@@ -24,8 +24,8 @@ The arguments of this pipeline are described in the table below:
...
@@ -24,8 +24,8 @@ The arguments of this pipeline are described in the table below:
| -profile | The profile to use. This can be **docker** or **singularity** to run the pipeline in docker or singularity container respectively. This can also be **psmn** to launch the analysis on the PSMN |
| -profile | The profile to use. This can be **docker** or **singularity** to run the pipeline in docker or singularity container respectively. This can also be **psmn** to launch the analysis on the PSMN |
| --input [path] | Path to the folder containing fast5 files. If skip basecalling option enabled, path to fastq files folder. |
| --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. |
| --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. HBV reference sequence preCore available in data folder. |
| --gtf [file] | Path to the gtf file containing the genome annotation. |
| --gtf [file] | Path to the gtf file containing the genome annotation. HBV reference preCore annotation available in data folder. |
| --skipBC [boolean] | Skip basecalling step. If truen give fastq folder as input. Default: true. |
| --skipBC [boolean] | Skip basecalling step. If truen give fastq folder as input. Default: true. |
