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fix panel annotation bug#313

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FerriolCalvet merged 2 commits intodevfrom
fix-panel-annotation
Jun 27, 2025
Merged

fix panel annotation bug#313
FerriolCalvet merged 2 commits intodevfrom
fix-panel-annotation

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@FerriolCalvet FerriolCalvet commented Jun 26, 2025

Here we are fixing a bug in the panel annotation process, by reimplementing the input of the script with click.
This makes sure that the only_canonical boolean is working.

  • only_canonical boolean working
  • not tested

FerriolCalvet and others added 2 commits May 17, 2025 18:32
@FerriolCalvet FerriolCalvet requested a review from Copilot June 26, 2025 21:43
Copilot AI reviewed Jun 26, 2025
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Pull Request Overview

This PR replaces the previous boolean string approach with a click-style flag for only_canonical and converts positional script arguments into named parameters.

  • Switch canonical_only from "True"/"False" strings to the --only_canonical flag
  • Update panel_postprocessing_annotation.py invocation to use --vep_output_file, --assembly, and --output_file flags
Comments suppressed due to low confidence (1)

modules/local/process_annotation/panel/main.nf:25

  • Add unit or integration tests to verify that the --only_canonical flag is correctly included when task.ext.canonical_only is true and omitted when false.
    def canonical_only = task.ext.canonical_only ? "--only_canonical" : ""

@FerriolCalvet FerriolCalvet self-assigned this Jun 26, 2025
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FerriolCalvet commented Jun 27, 2025

one more PR to review, this one is very small and is fixing a bug that I identified when trying to run some variation of the pipeline.

thanks in advance!!

FedericaBrando
FedericaBrando approved these changes Jun 27, 2025
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For the scope of this PR, the implementation of click does add a layer of consistency in the way the boolean flag is passed and solves the bug (Which I guess was in the passing the value from sys.argv).

I think there's also room for improvement in the modularity of the script itself (use function encapsulation instead of calling del etc) but maybe this is low priority and out of the scope of this PR. I would just leave it as a general comment.

This PR is ready! Great job! 🥳

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FerriolCalvet commented Jun 27, 2025

okay I will merge and then add this to some of the issues for the code review to take these details into account!

thanks for the quick reviews Fede!! ❤️
that's all for now

@FerriolCalvet FerriolCalvet merged commit 14c5246 into dev Jun 27, 2025
@FerriolCalvet FerriolCalvet deleted the fix-panel-annotation branch June 27, 2025 09:20
FerriolCalvet added a commit that referenced this pull request Jul 28, 2025
@FerriolCalvet
Squashed commit of the following:
8ec8b73 
commit 10c12aa
Author: FerriolCalvet <ferriolcalvet@gmail.com>
Date:   Thu Jul 24 12:35:40 2025 +0200

    update gnomAD threshold to 0.001

    - ignore errors in omega plot

commit 31e741e
Author: FerriolCalvet <ferriolcalvet@gmail.com>
Date:   Tue Jul 22 18:34:11 2025 +0200

    update description and fix broken link

commit 7b0fd9b
Merge: 72dc4d9 cb18adc
Author: Ferriol Calvet <38539786+FerriolCalvet@users.noreply.github.com>
Date:   Sun Jul 20 22:34:46 2025 +0200

    Merge pull request #315 from bbglab/dev

commit cb18adc
Author: FerriolCalvet <ferriolcalvet@gmail.com>
Date:   Sat Jul 19 12:40:39 2025 +0200

    fix bug in mut density & update omega container

commit 1b4a52d
Author: FerriolCalvet <ferriolcalvet@gmail.com>
Date:   Tue Jul 15 15:52:07 2025 +0200

    fix broken path for test_real

commit db6d640
Author: Ferriol Calvet <38539786+FerriolCalvet@users.noreply.github.com>
Date:   Fri Jul 11 15:50:45 2025 +0200

    Allow gene selection in consensus (#316)

