[Feature] Gene Score Computation #32

apeltzer · 2023-06-15T14:05:33Z

PR checklist

github-actions · 2023-06-15T14:07:11Z

`nf-core lint` overall result: Passed ✅

Posted for pipeline commit ba389f0

+| ✅ 160 tests passed       |+

✅ Tests passed:

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merge_markers - No merge markers found in pipeline files
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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 2.8
Run at 2023-06-22 12:55:40

…gene-score-computation

apeltzer · 2023-06-21T09:11:02Z

Needs this to be merged, too: BioContainers/multi-package-containers#2648

christopher-mohr

Do we need the flag parameter? Couple of things related to that and we have to wait for the new container anyway. :)

modules/local/compute_gene_scores.nf

conf/test_scores.config

nextflow.config

nextflow_schema.json

bin/compute_gene_scores.R

conf/test_scores.config

bin/compute_gene_scores.R

conf/test_scores.config

Co-authored-by: Christopher Mohr <contact.cmohr@gmail.com>

christopher-mohr

LGTM

Started adding R script back to pipeline

7c08646

apeltzer added 7 commits June 21, 2023 07:48

Added gene score computation

91dcc9b

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

60d0b06

…gene-score-computation

Add gene score computation

1130354

Add changelog

46dfd46

Added code to main workflow

3fa75c0

Added tests, depends on PR to testdata

f77b16a

Addd MultiQCC

aeda133

apeltzer marked this pull request as ready for review June 21, 2023 08:02

apeltzer mentioned this pull request Jun 21, 2023

Add gene score test YAML nf-core/test-datasets#942

Merged

apeltzer added 7 commits June 21, 2023 08:06

Nicer schema

2a77d94

Clean up editorconfig

80a8c8f

Added schema linting

dd3f7e4

Fix bits

317479f

Fix path

3948106

Add +x

8b6699d

Remove CBBD

2364bf1

apeltzer changed the title ~~Started adding R script back to pipeline~~ [Feature] Gene Score Computation Jun 21, 2023

christopher-mohr requested changes Jun 21, 2023

View reviewed changes

apeltzer added 8 commits June 22, 2023 08:23

Adjust to new mulled container

9ee8149

Cleaned up code substantially

b41e6cd

Schema ++

d209aed

Reformatting of count matrix

71d2e13

Ditch compute gene scores from test too

caedc53

Add configuration for output of gene scores

8844671

Should run through now :)

9a8cc4c

Fix EditorConfig

607b378

christopher-mohr requested changes Jun 22, 2023

View reviewed changes

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bin/compute_gene_scores.R Show resolved Hide resolved

apeltzer commented Jun 22, 2023

View reviewed changes

conf/test_scores.config Outdated Show resolved Hide resolved

Apply suggestions from code review

34a20bd

Co-authored-by: Christopher Mohr <contact.cmohr@gmail.com>

christopher-mohr approved these changes Jun 22, 2023

View reviewed changes

MOAR docs

de0f501

apeltzer mentioned this pull request Jun 22, 2023

Compute Gene Set Scores #16

Closed

apeltzer added 5 commits June 22, 2023 12:34

Add citations for Gene Set Scores

062670c

Adjust changelog for imminent release

8316afa

Add versions properly

a694bef

Fix table

a860405

Prettier

ba389f0

apeltzer merged commit 45d22c9 into dev Jun 22, 2023
6 checks passed

apeltzer deleted the add-gene-score-computation branch June 22, 2023 13:15

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[Feature] Gene Score Computation #32

[Feature] Gene Score Computation #32

apeltzer commented Jun 15, 2023 •

edited

github-actions bot commented Jun 15, 2023 •

edited

✅ Tests passed:

Run details

apeltzer commented Jun 21, 2023

christopher-mohr left a comment

christopher-mohr left a comment

[Feature] Gene Score Computation #32

[Feature] Gene Score Computation #32

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apeltzer commented Jun 15, 2023 • edited

PR checklist

github-actions bot commented Jun 15, 2023 • edited

nf-core lint overall result: Passed ✅

✅ Tests passed:

Run details

apeltzer commented Jun 21, 2023

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apeltzer commented Jun 15, 2023 •

edited

github-actions bot commented Jun 15, 2023 •

edited

`nf-core lint` overall result: Passed ✅