Finish singleR implementation by nictru · Pull Request #200 · nf-core/scdownstream

nictru · 2025-07-13T10:45:04Z

This builds up on #187 but aligns the implementation more with the existing pipeline architecture and nf-core guidelines
The following changes have been made:

There is now an additional CSV input, where each row represents one celldex reference
There are tests for all the newly added processes and subworkflows
Generally updated workflow hierarchy

@addityea please have a look at the changes, and let me know if these still resemble your original idea.

…for the celldex reference. There are downstream pipeline errors however.

…x column explicitly

celldex reference stored at the relative path: `celldex_references/celldex_hpca__2024-02-26_h5_se`` The reference was copied from the results of a run with profile test_full and should give identical results. This works on Dardel for me, e.g. with this command: ``` module load PDC java singularity export NXF_SINGULARITY_CACHEDIR="~/singularity_cache" ./nextflow run main.nf -profile pdc_kth,test_offline --project=naiss2024-22-1150 --outdir ./results ```

test_full profile. Added: - celldex_reference_label parameter with default value 'label.main' - support for multiple references in CELLTYPES_SINGLER - proper downloading of multiple references using CELLTYPES_CELLDEXDOWNLOAD

…oved to template; updated containers

…prints to stdout

…bled singleR in case unsupported env methods like Conda/mamba is used; removed unwanted lines and print statements from singleR

…moved them in logical group

…ort for previously missing SingleCellExperiment; removed some unwanted/ commented lines

…ted meta.yml, removed container switch logic

…-core-dev

… for cellDex reference.

Merging as tests have succeeded.

Implementation of SingleR module

nf-core-bot · 2025-07-13T10:45:38Z

Warning

Newer version of the nf-core template is available.

Your pipeline is using an old version of the nf-core template: 3.3.1.
Please update your pipeline to the latest version.

For more documentation on how to update your pipeline, please see the nf-core documentation and Synchronisation documentation.

github-actions · 2025-07-13T10:46:37Z

`nf-core pipelines lint` overall result: Passed ✅ ⚠️

Posted for pipeline commit 052b8cd

+| ✅ 273 tests passed       |+
!| ❗  20 tests had warnings |!

Details

❗ Test warnings:

files_exist - File not found: conf/igenomes.config
files_exist - File not found: conf/igenomes_ignored.config
readme - README contains the placeholder zenodo.XXXXXXX. This should be replaced with the zenodo doi (after the first release).
pipeline_todos - TODO string in nextflow.config: Optionally, you can add a pipeline-specific nf-core config at https://github.com/nf-core/configs
pipeline_todos - TODO string in README.md: Add citation for pipeline after first release. Uncomment lines below and update Zenodo doi and badge at the top of this file.
pipeline_todos - TODO string in README.md: Add bibliography of tools and data used in your pipeline
pipeline_todos - TODO string in base.config: Check the defaults for all processes
pipeline_todos - TODO string in base.config: Customise requirements for specific processes.
pipeline_todos - TODO string in methods_description_template.yml: #Update the HTML below to your preferred methods description, e.g. add publication citation for this pipeline
pipeline_todos - TODO string in awsfulltest.yml: You can customise AWS full pipeline tests as required
pipeline_todos - TODO string in main.nf: Optionally add in-text citation tools to this list.
pipeline_todos - TODO string in main.nf: Optionally add bibliographic entries to this list.
pipeline_todos - TODO string in main.nf: Only uncomment below if logic in toolCitationText/toolBibliographyText has been filled!
local_component_structure - unify_genes.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
local_component_structure - integrate.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
local_component_structure - finalize.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
local_component_structure - per_group.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
local_component_structure - scimilarity.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
local_component_structure - combine.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
local_component_structure - unify.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure

✅ Tests passed:

