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Updated the issue link so that issues are created with the "user requ…
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muffato committed Jun 18, 2024
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18 changes: 9 additions & 9 deletions markdown/resources/genome_after_party.md
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Expand Up @@ -17,7 +17,7 @@ A portal is being developed to automate the production of genome note publicatio

> You can see all planned features and requests on the [project board](https://github.com/orgs/sanger-tol/projects/3).
> Currently, we plan to **download** all primary and alternative ToL assemblies, as well as non-ToL (VGP, _Lepidoptera_, and requests) assemblies, and run the analysis pipelines **only on the primary** assemblies.
> [Let us know](https://github.com/sanger-tol/pipelines-website/issues/new?assignees=muffato&labels=pipeline%2Cenhancement&projects=&template=genome_after_party_feature_request.yaml&title=%5BFeature%5D%3A+) if some analyses would be useful to have on the other assemblies too.
> [Let us know](https://github.com/sanger-tol/pipelines-website/issues/new?assignees=muffato&labels=user%20request&projects=&template=genome_after_party_feature_request.yaml&title=%5BFeature%5D%3A+) if some analyses would be useful to have on the other assemblies too.
# INSDC Download {#insdcdownload}

Expand All @@ -37,7 +37,7 @@ A portal is being developed to automate the production of genome note publicatio
- Update pipeline template
- Update samplesheet validation steps

If you have an idea for a new feature – [send us your request](https://github.com/sanger-tol/pipelines-website/issues/new?assignees=muffato&labels=pipeline%2Cenhancement&projects=&template=genome_after_party_feature_request.yaml&title=%5BFeature%5D%3A+). You can see all planned features and requests on the [project board](https://github.com/orgs/sanger-tol/projects/3).
If you have an idea for a new feature – [send us your request](https://github.com/sanger-tol/pipelines-website/issues/new?assignees=muffato&labels=user%20request&projects=&template=genome_after_party_feature_request.yaml&title=%5BFeature%5D%3A+). You can see all planned features and requests on the [project board](https://github.com/orgs/sanger-tol/projects/3).

# Ensembl Repeat Download {#ensemblrepeatdownload}

Expand All @@ -55,7 +55,7 @@ If you have an idea for a new feature – [send us your request](https://github.
- Update pipeline template
- Update samplesheet validation steps

If you have an idea for a new feature – [send us your request](https://github.com/sanger-tol/pipelines-website/issues/new?assignees=muffato&labels=pipeline%2Cenhancement&projects=&template=genome_after_party_feature_request.yaml&title=%5BFeature%5D%3A+). You can see all planned features and requests on the [project board](https://github.com/orgs/sanger-tol/projects/3).
If you have an idea for a new feature – [send us your request](https://github.com/sanger-tol/pipelines-website/issues/new?assignees=muffato&labels=user%20request&projects=&template=genome_after_party_feature_request.yaml&title=%5BFeature%5D%3A+). You can see all planned features and requests on the [project board](https://github.com/orgs/sanger-tol/projects/3).

# Ensembl Gene Download {#ensemblgenedownload}

Expand All @@ -74,7 +74,7 @@ If you have an idea for a new feature – [send us your request](https://github.
- Update pipeline template
- Update samplesheet validation steps

If you have an idea for a new feature – [send us your request](https://github.com/sanger-tol/pipelines-website/issues/new?assignees=muffato&labels=pipeline%2Cenhancement&projects=&template=genome_after_party_feature_request.yaml&title=%5BFeature%5D%3A+). You can see all planned features and requests on the [project board](https://github.com/orgs/sanger-tol/projects/3).
If you have an idea for a new feature – [send us your request](https://github.com/sanger-tol/pipelines-website/issues/new?assignees=muffato&labels=user%20request&projects=&template=genome_after_party_feature_request.yaml&title=%5BFeature%5D%3A+). You can see all planned features and requests on the [project board](https://github.com/orgs/sanger-tol/projects/3).

# Sequence Composition {#sequencecomposition}

Expand Down Expand Up @@ -110,7 +110,7 @@ _Only if there is an actual demand! Use the form below to indicate interest._
- Telomeric repeat annotation (tool to be confirmed)
- Centromeric repeat annotation (tool to be confirmed)

If you have an idea for a new feature or would like this pipeline to run on other assemblies – [send us your request](https://github.com/sanger-tol/pipelines-website/issues/new?assignees=muffato&labels=pipeline%2Cenhancement&projects=&template=genome_after_party_feature_request.yaml&title=%5BFeature%5D%3A+). You can see all planned features and requests on the [project board](https://github.com/orgs/sanger-tol/projects/3).
If you have an idea for a new feature or would like this pipeline to run on other assemblies – [send us your request](https://github.com/sanger-tol/pipelines-website/issues/new?assignees=muffato&labels=user%20request&projects=&template=genome_after_party_feature_request.yaml&title=%5BFeature%5D%3A+). You can see all planned features and requests on the [project board](https://github.com/orgs/sanger-tol/projects/3).

