diff --git a/docs/usage.md b/docs/usage.md index 76f8a2a..520f53e 100755 --- a/docs/usage.md +++ b/docs/usage.md @@ -9,16 +9,22 @@ This is a sister pipeline to [TreeVal](https://github.com/sanger-tol/treeval/) which generated a plurality of data for the curation of reference-quality genomes. curationpretext is a subset of TreeVal that produces soley the Pretext maps and accessory files Currently, the pipeline expects input data to be in a specific format. + The `--input` should be `.fasta` or `.fa` (the same format but differing suffix). + The `--cram` should point to the folder containing `.cram` files along with a `.crai` per `.cram`. + The `--pacbio` should point to the folder containing `.fasta.gz` files. If you do not have these file formats we have also included instructions on converting from common formats to our preferred format. If there is a popular public preference for a particular format, we can modify the pipeline to utilise those formats. Just submit an issue. -The conversion documentation can be found in the [TreeVal Wiki](https://github.com/sanger-tol/treeval/wiki/Data-Preparation). +The conversion documentation can be found in: + + - [TreeVal Wiki - PacBio Data](https://github.com/sanger-tol/treeval/wiki/Data-Preparation#pacbio-data). + - [TreeVal Wiki - Cram Data](https://github.com/sanger-tol/treeval/wiki/Data-Preparation#hic-data). -The pipeline currently does not ingest the accessory files into the pretext map for you, however, we have included this code in the [TreeVal Wiki](https://github.com/sanger-tol/treeval/wiki/Ingesting-PreText-Accessory-Files). +The pipeline currently does not ingest the accessory files into the pretext map for you, however, we have included this code in the [TreeVal Wiki - Ingesting PreText Accessory Files](https://github.com/sanger-tol/treeval/wiki/Ingesting-PreText-Accessory-Files). ## Running the pipeline