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nextflow_config - Config timeline.enabled had correct value: true
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nextflow_config - Config trace.enabled had correct value: true
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nextflow_config - Config default value correct: params.duplicate_var_resolution= sum
nextflow_config - Config default value correct: params.ambient_removal= decontx
nextflow_config - Config default value correct: params.doublet_detection= scrublet
nextflow_config - Config default value correct: params.doublet_detection_threshold= 1
nextflow_config - Config default value correct: params.cellbender_epochs= 150
nextflow_config - Config default value correct: params.integration_methods= scvi
nextflow_config - Config default value correct: params.integration_hvgs= 0
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nextflow_config - Config default value correct: params.base_label_col= label
nextflow_config - Config default value correct: params.clustering_resolutions= 0.5,1.0
nextflow_config - Config default value correct: params.cluster_global= true
nextflow_config - Config default value correct: params.memory_scale= 1
nextflow_config - Config default value correct: params.scvi_n_latent= 30
nextflow_config - Config default value correct: params.scvi_n_hidden= 128
nextflow_config - Config default value correct: params.scvi_n_layers= 2
nextflow_config - Config default value correct: params.scvi_dispersion= gene
nextflow_config - Config default value correct: params.scvi_gene_likelihood= zinb
nextflow_config - Config default value correct: params.pseudobulk_groupby_labels= batch
nextflow_config - Config default value correct: params.pseudobulk_min_num_cells= 5
nextflow_config - Config default value correct: params.custom_config_version= master
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nextflow_config - Config default value correct: params.publish_dir_mode= copy
nextflow_config - Config default value correct: params.max_multiqc_email_size= 25.MB
nextflow_config - Config default value correct: params.validate_params= true
nextflow_config - Config default value correct: params.pipelines_testdata_base_path= https://raw.githubusercontent.com/nf-core/test-datasets/be82517a080e70628dce694c61eb91821850aea9/
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actions_awsfulltest - .github/workflows/awsfulltest.yml does not use -profile test
readme - README Nextflow minimum version badge matched config. Badge: 24.04.2, Config: 24.04.2
readme - README nf-core template version badge found.
pipeline_if_empty_null - No ifEmpty(null) strings found
plugin_includes - No wrong validation plugin imports have been found
pipeline_name_conventions - Name adheres to nf-core convention
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multiqc_config - assets/multiqc_config.yml contains a matching 'report_comment'.
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modules_structure - modules directory structure is correct 'modules/nf-core/TOOL/SUBTOOL'
local_component_structure - local modules directory structure is correct 'modules/local/TOOL/SUBTOOL'
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modules_config - conf/modules.config found and not ignored.
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modules_config - CELDA_DECONTX found in conf/modules.config and Nextflow scripts.
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modules_config - SCANPY_COMBAT found in conf/modules.config and Nextflow scripts.
modules_config - SCIMILARITY_EMBED found in conf/modules.config and Nextflow scripts.
modules_config - SCIMILARITY_ANNOTATE found in conf/modules.config and Nextflow scripts.
modules_config - ADATA_MERGEEMBEDDINGS found in conf/modules.config and Nextflow scripts.
modules_config - CELLDEX_FETCHREFERENCE found in conf/modules.config and Nextflow scripts.
modules_config - CELLTYPES_SINGLER found in conf/modules.config and Nextflow scripts.
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modules_config - SCANPY_RANKGENESGROUPS found in conf/modules.config and Nextflow scripts.
modules_config - MULTIQC found in conf/modules.config and Nextflow scripts.
nfcore_yml - Repository type in .nf-core.yml is valid: pipeline
nfcore_yml - nf-core version in .nf-core.yml is set to the latest version: 3.3.1
rocrate_readme_sync - RO-Crate descriptions are in sync with README.md.

Run details

nf-core/tools version 3.3.1
Run at 2025-07-14 08:05:51

addityea · 2025-07-14T06:27:40Z

This builds up on #187 but aligns the implementation more with the existing pipeline architecture and nf-core guidelines The following changes have been made:
* There is now an additional CSV input, where each row represents one celldex reference

* There are tests for all the newly added processes and subworkflows

* Generally updated workflow hierarchy
@addityea please have a look at the changes, and let me know if these still resemble your original idea.