# Read Mapping {#readmapping}

Expand All @@ -137,7 +137,7 @@ If you have an idea for a new feature or would like this pipeline to run on othe
- Support compression with `crumble` for aligned files
- Support multiple output options – BAM, compressed BAM, CRAM, compressed CRAM

If you have an idea for a new feature or would like this pipeline to run on other assemblies – [send us your request](https://github.com/sanger-tol/pipelines-website/issues/new?assignees=muffato&labels=pipeline%2Cenhancement&projects=&template=genome_after_party_feature_request.yaml&title=%5BFeature%5D%3A+). You can see all planned features and requests on the [project board](https://github.com/orgs/sanger-tol/projects/3).
If you have an idea for a new feature or would like this pipeline to run on other assemblies – [send us your request](https://github.com/sanger-tol/pipelines-website/issues/new?assignees=muffato&labels=user%20request&projects=&template=genome_after_party_feature_request.yaml&title=%5BFeature%5D%3A+). You can see all planned features and requests on the [project board](https://github.com/orgs/sanger-tol/projects/3).

# Variant Calling {#variantcalling}

Expand All @@ -162,7 +162,7 @@ If you have an idea for a new feature or would like this pipeline to run on othe
- Add variant calling for short read data
- Ability to process and analyse population genomics data

If you have an idea for a new feature or would like this pipeline to run on other assemblies – [send us your request](https://github.com/sanger-tol/pipelines-website/issues/new?assignees=muffato&labels=pipeline%2Cenhancement&projects=&template=genome_after_party_feature_request.yaml&title=%5BFeature%5D%3A+). You can see all planned features and requests on the [project board](https://github.com/orgs/sanger-tol/projects/3).
If you have an idea for a new feature or would like this pipeline to run on other assemblies – [send us your request](https://github.com/sanger-tol/pipelines-website/issues/new?assignees=muffato&labels=user%20request&projects=&template=genome_after_party_feature_request.yaml&title=%5BFeature%5D%3A+). You can see all planned features and requests on the [project board](https://github.com/orgs/sanger-tol/projects/3).

# BlobToolKit {#blobtoolkit}

Expand All @@ -185,7 +185,7 @@ If you have an idea for a new feature or would like this pipeline to run on othe

- Update pipeline template

If you have an idea for a new feature or would like this pipeline to run on other assemblies – [send us your request](https://github.com/sanger-tol/pipelines-website/issues/new?assignees=muffato&labels=pipeline%2Cenhancement&projects=&template=genome_after_party_feature_request.yaml&title=%5BFeature%5D%3A+). You can see all planned features and requests on the [project board](https://github.com/orgs/sanger-tol/projects/3).
If you have an idea for a new feature or would like this pipeline to run on other assemblies – [send us your request](https://github.com/sanger-tol/pipelines-website/issues/new?assignees=muffato&labels=user%20request&projects=&template=genome_after_party_feature_request.yaml&title=%5BFeature%5D%3A+). You can see all planned features and requests on the [project board](https://github.com/orgs/sanger-tol/projects/3).

# Genome Note {#genomenote}

Expand All @@ -206,4 +206,4 @@ If you have an idea for a new feature or would like this pipeline to run on othe
- Support Merqury and Meryl for k-mer analysis
- Run GFA stats

If you have an idea for a new feature or would like this pipeline to run on other assemblies – [send us your request](https://github.com/sanger-tol/pipelines-website/issues/new?assignees=muffato&labels=pipeline%2Cenhancement&projects=&template=genome_after_party_feature_request.yaml&title=%5BFeature%5D%3A+). You can see all planned features and requests on the [project board](https://github.com/orgs/sanger-tol/projects/3).
If you have an idea for a new feature or would like this pipeline to run on other assemblies – [send us your request](https://github.com/sanger-tol/pipelines-website/issues/new?assignees=muffato&labels=user%20request&projects=&template=genome_after_party_feature_request.yaml&title=%5BFeature%5D%3A+). You can see all planned features and requests on the [project board](https://github.com/orgs/sanger-tol/projects/3).

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