Ajout de la commande find pour le basecalling

src/bolero.nf

@@ -31,8 +31,8 @@ def helpMessage() {
     Mandatory arguments:
       --input [path]                  Path to the folder containing fast5 files. 
                                       If skip basecalling option enabled, path to fastq files folder.
-      --adapt [str]                   Sequence of 5'RACE adapter.
-      --gsp [str]                     Sequence of gene-specific primer used in 5'RACE amplification step.
+      --adapt [file]                  Path to the txt/fasta file containing the sequence of 5'RACE adapter.
+      --gsp [file]                    Path to the txt/fasta file containing the sequence of gene-specific primer used in 5'RACE amplification step.
       
     References:
       --genome [file]                 Path to the fasta file containing the genome.
@@ -128,11 +128,18 @@ Channel
     .ifEmpty { error "No fast5/q folder defined." }
     .set { input }
 
+/*
 Channel
-    .of( params.adapt )
+    .fromPath( params.adapt )
     .ifEmpty { error "No adapter sequence defined." }
     .set { adapt }
 
+Channel
+    .fromPath( params.gsp )
+    .ifEmpty { error "No adapter sequence defined." }
+    .set { gsp }
+*/
+
 Channel
     .fromPath( params.genome )
     .ifEmpty { error "No genome defined, a fasta file containing the full length preC RNA from HBV genome." }
@@ -164,7 +171,6 @@ if(!params.skipBC) {
   }
 }
 
-include { barecode } from "./nf_modules/barecode/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"
@@ -187,7 +193,6 @@ include { rna_count } from "./nf_modules/rna_count/main.nf"
 
 workflow {
 
-
   //######################## BASECALLING ########################
 
   if(params.skipBC) { // we take fastq files as input and skip basecalling

src/nf_modules/junction_nanosplicer/main.nf

@@ -23,6 +23,5 @@ process junctions_nanosplicer{
     mkdir ${barcode}
     cd ${barcode}/
     Rscript /Junctions_NanoSplicer.R -c ../${txt} -j ../${csv}
-    mv identified_SPvariants.csv ${barcode}_identified_SPvariants.csv
     """
 }
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src/nf_modules/ont-guppy/main.nf

@@ -39,8 +39,10 @@ process basecall_fast5_gpu {
 """
 echo "Start basecalling using GPUs."
 # guppy_basecaller --print_workflows
+find -type f -name "*.fast5" > allfast5files.txt
 guppy_basecaller --compress_fastq \
    -i ${fast5_folder} \
+   --input_file_list allfast5files.txt \
    -s . \
    --flowcell ${params.flowcell} \
    --kit ${params.kit} \
@@ -82,8 +84,10 @@ process basecall_fast5_cpu {
   script:
 """
 echo "Start basecalling using CPUs."
+find ${fast5_folder} -type f -name "*.fast5" > allfast5files.txt
 guppy_basecaller --compress_fastq \
-   -i ${fast5_folder} \
+   -i / \
+   --input_file_list allfast5files.txt \
    -s . \
    --cpu_threads_per_caller ${params.cpu_threads_per_caller} \
    --num_callers ${params.num_callers} \

src/nf_modules/start_positions/main.nf

@@ -23,8 +23,6 @@ process start_position_individuals{
     mkdir ${barcode}
     cd ${barcode}/
     Rscript /Start_positions.R -i ../${start_position_counts}
-    mv classification_of_reads_per_RNA.txt ${barcode}_classification_of_reads_per_RNA.txt
-    mv Count_reads_per_promoter.tsv ${barcode}_count_reads_per_promoter.tsv
     mv Rplots.pdf ${barcode}_Rplots.pdf
     """
 }
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