Hey @nictru , Yes, the implementation of singleR is still following the ideas we had! All good from my end! Thanks!

addityea and others added 30 commits May 21, 2025 16:27

NBIS Hackathon day 1 progress

d433f0f

SingleR now runs and an HDF5-serialized SumamrizedExperiment is used …

8dcc0ac

…for the celldex reference. There are downstream pipeline errors however.

It now runs with singler,, loading a csv required specifying the inde…

07f37d1

…x column explicitly

Fixing accidental inclusion of singleR.R in .gitignore

3046efa

Add functionality to handle multiple SingleR references in a single run.

c29182c

Fix a couple of small things in singleR.R

292804c

Adding paths for local celldex reference folder to .gitignore

edbabca

Added celldex_reference_label to schema, fixed celldexD for Docker; m…

6547807

…oved to template; updated containers

Moved away from 'for' loops to 'each' method; removed diagnostic log …

7861b1d

…prints to stdout

Updated containers

ff3dd6c

detached celldex_reference_processing into it's own subworkflow; Disa…

fbc1770

…bled singleR in case unsupported env methods like Conda/mamba is used; removed unwanted lines and print statements from singleR

Updated schema with descriptions for the celldex/ singleR module and …

407e1bc

…moved them in logical group

Added citations for major tools used in singleR module

5bdb8ed

CelldexDownload moved to new Seqera container; added version info exp…

fd91a64

…ort for previously missing SingleCellExperiment; removed some unwanted/ commented lines

Brushing up for PR

60a87ed

Merge branch 'dev' into singleR

8557a9d

Removing local debugging files

7bc42d4

Added warning text when conda used; removed TODO texts; deleted unwan…

5150fa2

…ted meta.yml, removed container switch logic

Deleted non-functional celldexdownload test file

c75631e

Fix: Pre-commit editorconfig-checker errors

343afa0

Merge branch 'nf-core:dev' into singleR

c1a8c31

Merge branch 'dev' of https://github.com/nf-core/scdownstream into nf…

9aad8ad

…-core-dev

Merge branch 'dev' of https://github.com/nf-core/scdownstream into nf…

030840d

…-core-dev

Merge branch 'nf-core-dev' into singleR

07a289a

Enabled offline singleR testing: Moved to tar.gz instead of directory…

54bc8ed

… for cellDex reference.

Merge pull request #2 from NBISweden/singleR_offline

e071b37

Merging as tests have succeeded.

applied pre-commit linting

a9f1283

Merge branch 'nf-core:dev' into singleR

4f5d92c

nictru added 8 commits July 12, 2025 15:04

Merge pull request #187 from NBISweden/singleR

8f48296

Implementation of SingleR module

Reset gitignore

33d0385

Clean up singleR implementation

3bd0a48

Add some singleR tests

1de9deb

Switch to samplesheet-based singleR configuration

a7db4be

Update singleR tests

4575636

Update subworkflow tests

e9b243e

Fix celldex_reference parameter name inconsistency

5b7f78b

nictru added 10 commits July 13, 2025 12:58

Fix channel structure issues

9bfe256

Update some test snap

9082242

Update singleR output structure

90b44f6

Update singleR test snapshots

0b8cb1a

update pipeline-level test snapshots

b780eba

Update some test snapshots

c74a03c

Usa larger disks for nf-tests

828de42

Update decontX tests

a423a32

Update QC subworkflow test snaps

6e9355e

Update ambient RNA removal test snaps

1b353c2

nictru added 2 commits July 14, 2025 10:03

Update celltype_assignment tests

a8f7f58

Update celltype assignment docs

052b8cd

nictru marked this pull request as ready for review July 14, 2025 09:50

nictru merged commit 283f4ea into dev Jul 14, 2025
77 of 91 checks passed

nictru deleted the singleR branch July 14, 2025 09:50

nictru mentioned this pull request Jul 14, 2025

Implement SingleR cell type assignment #24

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Finish singleR implementation#200

Finish singleR implementation#200
nictru merged 50 commits intodevfrom
singleR

nictru commented Jul 13, 2025 •

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nf-core pipelines lint overall result: Passed ✅ ⚠️

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nictru commented Jul 13, 2025 •

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`nf-core pipelines lint` overall result: Passed ✅ ⚠️