Added annotation statistics subworkflow #150

BethYates · 2024-11-13T17:55:14Z

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
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).

…AGAT_SQSTATBASIC'

Added new subworkflow 'ANNOTATION_STATS' and new parameter --annotation_set to solve issue #121

…s information from the txt files

…sic processes

…from BUSCO json file

Added Busco to run in protein mode

… document when assembly annotation has been provided as input

github-actions · 2024-11-13T17:56:44Z

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

Posted for pipeline commit 06e2b20

+| ✅ 131 tests passed       |+
#| ❔  21 tests were ignored |#
!| ❗   1 tests had warnings |!

❗ Test warnings:

nextflow_config - Config manifest.version should end in dev: '2.0.0'

❔ Tests ignored:

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template_strings - template_strings

✅ Tests passed:

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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 2024-11-14 12:39:04

…sing mrna rather than cds/transcript

SandraBabirye and others added 30 commits August 15, 2024 20:06

added two new nf-core modules 'agat/sptatistics and agat/sqstatbasic'

7dc9838

added two new nf-core modules 'agat/sptatistics and agat/sqstatbasic'

0548d90

added new subworkflow to obtain annotation summary statistics

cfafbaa

added params.annotation_set

ddc3edc

added documentation for params.annotation_set

3bd733a

added annotation_stats as specific output directory

131b7b8

allocated resources for the two new processes 'AGAT-SPSTATISTICS and …

e98a375

…AGAT_SQSTATBASIC'

added new subworkflow and params.annotation_set

5a2abe7

added path to the test annotation file

c35db05

modified the file after running prettier

2fc43e8

added a new subworkflow 'ANNOTATION_STATS)

a8dbd78

Edited annotation_statistics.nf file

da91c57

edited the pattern for --annotation_set to include gff rather than gff3

65b463e

edited the pattern for --annotation_set to include gff rather than gff3

85ac505

Merge pull request #135 from sanger-tol/annotation_statistics

7e201c7

Added new subworkflow 'ANNOTATION_STATS' and new parameter --annotation_set to solve issue #121

added a python script that extracts the relevant annotation statistic…

26bd58c

…s information from the txt files

added a new local module to extract annotation statistics information

fe3c78e

edited the annotation_stats subworkflow to include the new local module

fd0d992

adjusted the allocated memory for agat_spstatistics and agat_sqstatba…

e6c6778

…sic processes

edited the annotation_stats subworkflow to include the new local module

ead4298

edited the annotation_stats subworkflow to include the new local module

a52bc5d

edited the annotation_stats subworkflow and removed .out

054dade

edited the modules.confif file

0e316cd

edited the file

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edited the file

0f8b9ae

edited file

5b6db7a

edited file

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edited file

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edited file

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edited file

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SandraBabirye and others added 23 commits October 23, 2024 13:24

edited the file to run busco in protein mode

6db6859

edited python script to include the busco stats file

1feb2a6

edited files

ee4e2a9

edited files

21f2b4d

fixed black linting issues

64a39d5

added a busco stats file as parameter

8e5490c

edited the arguments

208e3ab

fixing black linting issues

b060f6e

edited the python script to extract busco stats

80301fe

edited the input channels for buscoproteins process

f4d28c7

Changed the order of inputs for ANNOTATION_STATS

d95f4b5

edited the busco output file channel to json

164b74d

edited the python script to extract the one_line_summary information …

99a6e26

…from BUSCO json file

Updated annotation_statistics.nf file

dfdb0cf

fixing black issues

fbc3deb

fixing linting issues

af3a412

remove trailing whitespace

7acb7b8

removed the left padding space

5ad88dd

removed the left padding space

cf1e9d1

updated modules.config

067833c

Merge pull request #142 from SandraBabirye/busco_feature

05114c8

Added Busco to run in protein mode

Merge branch 'annotation_stats_dev' into public_dev

0ebe932

Added annotation statistics to the full parameter list and genomenote…

7a08874

… document when assembly annotation has been provided as input

BethYates added 4 commits November 13, 2024 17:58

typo

37b9838

corrected some of the statistics being being returned, we should be u…

70a80b8

…sing mrna rather than cds/transcript

updated docs to include annotation statistics subworkflow

96cf0bd

prettier fixes

06e2b20

BethYates requested review from tkchafin and muffato November 14, 2024 12:39

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Added annotation statistics subworkflow #150

Added annotation statistics subworkflow #150

BethYates commented Nov 13, 2024

github-actions bot commented Nov 13, 2024 •

edited

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Added annotation statistics subworkflow #150

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Added annotation statistics subworkflow #150

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BethYates commented Nov 13, 2024

PR checklist

github-actions bot commented Nov 13, 2024 • edited Loading

nf-core lint overall result: Passed ✅ ⚠️

❗ Test warnings:

❔ Tests ignored:

✅ Tests passed:

Run details

github-actions bot commented Nov 13, 2024 •

edited

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