${barcode}/
-samtools view -F 260 ../${bam} |
+samtools view -F 260 ${bam} |
   cut -f 1,4 |
-  sort > ${barcode}_start_positions_counts.txt
+  sort > ${barcode}/${barcode}_start_positions_counts.txt
 """
 }