Contribution instructions, fix MPXV Erasmus URLs

README.md

@@ -4,28 +4,48 @@
 
 **🚨 Migration to v1 scheme specification in progress**
 
-A versioned and schematised community repository of tiled amplicon primer scheme definitions (created with e.g. [Primal Scheme](https://primalscheme.com)) for pathogen sequencing, made with the objective of eliminating ambiguity in scheme naming and versioning and maximising the findability, accessibility, interoperability and reusability ([FAIRness](https://www.go-fair.org/fair-principles/)) of primer scheme definitions and associated sequencing data.
+A versioned and schematised community repository of tiled amplicon primer scheme definitions (created with e.g. [Primal Scheme](https://primalscheme.com)) for pathogen sequencing, made with the objective of eliminating ambiguity in scheme naming and versioning and maximising the findability, accessibility, interoperability and reusability ([FAIRness](https://www.go-fair.org/fair-principles/)) of primer schemes and associated sequencing data. An example of a canonical primer scheme name is `sars-cov-2/midnight/1200/v1.0.0`.
+
+The repository includes a top-level machine readable [index](https://github.com/pha4ge/primer-schemes/blob/main/index.yml) of available primer scheme definitions.
+
 
 
 ## Scheme specification
 
 A scheme definition has three components:
 
-1.  A reference sequence ([`reference.fasta`](https://github.com/pha4ge/primer-schemes/blob/main/sars-cov-2/artic/v4.1/reference.fasta))
-2.  A seven column BED file of primer sequences & positions in reference coordinates ([`primer.bed`](https://github.com/pha4ge/primer-schemes/blob/main/sars-cov-2/artic/v4.1/primer.bed))
-3.  A metadata file in YAML format adhering to [this schema](https://github.com/pha4ge/primaschema/blob/main/src/primaschema/schema/info.yml) ([`info.yml`](https://github.com/pha4ge/primer-schemes/blob/main/schemes/sars-cov-2/artic/400/v4.1.0/info.yml))
+1.  A reference sequence (e.g. [`reference.fasta`](https://github.com/pha4ge/primer-schemes/blob/main/schemes/sars-cov-2/artic/400/v4.1.0/reference.fasta))
+2.  A seven column Primal Scheme-like BED file of primer sequences & coordinates (e.g. [`primer.bed`](https://github.com/pha4ge/primer-schemes/blob/main/schemes/sars-cov-2/artic/400/v4.1.0/primer.bed))
+3.  A metadata file in YAML format adhering to a [schema](https://github.com/pha4ge/primaschema/blob/main/src/primaschema/schema/info.yml) (e.g. [`info.yml`](https://github.com/pha4ge/primer-schemes/blob/main/schemes/sars-cov-2/artic/400/v4.1.0/info.yml))
+
 
 
+## Tooling
 
-## Contributing new schemes
+The repository's companion tool [Primaschema](https://github.com/pha4ge/primaschema) is used to automatically validate schemes in this repository, create graphics and manage checksums, as well as generate a six column scheme.bed for legacy tool compatibility. It may be installed standalone using `pip install` for fetching, validating and interrogating primer schemes.
 
-*Coming soon*
 
 
+## Contributing new scheme definitions
 
-## Tooling
+We encourage contributions of any schemes the others might wish to use, especially if sequencing data has been or will be deposited publicly. We're working to make this process easier, but in the meantime please either follow the instructions below to send us a draft scheme, or create a pull request using GitHub if comfortable doing so.
+
+A scheme definition comprises *i)* a reference sequence (`reference.fasta`), *ii)* a BED file of primer sequences & reference coordinates (`primer.bed`), and *iii)*, a metadata file in YAML format adhering to [this schema](https://github.com/pha4ge/primaschema/blob/main/src/primaschema/schema/info.yml), called `info.yml`. If you've created a scheme you probably already have i) and ii), and need to make `info.yml`. It's easiest to begin by modifying a copy of an existing `info.yml` [such as this one](https://github.com/pha4ge/primer-schemes/blob/main/schemes/sars-cov-2/eden/2500/v1.0.0/info.yml).
 
