Skip to content

Point the full run scripts at build/main #129

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Merged
rcannood merged 2 commits into from
Jul 28, 2026
Merged

Point the full run scripts at build/main #129

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
2 commits
Select commit Hold shift + click to select a range
940767d
point the full run scripts at build/main
rcannood Jul 28, 2026
fec0557
update changelog
rcannood Jul 28, 2026
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
5 changes: 4 additions & 1 deletion CHANGELOG.md
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -239,4 +239,7 @@
and thus can't be directly overriden (new values given by get_donor_batch_map is int) (PR #119).

* Update flowsom mapping similarity so we subset to just markers to correct, and lisi to remove control samples
and unlabelled cells (PR #119).
and unlabelled cells (PR #119).

* Point `scripts/run_benchmark/wehi_hpc/run_full_hpc.sh` at `build/main` instead of
`build/update_ilisi`, and label the seqera full run as `full` instead of `test_subset` (PR #129).
2 changes: 1 addition & 1 deletion scripts/run_benchmark/run_full_seqeracloud.sh
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -28,4 +28,4 @@ tw launch https://github.com/openproblems-bio/task_cyto_batch_integration.git \
--params-file /tmp/params.yaml \
--entry-name auto \
--config common/nextflow_helpers/labels_tw.config \
--labels task_cyto_batch_integration,test_subset
--labels task_cyto_batch_integration,full
2 changes: 1 addition & 1 deletion scripts/run_benchmark/wehi_hpc/run_full_hpc.sh
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -21,7 +21,7 @@ publish_dir: "$publish_dir"
HERE

tw launch https://github.com/openproblems-bio/task_cyto_batch_integration.git \
--revision build/update_ilisi \
--revision build/main \
--pull-latest \
--main-script target/nextflow/workflows/run_benchmark/main.nf \
--workspace 80689470953249 \
Expand Down
Loading