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Commit cd8b888d authored by Xavier Grand's avatar Xavier Grand
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Merge branch 'Alia' into 'master'

Mise à jour du readme

See merge request testoni-lab/bolero!4
parents 62517165 a1448e34
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...@@ -13,6 +13,8 @@ git clone git@gitbio.ens-lyon.fr:xgrand/bolero.git ...@@ -13,6 +13,8 @@ git clone git@gitbio.ens-lyon.fr:xgrand/bolero.git
## Getting Started ## Getting Started
The pipeline `src/bolero.nf` works a nextflow configuration file `src/nextflow.config`. 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: 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: ...@@ -24,11 +26,17 @@ The arguments of this pipeline are described in the table below:
| --adapt [str] | Sequence of 5'RACE adapter. | | --adapt [str] | Sequence of 5'RACE adapter. |
| --genome [file] | Path to the fasta file containing the genome. | | --genome [file] | Path to the fasta file containing the genome. |
| --gtf [file] | Path to the gtf file containing the genome annotation. | | --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. | | --flowcell [str] | Nanopore flowcell. Default = FLO-MIN106. |
| --kit [str] | Nanopore kit. Default = SQK-PBK004. | | --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". | | --gpu_mode [str] | Guppy basecaller configuration. Default: false.
| --skipBC [Boolean] | Skip basecalling step. If TRUE, give fastq folder as input. | "gpu" mode is dedicated to NVIDIA Cuda compatible system according to Guppy specifications. |
| --help | Display this help message. | | --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 ## Contributing
...@@ -45,4 +53,6 @@ This project is licensed under the CeCiLL License- see the [LICENSE](LICENSE) fi ...@@ -45,4 +53,6 @@ This project is licensed under the CeCiLL License- see the [LICENSE](LICENSE) fi
## To Do: ## 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
...@@ -69,7 +69,7 @@ ggplot(df_parsed, aes(Start_position, nb_reads)) + ...@@ -69,7 +69,7 @@ ggplot(df_parsed, aes(Start_position, nb_reads)) +
theme(axis.text.x = element_text(angle = 45) theme(axis.text.x = element_text(angle = 45)
) )
ggsave(paste0(filename,".jpg"), ggsave(paste0(filename,".png"),
plot = last_plot(), plot = last_plot(),
scale = 2, scale = 2,
width = 1920, width = 1920,
...@@ -201,7 +201,7 @@ plot_camembert <- function(barcode, df, tot) { ...@@ -201,7 +201,7 @@ plot_camembert <- function(barcode, df, tot) {
print(camembert) print(camembert)
ggsave(filename = paste0("./Reads_start_promoters_", barcode, "_camembert.jpg"), ggsave(filename = paste0("./Reads_start_promoters_", barcode, "_camembert.png"),
plot = last_plot(), plot = last_plot(),
scale = 1, scale = 1,
width = 1920, width = 1920,
......
...@@ -17,7 +17,7 @@ process junctions_nanosplicer{ ...@@ -17,7 +17,7 @@ process junctions_nanosplicer{
output: output:
path("Rplots.pdf") path("Rplots.pdf")
path("JWR_check_parsed.csv") path("JWR_check_parsed.csv")
path("*.jpg") path("*.png")
path("identified_SPvariants.csv"), emit: identified_SPvariants path("identified_SPvariants.csv"), emit: identified_SPvariants
script: script:
......
...@@ -17,7 +17,7 @@ process rna_count{ ...@@ -17,7 +17,7 @@ process rna_count{
output: output:
path("*.csv") path("*.csv")
path("*.pdf") path("*.pdf")
path("*.jpg") path("*.png")
script: script:
""" """
......
...@@ -14,7 +14,7 @@ process start_position_individuals{ ...@@ -14,7 +14,7 @@ process start_position_individuals{
output: output:
path("Rplots.pdf") path("Rplots.pdf")
path("*.jpg") path("*.png")
path("Count_reads_per_promoter.tsv") path("Count_reads_per_promoter.tsv")
path("classification_of_reads_per_RNA.txt"), emit: classification_of_reads path("classification_of_reads_per_RNA.txt"), emit: classification_of_reads
......
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