The download_probeset process wasn't used anymore anyway
The download_reference can be replaced with the untar module from nf-core/modules, thereby reducing the amount of custom code required.
In the future, it could be considered to support custom references with spaceranger/mkgtf and spaceranger/mkref, but I suppose 99% of use-cases are covered with prebuilt 10x references, and it is definitely not a priority for me.
PR checklist
[x] This comment contains a description of changes (with reason).
[ ] If you've fixed a bug or added code that should be tested, add tests!
[ ] If you've added a new tool - have you followed the pipeline conventions in the contribution docs
[ ] If necessary, also make a PR on the nf-core/spatialtranscriptomics branch on the nf-core/test-datasets repository.
[x] Make sure your code lints (nf-core lint).
[ ] Ensure the test suite passes (nextflow run . -profile test,docker --outdir <OUTDIR>).
[ ] Usage Documentation in docs/usage.md is updated.
[ ] Output Documentation in docs/output.md is updated.
[x] CHANGELOG.md is updated.
[ ] README.md is updated (including new tool citations and authors/contributors).
download_probeset
process wasn't used anymore anywaydownload_reference
can be replaced with theuntar
module fromnf-core/modules
, thereby reducing the amount of custom code required.In the future, it could be considered to support custom references with
spaceranger/mkgtf
andspaceranger/mkref
, but I suppose 99% of use-cases are covered with prebuilt 10x references, and it is definitely not a priority for me.PR checklist
nf-core lint
).nextflow run . -profile test,docker --outdir <OUTDIR>
).docs/usage.md
is updated.docs/output.md
is updated.CHANGELOG.md
is updated.README.md
is updated (including new tool citations and authors/contributors).