Integrate Cellranger-atac #175

heylf · 2022-11-02T16:21:27Z

PR checklist

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/scrnaseq branch on the nf-core/test-datasets repository.
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.
CHANGELOG.md is updated.
README.md is updated (including new tool citations and authors/contributors).

…ges to lib/WorkflowScrnaseq.groovy

…or cellranger-atac

Dev

heylf · 2022-11-02T16:22:45Z

Currently the modules are local. PR for nf-core modules are in place already: nf-core/modules#2450

github-actions · 2022-11-02T16:23:19Z

`nf-core lint` overall result: Passed ✅

Posted for pipeline commit 07ccbd2

+| ✅ 158 tests passed       |+

✅ 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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pipeline_todos - No TODO strings found
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template_strings - Did not find any Jinja template strings (124 files)
schema_lint - Schema lint passed
schema_lint - Schema title + description lint passed
schema_lint - Input mimetype lint passed: 'text/csv'
schema_params - Schema matched params returned from nextflow config
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merge_markers - No merge markers found in pipeline files
modules_json - Only installed modules found in modules.json
multiqc_config - 'assets/multiqc_config.yml' follows the ordering scheme of the minimally required plugins.
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'

Run details

nf-core/tools version 2.6
Run at 2022-11-16 13:31:33

heylf · 2022-11-02T16:24:42Z

Should I include an individual test for cellranger-atac? Because cellranger-atac needs different type of data and input format.

apeltzer · 2022-11-03T22:52:47Z

In such a case definitely some extra test profile + test data is justified 👍🏻

apeltzer · 2022-11-03T22:53:00Z

And in general: More tests do not hurt ;-)

heylf · 2022-11-04T08:05:26Z

@nf-core-bot fix linting

heylf · 2022-11-04T09:37:55Z

Waiting for test data to arrive in the nf-core nf-core/test-datasets#687

heylf · 2022-11-04T13:48:13Z

Pipeline misses right now a container that has scanpy and muon (needed for mtx_to_h5ad)

apeltzer · 2023-02-17T15:16:19Z

Can you attempt at fixing the conflicts so this can be merged soon @heylf ?

klkeys · 2023-05-19T18:00:05Z

Waiting for test data to arrive in the nf-core nf-core/test-datasets#687

that pull is obselete and unmerged, leaving note here about suitable and successfully merged test data in nf-core/test-datasets#847

heylf added 30 commits October 21, 2022 10:59

Adding first version of cellranger-atac modules

d0fa753

Changes to nextflow.config to hold cellranger-atac parameters

2e48aae

changes to nextflow_schema.json to allow for cellranger-atac

040b62c

Adding cellranger-atac call to scranseq.nf

19c32e5

adding cellranger-atac subworkflow

59ee97d

Changes to scrnseq.nf

28ae3cf

Chenages to cellranger-atac subworkflow

1ff9e46

Changes to nextflow_schema.json

397e1f2

Changes to module.config for cellranger-atac

b1ea9ef

changes to cellranger-atac count meta and main

b589b87

Changes to cellranger-atac mkref meta and main

f22a075

Temporary change to test.config

9c9e0ad

Changes to usage.md and output.md

6b43116

Changes to meta.yml of cellranger-atac mkref

8477ca5

changes to scranseq.nf

4e0dc52

changes to align_cellranger_atac.nf

64aed03

Changes to check_samplesheet.py

094b93b

Changes to nextflow config and schema.json

aedff87

Changes to scranseq.nf

e838cf7

Changes to scrnaseq.nf

1cf8c83

Changes to align_cellranger_atac.nf

f83fe02

Changes to nextflow.config remove unnecesary params for cellranger.atac

80f4bdc

Set test.config as in the dev branch

5b815a4

Changes to modules.config to remove ext.params from cellranger-atac

9a301ac

Adding barcode file for cellranger-atac in input_check

ebe4001

cellranger-atac can work without --fasta/--gtf and --genome thus chan…

2ce645e

…ges to lib/WorkflowScrnaseq.groovy

Changes to bin/check_samplesheet.py to check for fastq barcode file f…

9ee156d

…or cellranger-atac

changes to usage.md

db9db83

Changes to meta.yml for cellranger-atac count

4dc4f64

Changes to scrnaseq.nf

079f0f6

heylf added 5 commits November 2, 2022 13:47

Add cellranger-atac to readme

2ae349b

Changes to nextflow_schema.json missing cellranger-atac for allOf

605e294

Merge pull request #1 from heylf/dev

ca06abc

Dev

Adding fasta, gtf, and motifs file for cellranger-atac

6625b0b

changes to usage text of cellranger-atac

05ac1a8

eclint lib/WorkflowScrnaseq.groovy

e52706b

nf-core-bot and others added 2 commits November 4, 2022 08:05

[automated] Fix linting with Prettier

0429fdf

black lint reformatting for bin/check_samplesheet.py

4d876f0

Changes to mtx_to_h5ad because of cellranger-atac

0bdacf9

heylf added 3 commits November 4, 2022 14:51

black linting

765c309

Two small bugfixes

0bcf4cc

Changes to usage

07ccbd2

heylf self-assigned this Mar 29, 2023

heylf added the DO_NOT_MERGE label Mar 29, 2023

klkeys linked an issue May 19, 2023 that may be closed by this pull request

Add ATAC-Seq data support #129

Closed

heylf closed this May 23, 2023

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Integrate Cellranger-atac #175

Integrate Cellranger-atac #175

heylf commented Nov 2, 2022 •

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✅ Tests passed:

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heylf commented Nov 2, 2022

apeltzer commented Nov 3, 2022

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apeltzer commented Feb 17, 2023

klkeys commented May 19, 2023 •

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Integrate Cellranger-atac #175

Integrate Cellranger-atac #175

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heylf commented Nov 2, 2022 • edited Loading

PR checklist

heylf commented Nov 2, 2022

github-actions bot commented Nov 2, 2022 • edited Loading

nf-core lint overall result: Passed ✅

✅ Tests passed:

Run details

heylf commented Nov 2, 2022

apeltzer commented Nov 3, 2022

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heylf commented Nov 4, 2022

heylf commented Nov 4, 2022

heylf commented Nov 4, 2022

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`nf-core lint` overall result: Passed ✅

klkeys commented May 19, 2023 •

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