Benchmarking #118

Fabian-Boehm · 2024-05-08T10:07:02Z

Implementation of benchmarking and statistics based on the comparison of polyA selected RNA and total RNA

modules/local/benchmarking/bed_to_csv/main.nf

modules/local/benchmarking/bed_to_csv/templates/starts_bed.py

github-actions · 2024-06-18T13:11:23Z

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

Posted for pipeline commit c4f4b3c

+| ✅ 248 tests passed       |+
!| ❗   1 tests had warnings |!

❗ Test warnings:

readme - README contains the placeholder zenodo.XXXXXXX. This should be replaced with the zenodo doi (after the first release).

✅ Tests passed:

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nextflow_config - Config default value correct: params.mirna_min_reads= 5
nextflow_config - Config default value correct: params.mirna_correlation= pearson
nextflow_config - Config default value correct: params.tools= circexplorer2
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nextflow_config - Config default value correct: params.min_trimmed_reads= 10000
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nextflow_config - Config default value correct: params.max_cpus= 50
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modules_config - TARGETSCAN_DATABASE found in conf/modules.config and Nextflow scripts.
modules_config - TARGETSCAN found in conf/modules.config and Nextflow scripts.
modules_config - MIRANDA found in conf/modules.config and Nextflow scripts.
modules_config - MIRNA_TARGETS found in conf/modules.config and Nextflow scripts.
modules_config - COMBINE_BINDINGSITES found in conf/modules.config and Nextflow scripts.
modules_config - MAJORITY_VOTE found in conf/modules.config and Nextflow scripts.
modules_config - CIRCTEST_PREPARE found in conf/modules.config and Nextflow scripts.
modules_config - CIRCTEST_CIRCTEST 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: 2.14.1

Run details

nf-core/tools version 2.14.1
Run at 2024-09-16 10:38:28

nictru

Good start :)

modules/local/benchmarking/average_tsv/templates/average.py

modules/local/benchmarking/location_plots/main.nf

modules/local/benchmarking/location_plots/templates/create_plots.py

modules/local/benchmarking/overlap_plot/main.nf

modules/local/benchmarking/average_tsv/main.nf

modules/local/benchmarking/location_plots/main.nf

modules/local/benchmarking/overlap_plot/main.nf

modules/local/benchmarking/png_json/main.nf

modules/local/benchmarking/seq_depth_plot/main.nf

…Pearson-correllation. Implemented collection of correlation values.

…on plots

…tion was calculated from the wrong files

…sometimes apear the wrong way round

…ecessary inputs after the merge

modules/local/benchmarking/location_plots/main.nf

modules/local/benchmarking/overlap_plot/main.nf

nictru · 2024-09-05T15:51:08Z

modules/local/benchmarking/overlap_plot/templates/create_plots.py

+def read_bed_file(file_path):
+    data = {'chromosome': [], 'start': [], 'strand': []}
+    with open(file_path, 'r') as file:
+        reader = csv.reader(file, delimiter='\t')


modules/local/benchmarking/png_json/main.nf

nictru · 2024-09-05T15:53:11Z

modules/local/benchmarking/seq_depth_plot/main.nf

+    conda "bioconda::matplotlib=3.5.1 bioconda::seaborn=0.11.2"
+    container 'https://depot.galaxyproject.org/singularity/bionumpy:0.2.12--pyha8f3691_0'


nextflow_schema.json

subworkflows/local/benchmarking.nf

Fabian-Boehm requested a review from nictru May 8, 2024 10:07

nictru requested changes May 13, 2024

View reviewed changes

modules/local/benchmarking/bed_to_csv/main.nf Outdated Show resolved Hide resolved

modules/local/benchmarking/bed_to_csv/templates/starts_bed.py Outdated Show resolved Hide resolved

nictru linked an issue Jun 9, 2024 that may be closed by this pull request

Implement polyA-Benchmarking #143

Open

nictru requested changes Jul 15, 2024

View reviewed changes

nictru and others added 21 commits July 18, 2024 13:31

Replicate circRNA discovery for benchmarking

88931b2

Implement Jaccard calculation

56d6bd5

Implement jaccard file collection

31dc5e8

Add benchmarking multiqc configuration

650480c

Group benchmark multiqc sections

d506c8b

implemented location mapping

fac07a4

diagnostics: ch_joined not found, added files

a1a9594

Added Overlap location plots

9c1aae1

prepare seq_depth data, trimgalore reports in benchmarking.nf

31ff400

sequencing depth pearson correllation computation

1d036fb

config files added to git

bda9c59

Postmerge fixes

e0bc4f0

diagnostic: comparison to older version needed

7e6a944

Fixed benchmarking.nf input to be tool specific as previously. Fixed …

4a06426

…Pearson-correllation. Implemented collection of correlation values.

added sequence depth to mulitiqc. Changed labels and layout of locati…

931698d

…on plots

pre-commit run pass. Deleted redundant module

5bb7aa9

Added sections to multiqc, fixed an issue where the Seq-depth-correla…

1e12d20

…tion was calculated from the wrong files

Fixed an issue, where the Strands in the multiqc locationplots would …

0fda391

…sometimes apear the wrong way round

cosmetic cleanup of the benchmarking module.

b7cbd04

Fixed an issue where CIRCRNA_DISCOVERY_BENCHMARKING did not get all n…

3039a80

…ecessary inputs after the merge

readded missing module configs after rebase

4265950

Fabian-Boehm force-pushed the benchmarking branch from 8983c35 to 4265950 Compare July 18, 2024 12:57

Fabian-Boehm added 3 commits August 1, 2024 11:46

Ensured correct syntax, removed unnecessary specifications

1fefca7

Merge branch 'dev' into benchmarking after find_circ fix

9e1717e

removed debugging statements

74a243a

Fabian-Boehm and others added 5 commits August 19, 2024 15:07

added version control as per requested changes (15.07.24) and GENOMECOV

78e8c11

Merge remote-tracking branch 'origin/dev' into benchmarking

3e62a86

Minor adjustments for compatibility

f7bbcbb

Remove outdated module configs

c2b76e6

Remove some unnecessary imports

467e617

nictru requested changes Sep 5, 2024

View reviewed changes

nictru marked this pull request as ready for review September 5, 2024 15:58

Fabian-Boehm added 2 commits September 13, 2024 12:44

implemented requested changes from 5.9.24

a06a53a

fixed some issues that pervented termination

c4f4b3c

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Benchmarking #118

Benchmarking #118

Fabian-Boehm commented May 8, 2024 •

edited by nictru

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github-actions bot commented Jun 18, 2024 •

edited

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❗ Test warnings:

✅ Tests passed:

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nictru Sep 5, 2024

nictru Sep 5, 2024

		conda "bioconda::matplotlib=3.5.1 bioconda::seaborn=0.11.2"
		container 'https://depot.galaxyproject.org/singularity/bionumpy:0.2.12--pyha8f3691_0'

Benchmarking #118

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Benchmarking #118

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Fabian-Boehm commented May 8, 2024 • edited by nictru Loading

github-actions bot commented Jun 18, 2024 • edited Loading

nf-core lint overall result: Passed ✅ ⚠️

❗ Test warnings:

✅ Tests passed:

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Fabian-Boehm commented May 8, 2024 •

edited by nictru

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github-actions bot commented Jun 18, 2024 •

edited

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