Merge branch 'Alia' into 'master'

Mise à jour du readme

See merge request testoni-lab/bolero!4

README.md

@@ -13,6 +13,8 @@ git clone git@gitbio.ens-lyon.fr:xgrand/bolero.git
 ## Getting Started
 
 The pipeline `src/bolero.nf` works a nextflow configuration file `src/nextflow.config`.
+The typical command for running the pipeline is as follows:
+`nextflow ./src/bolero.nf -c ./src/nextflow.config -profile singularity`
 
 The arguments of this pipeline are described in the table below:
 
@@ -24,11 +26,17 @@ The arguments of this pipeline are described in the table below:
 | --adapt [str] | Sequence of 5'RACE adapter. |
 | --genome [file] | Path to the fasta file containing the genome. |
 | --gtf [file] | Path to the gtf file containing the genome annotation. |
+| --skipBC [boolean] | Skip basecalling step. If truen give fastq folder as input. Default: true. |
 | --flowcell [str] | Nanopore flowcell. Default = FLO-MIN106. |
 | --kit [str] | Nanopore kit. Default = SQK-PBK004. |
-| --mode [str] | Configuration to Guppy basecaller. Available: cpu, gpu. "gpu" mode is dedicated to NVIDIA Cuda compatible system according to Guppy specifications, default "cpu". |
-| --skipBC [Boolean] | Skip basecalling step. If TRUE, give fastq folder as input. |
-| --help | Display this help message. |
+| --gpu_mode [str] | Guppy basecaller configuration. Default: false. 
+"gpu" mode is dedicated to NVIDIA Cuda compatible system according to Guppy specifications. |
+| --min_qscore [float] | Minimum quality score threshold, default = 7.0. |
+| --gpu_runners_per_device [int] | Number of runner per device, default = 32 (refer to guppy manual). |
+| --num_callers [int] | Number of callers, default = 16 (refer to guppy manual). |
+| --chunks_per_runner [int] | Number of chunks per runner, default = 512 (refer to guppy manual). |
+| --chunks_size [int] | Chunck size, default = 1900 (refer to guppy manual). |
+| --help --h | Display this help message. |
 
 ## Contributing
 
@@ -45,4 +53,6 @@ This project is licensed under the CeCiLL License- see the [LICENSE](LICENSE) fi
 
 ## To Do:
 
-Give the user the possibility to choose the basecalling configuration file.
+* Give the user the possibility to choose the basecalling configuration file
+* Change jpg to png in Start_positions.R
+* Correct seqkit concatenate

src/.docker_modules/r-bolero/1.0/Start_positions.R

@@ -69,7 +69,7 @@ ggplot(df_parsed, aes(Start_position, nb_reads)) +
   theme(axis.text.x = element_text(angle = 45)
   )
 
-ggsave(paste0(filename,".jpg"),
+ggsave(paste0(filename,".png"),
        plot = last_plot(),
        scale = 2,
        width = 1920,
@@ -201,7 +201,7 @@ plot_camembert <- function(barcode, df, tot) {
   
   print(camembert)
   
-  ggsave(filename = paste0("./Reads_start_promoters_", barcode, "_camembert.jpg"),
+  ggsave(filename = paste0("./Reads_start_promoters_", barcode, "_camembert.png"),
          plot = last_plot(),
          scale = 1,
          width = 1920,

src/nf_modules/junction_nanosplicer/main.nf

@@ -17,7 +17,7 @@ process junctions_nanosplicer{
   output:
     path("Rplots.pdf")
     path("JWR_check_parsed.csv")
-    path("*.jpg")
+    path("*.png")
     path("identified_SPvariants.csv"), emit: identified_SPvariants
 
   script:

src/nf_modules/rna_count/main.nf

@@ -17,7 +17,7 @@ process rna_count{
   output:
     path("*.csv")
     path("*.pdf")
-    path("*.jpg")
+    path("*.png")
 
   script:
     """

src/nf_modules/start_positions/main.nf

@@ -14,7 +14,7 @@ process start_position_individuals{
 
   output:
     path("Rplots.pdf")
-    path("*.jpg")
+    path("*.png")
     path("Count_reads_per_promoter.tsv")
     path("classification_of_reads_per_RNA.txt"), emit: classification_of_reads