-The repository's companion tool [Primaschema](https://github.com/pha4ge/primaschema) is used to automatically validate schemes in this repository and create plots, as well as generate a six column scheme.bed for legacy tool compatibility. It can also be installed standalone.
+1. Check that the `organism` field in your scheme's `info.yml` references the correct pathogen. If there are no existing schemes for the target pathogen, please [open a GitHub issue](https://github.com/pha4ge/primer-schemes/issues) to request it be added.
+2. Choose a scheme name and version, e.g `midnight` and `v1.0.0`. The name should not include special characters except hyphens.
+    - If adding a new scheme, choose any name, preferably not referencing the organism name. 
+    - If updating your existing scheme, keep the same name and update the version:
+      - Versions must take the form `v{major}.{minor}.{patch}`
+      - For primer changes beyond adding primers, increment the *major* version
+      - If only adding primers with respect to an existing version, increment the *minor* version
+      - For smaller technical changes, the *patch* version may be incremented
+    - If updating a third party's existing scheme, you may propose a new scheme name with version `v1.0.0` rather than increment the existing scheme's version.
+3. Complete the `name` and `version` fields inside your new scheme's `info.yml`, along with the other required fields:
+    - `amplicon_size`: the approximate integer amplicon length in bp
+    - `developers`: a list of developer names or organisations
+4. [Open a GitHub issue](https://github.com/pha4ge/primer-schemes/issues) attaching or linking to your `reference.fasta`, `primer.bed` and `info.yml` files.
+5. If you wish, you may install [primaschema](https://github.com/pha4ge/primaschema) and run `primaschema build {scheme-directory}`to validate your newly created scheme and add checksums etc. However this is not necessary.
 
 
 

index.yml

@@ -24,13 +24,13 @@ schemes:
   - Matthijs Welkers
   - Marcel Jonges
   - Anton van den Ouden
-  definition_url: https://github.com/pha4ge/primer-schemes/tree/main/sars-cov-2/artic/v4.1
-  source_url: https://github.com/quick-lab/primerschemes/tree/main/primerschemes/artic-sars-cov-2/400/v4.1.0
+  definition_url: https://github.com/pha4ge/primer-schemes/tree/main/schemes/mpxv/erasmus/2500/v1.0.0
+  source_url: https://www.protocols.io/view/monkeypox-virus-whole-genome-sequencing-using-comb-n2bvj6155lk5
   citations:
   - https://www.protocols.io/view/monkeypox-virus-whole-genome-sequencing-using-comb-n2bvj6155lk5
   license: CC-BY-SA-4.0
   primer_checksum: primaschema:9acd3f5ce5711ed2
-  reference_checksum: primaschema:31ff1b123bbce197
+  reference_checksum: primaschema:17cbcde0cfff7158
 - organism: mpxv
   name: yale
   amplicon_size: 2000
@@ -236,16 +236,16 @@ schemes:
   license: CC-BY-SA-4.0
   primer_checksum: primaschema:294136d77eb67db8
   reference_checksum: primaschema:b1acd7163146bf17
-- name: eden
+- organism: sars-cov-2
+  name: eden
   amplicon_size: 2500
   version: v1.0.0
-  organism: sars-cov-2
   aliases:
   - sydney
   developers:
   - John-Sebastian Eden
   - Eby Sim
-  definition_url: https://github.com/pha4ge/primer-schemes/tree/main/sars-cov-2/eden/v1
+  definition_url: https://github.com/pha4ge/primer-schemes/blob/main/schemes/sars-cov-2/eden/2500/v1.0.0
   citations:
   - https://dx.doi.org/10.17504/protocols.io.befyjbpw
   notes:

schemes/mpxv/erasmus/2500/v1.0.0/info.yml

@@ -7,8 +7,7 @@ developers:
 - Matthijs Welkers
 - Marcel Jonges
 - Anton van den Ouden
-definition_url: https://github.com/pha4ge/primer-schemes/tree/main/sars-cov-2/artic/v4.1
-source_url: https://github.com/quick-lab/primerschemes/tree/main/primerschemes/artic-sars-cov-2/400/v4.1.0
+definition_url: https://github.com/pha4ge/primer-schemes/tree/main/schemes/mpxv/erasmus/2500/v1.0.0
 citations:
 - https://www.protocols.io/view/monkeypox-virus-whole-genome-sequencing-using-comb-n2bvj6155lk5
 license: CC-BY-SA-4.0

schemes/sars-cov-2/eden/2500/v1.0.0/info.yml

@@ -1,14 +1,14 @@
 schema_version: 1.0.0a
+organism: sars-cov-2
 name: eden
 amplicon_size: 2500
 version: v1.0.0
-organism: sars-cov-2
 aliases:
 - sydney
 developers:
 - John-Sebastian Eden
 - Eby Sim
-definition_url: https://github.com/pha4ge/primer-schemes/tree/main/sars-cov-2/eden/v1
+definition_url: https://github.com/pha4ge/primer-schemes/blob/main/schemes/sars-cov-2/eden/2500/v1.0.0
 citations:
 - https://dx.doi.org/10.17504/protocols.io.befyjbpw
 notes: