README.md modif

README.md

@@ -16,6 +16,9 @@ The pipeline `src/bolero.nf` works a nextflow configuration file `src/nextflow.c
 The typical command for running the pipeline is as follows:
 `nextflow ./src/bolero.nf -c ./src/nextflow.config -profile singularity`
 
+The typical command to obtain help:
+`nextflow ./src/bolero.nf --help`
+
 The arguments of this pipeline are described in the table below:
 
 |         Arguments           |                             Description                             | 
@@ -37,6 +40,31 @@ The arguments of this pipeline are described in the table below:
 | --chunks_size [int] | Chunck size, default = 1900 (refer to guppy manual). |
 | --help --h | Display this help message. |
 
+## Test Bolero
+
+1. simulate 5'RACE sequenced reads:
+Require pbsim3 software: https://github.com/yukiteruono/pbsim3
+
+To produce a complete transcriptome you can run:
+```
+mkdir -p 01_basecalling
+for i in $(seq 1 30)
+do
+	extract=$(cut -f1 expression.transcript_${i})
+	mkdir 01_basecalling/${extract}
+	pbsim --strategy trans --transcript expression.transcript_${i} --id-prefix ${extract} --method errhmm --errhmm <PATH_TO_pbsim3>/data/ERRHMM-ONT.model
+	mv sd.fastq 01_basecalling/${extract}/${extract}.fastq
+	mv sd.maf 01_basecalling/${extract}/${extract}.maf
+	gzip 01_basecalling/${extract}/${extract}.fastq
+done
+```
+
+2. run Bolero:
+```
+cd <PATH_TO_Bolero>
+nextflow ./src/bolero.nf -c ./src/nextflow.config -profile <PROFILE> --input 01_basecalling
+```
+
 ## Reference sequence
 
 The HBV reference sequence, genotype D ayw, is available in "data" folder.
@@ -51,9 +79,10 @@ If you want to add more tools to this project, please read the [CONTRIBUTING.md]
 * **Alia Rifki** - *Contributor*
 
 ## License
-
+[Info](#){.btn .btn-info}
 This project is licensed under the CeCiLL License- see the [LICENSE](LICENSE) file for details.
 
+[Warning](#){.btn .btn-warning}
 The optional basecalling and demultiplexing steps may be carried out if necessary but are not executed automatically. 
 To execute these steps, it is essential to adhere to the guidelines provided with the Guppy software from Oxford Nanopore Technologies.