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Merged
wes-lewis merged 5 commits into from
Aug 19, 2025
Merged

Bump Viash version and update dependencies to OpenProblems #32

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f82cc48
bump viash version
rcannood Aug 11, 2025
1a694db
use openproblems dependencies
rcannood Aug 11, 2025
16c74d4
update changelog
rcannood Aug 11, 2025
c9359ac
update submodule
rcannood Aug 11, 2025
bda8b90
update script
rcannood Aug 11, 2025
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12 changes: 12 additions & 0 deletions CHANGELOG.md
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Original file line number Diff line number Diff line change
@@ -1,8 +1,20 @@
# denoising devel

## NEW FUNCTIONALITY

* Add new method: CellMapper (PR #31)

## MINOR CHANGES

* Update the Viash version to 0.9.4 (PR #32)

* Dependencies were moved to main openproblems repository (PR #32)

## BUG FIXES

* Update scPRINT, including a new default model (PR #26)


# denoising v1.0.0

## BREAKING CHANGES
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10 changes: 5 additions & 5 deletions _viash.yaml
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Expand Up @@ -3,6 +3,8 @@ organization: openproblems-bio
version: dev
license: MIT

viash_version: 0.9.4

label: Denoising
keywords: [single-cell, openproblems, benchmark, denoising]
summary: "Removing noise in sparse single-cell RNA-sequencing count data"
Expand Down Expand Up @@ -80,14 +82,12 @@ authors:
info:
github: marius1311
orcid: 0000-0002-4846-1266

repositories:
- name: core
- name: openproblems
type: github
repo: openproblems-bio/core
repo: openproblems-bio/openproblems
tag: build/main
path: viash/core

viash_version: 0.9.0

config_mods: |
.runners[.type == "nextflow"].config.labels := { lowmem : "memory = 20.Gb", midmem : "memory = 50.Gb", highmem : "memory = 100.Gb", lowcpu : "cpus = 5", midcpu : "cpus = 15", highcpu : "cpus = 30", lowtime : "time = 1.h", midtime : "time = 4.h", hightime : "time = 8.h", veryhightime : "time = 24.h" }
2 changes: 1 addition & 1 deletion common
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Submodule common updated from 65e05a to 79b884
5 changes: 2 additions & 3 deletions scripts/run_benchmark/run_full_seqeracloud.sh
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Expand Up @@ -10,7 +10,7 @@ set -e

# generate a unique id
RUN_ID="run_$(date +%Y-%m-%d_%H-%M-%S)"
publish_dir="s3://openproblems-data/resources/task_denoising/results/${RUN_ID}"
publish_dir="s3://openproblems-data/resources/results/${RUN_ID}"
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@lazappi lazappi Aug 12, 2025

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I guess you meant to remove the task name from here?

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@rcannood rcannood Aug 12, 2025

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No, the results need to be published in the task specific subdirs ^^ Coincidentally I had make the same changes but then reverted them because I realised that this in fact made sense


# write the parameters to file
cat > /tmp/params.yaml << HERE
Expand All @@ -21,11 +21,10 @@ publish_dir: "$publish_dir"
HERE

tw launch https://github.com/openproblems-bio/task_denoising.git \
--revision v1.0.0 \
--revision build/main \
--pull-latest \
--main-script target/nextflow/workflows/run_benchmark/main.nf \
--workspace 53907369739130 \
--compute-env 5DwwhQoBi0knMSGcwThnlF \
--params-file /tmp/params.yaml \
--entry-name auto \
--config common/nextflow_helpers/labels_tw.config \
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4 changes: 2 additions & 2 deletions src/workflows/process_datasets/config.vsh.yaml
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Expand Up @@ -23,8 +23,8 @@ resources:
entrypoint: run_wf
- path: /common/nextflow_helpers/helper.nf
dependencies:
- name: schema/verify_data_structure
repository: core
- name: validation/check_dataset_with_schema
repository: openproblems
- name: data_processors/process_dataset
runners:
- type: nextflow
2 changes: 1 addition & 1 deletion src/workflows/process_datasets/main.nf
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Expand Up @@ -14,7 +14,7 @@ workflow run_wf {
main:
output_ch = input_ch

| verify_data_structure.run(
| check_dataset_with_schema.run(
fromState: { id, state ->
def schema = findArgumentSchema(meta.config, "input")
def schemaYaml = tempFile("schema.yaml")
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4 changes: 2 additions & 2 deletions src/workflows/run_benchmark/config.vsh.yaml
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Expand Up @@ -67,8 +67,8 @@ resources:
- path: /common/nextflow_helpers/helper.nf

dependencies:
- name: h5ad/extract_uns_metadata
repository: core
- name: utils/extract_uns_metadata
repository: openproblems
- name: control_methods/no_denoising
- name: control_methods/perfect_denoising
- name: methods/alra
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