Introduction

On this page you can see the beating heart of sanger-tol - the size of our community and the output of our work.

Please bear in mind the following points when looking over these numbers:

  • Pipelines maybe worked on before they are transferred to sanger-tol. The age, stars and other metrics of the original parent repository are not shown.
  • Metrics are for the default (main) branch only
  • Commits and contributors are only counted if associated with a GitHub account
  • nextflow pull and nextflow run uses git to clone a remote repo the first time it runs, so the clones count gives some idea of usage. However:
    • Unique cloners is based on IP address, so will under-represent institutional users sharing a single external IP address
    • Unique cloners is based on IP address, so will over-represent cloud users using multiple IP addresses
    • Traditional HPC centres may share workflow installations, so only have one clone for many users  /  pipeline runs
    • Cloud users will typically spin up a new instance and clone the workflow every time that they run a pipeline.
  • Clone counts and repositoriy views are only available for two weeks - longer term data collection for sanger-tol repos started in July 2023 This is when we started counting the totals.
  • Metrics are fetched once per day (last checked 2024-10-13).

Community

The numbers below track our growth over the various channels that the sanger-tol community operates in.

Click a number to see how the community has grown over time

34

GitHub organisation members

39

GitHub contributors

GitHub organisation members

We use GitHub to manage all of the code written for sanger-tol. It's a fantastic platform and provides a huge number of tools. We have a GitHub organisation called sanger-tol.

It is not required to be a member of the sanger-tol GitHub organisation to contribute. However, members get the sanger-tol logo listed on their profile page and full write-access to all sanger-tol repositories.

By default, organisation membership is private. This is why you'll see a lower number if you visit the sanger-tol organisation page and are not a member.

Download as SVG  /  Reset zoom

GitHub contributors

Anybody can fork sanger-tol repositories and open a pull-request. Here we count how many different people have contributed at least one commit to an sanger-tol repository, or created or commented on an issue or pull-request.

Plot truncated to start of 2022 (some pipelines moved to sanger-tol so have older contributions).

Download as SVG  /  Reset zoom

Code stats

Whilst we always prefer quality over quantity, these numbers reflect the work output from the sanger-tol community.

18

Repositories

543

Pull Requests

5.45K

Commits

507

Issues

Repository traffic

Every time a nextflow user pulls a sanger-tol pipeline, the repository is cloned. Here we can track how much that happens across all sanger-tol repositories. Please note that these numbers come with some caveats [ see more ].

Additionally, GitHub tracks how many times people view repository web pages on github.com.

SVG  /  Reset zoom Git clones: All sanger-tol repositories
SVG  /  Reset zoom Visitors: All sanger-tol repositories

Pull Requests

When people contribute code to a sanger-tol repository, we conduct a "Pull request" - other members of the sanger-tol community review the proposed code and make suggestions, before merging into the main repository.

Pull Request response times

Pull-requests are reviewed by the sanger-tol community - they can contain discussion on the code and can be merged and closed. We aim to be prompt with reviews and merging. Note that some PRs can be a simple type and so very fast to merge, others can be major pipeline updates.

First response is when a comment is made by a GitHub user other than the original PR author

Download as SVG  /  Reset zoom

Issues

GitHub issues can be created to log feature requests, bug reports or questions.

Issue response times

A sign of an active community is a quick response time to issues. Here we see a frequency histogram of how long it takes to respond to and close issues.

First response is when a comment is made by a GitHub user other than the original issue author

Download as SVG  /  Reset zoom

Contributor Leaderboard

We value each and every contribution to sanger-tol, no matter how small. However, that doesn't mean that we can not get competitive!

Here are the latest stats of who has contributed the greatest number of commits.

Remember
  • There is more to contributing than commits! We're not counting issue comments, reviews or anything else here.
  • People merging pull-requests get bonus commit counts from those merge commits.
  • Some people commit often, others not so much. So it's not a perfect representation of amount of work - just a bit of fun!
  • main branch only, and all of the other caveats..
@DLBPointon
1841
treeval 1369
@muffato
1116
blobtoolkit 196
@yumisims
519
treeval 390
@priyanka-surana
448
readmapping 150
@weaglesBio
436
treeval 419
@gq1
316
variantcalling 230
@BethYates
220
genomenote 218
@alxndrdiaz
177
blobtoolkit 177
@zb32
121
blobtoolkit 121
@tkchafin
110
readmapping 99
@SandraBabirye
genomenote 59
@ksenia-krasheninnikova
genomeassembly 52
@reichan1998
readmapping 10
@eeaunin
ascc 13
@sanger-tolsoft
variantcalling 2
@nf-core-bot
variantcalling 2
@sujaikumar
blobtoolkit 2
@scorreard
curationpretext 1

Pipeline numbers

All sanger-tol pipelines are only considered stable when they have at least one release. Until then, they are classed as "in development".

Pipelines

Click a row to see detailed statistics for that repository.

  Name Age Releases Committers Commits Stargazers Watchers Network Forks Clones Unique cloners Repo views Unique repo visitors
  Total: 15 pipelines 39 18 unique 5450 104 114 27 16306 3526 70751 7653
sanger-tol/blobtoolkit 2 years 5 7 626 11 7 1 1291 275 5697 684
sanger-tol/ensemblgenedownload 2 years 3 2 137 1 7 1 361 127 463 106
sanger-tol/ensemblrepeatdownload 2 years 2 2 146 1 6 0 345 119 406 89
sanger-tol/genomeassembly 2 years 0 7 144 20 11 2 1927 316 11272 1069
sanger-tol/genomenote 2 years 8 7 590 24 8 6 2007 440 8074 1060
sanger-tol/insdcdownload 2 years 3 3 208 1 7 2 639 202 1330 162
sanger-tol/readmapping 3 years 7 5 376 9 6 6 1013 230 7220 751
sanger-tol/sequencecomposition 2 years 1 1 78 2 7 0 338 112 382 84
sanger-tol/treeval 2 years 3 6 2249 22 7 3 3868 626 22361 2264
sanger-tol/variantcalling 2 years 5 5 272 3 11 2 1018 259 3712 442
sanger-tol/curationpretext 1 year 1 5 154 5 8 3 1397 386 2767 400
sanger-tol/ascc 1 year 0 4 414 3 8 0 1929 350 6607 471
sanger-tol/longreadmag 7 months 0 1 2 1 5 0 36 34 83 16
sanger-tol/genealignment 4 months 0 1 1 0 4 0 30 24 74 20
sanger-tol/ear 3 months 1 1 53 0 5 0 107 26 303 35
sanger-tol/MicroFinder 1 month 0 0 1 3 1
sanger-tol/Pretext-curation-tools 3 days 0 0 0 2 0
sanger-tol/rapid-curation 2 days 0 0 0 2 0
  Name Age Releases Committers Commits Stargazers Watchers Network Forks Clones Unique cloners Repo views Unique repo visitors