    * update consensus building to filter genes

    - add consensus compliance param
    - add list of genes param
    - NOT tested

    * tested gene filter implementation

    - consensus panels implemented in polars
    - allowing subset for specific genes

commit b92c2b9
Author: FerriolCalvet <ferriolcalvet@gmail.com>
Date:   Thu Jul 10 23:56:47 2025 +0200

    add metro map

commit 11fb1c5
Author: FerriolCalvet <ferriolcalvet@gmail.com>
Date:   Thu Jul 10 08:25:31 2025 +0200

    update description in main README

commit 628f282
Author: Ferriol Calvet <38539786+FerriolCalvet@users.noreply.github.com>
Date:   Mon Jul 7 19:14:21 2025 +0200

    Add more complete docs (#306)

    * first doc update

    * update in usage documentation

    - list params
    - list structural parameters and files

    * backbone of output docs

    * update usage description with custom sets of mutations

    * fix headers

    * docs: Update usage with vep information

    * update output description

    * update order of usage information

    * update distribution of information in the docs

    * fix typo in docs/output.md

    Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>

    * fix markdown linting

    * remove unnecessary validation params from config

    - REQUIRES TESTING

    * remove remaining references to download VEP cache

    * update dag format to mmd

    * update in usage

    * update documentation of file formatting and some params

    * add examples in file formatting docs

    * apply review comments

    * remove Nextflow parameters section

    * minor fix in nextflow.config

    ---------

    Co-authored-by: Miquel L. Grau <miguel.grau@irbbarcelona.org>
    Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>

commit 72dc4d9
Author: FerriolCalvet <ferriolcalvet@gmail.com>
Date:   Mon Jul 7 15:53:47 2025 +0200

    temporary LICENSE definition

commit 14c5246
Author: Ferriol Calvet <38539786+FerriolCalvet@users.noreply.github.com>
Date:   Fri Jun 27 11:19:45 2025 +0200

    fix bug in panel_annotation (#313)

    reimplement it with click solved the problem
    - only_canonical boolean working
    - not tested

commit 764782a
Author: Ferriol Calvet <38539786+FerriolCalvet@users.noreply.github.com>
Date:   Thu Jun 26 23:23:05 2025 +0200

    Update mutation rate to mutation density (#307)

    * rename mutrate to mut density

    - reimplement with click
    - partial renaming
    - simplification of sample_name logic

    * full update of mutation rate to mutation density

    * define other_sample_SNP based on all VAF

    * update mutation density functions

    - clean code
    - add explanation on mutation density

    * apply review changes

commit aae8f0b
Author: Ferriol Calvet <38539786+FerriolCalvet@users.noreply.github.com>
Date:   Thu Jun 26 10:49:00 2025 +0200

    Ensure POSTPROCESSVEPPANEL in output (#311)

    * fix relative mutabilities output

    * explicitly define postprocessveppanel outdir

    * force outputting postprocesspanel

    * update storing fixes

commit dd25b9b
Merge: 05c80ee 26d5d9b
Author: Ferriol Calvet <38539786+FerriolCalvet@users.noreply.github.com>
Date:   Wed Jun 4 23:09:29 2025 +0200

    Merge pull request #303 from bbglab/dev

    First pre-release merge

commit 05c80ee
Merge: ea9a301 e06218a
Author: Ferriol Calvet <38539786+FerriolCalvet@users.noreply.github.com>
Date:   Tue Apr 29 10:30:23 2025 +0200

    Merge pull request #289 from bbglab/tmp-dev

    First release

commit e06218a
Merge: 7559d7f ea9a301
Author: Ferriol Calvet <38539786+FerriolCalvet@users.noreply.github.com>
Date:   Tue Apr 29 10:11:05 2025 +0200

    Merge branch 'main' into tmp-dev

commit ea9a301
Author: FerriolCalvet <ferriolcalvet@gmail.com>
Date:   Thu Jul 25 16:05:10 2024 +0200

    update schema
FerriolCalvet added a commit that referenced this pull request Aug 1, 2025
@FerriolCalvet
Add plotting selection and saturation (#333)
fd48355 
* plotting wishlist

- subworkflow definition
- shortlisting plots to add

missing:
- nf scripts for the modules
- python scripts for the plots

* add raw version of supplementary figure plotting

* update omega plotting

* plotting update: omega & needles & stacked

* update plotting cohort plots working

* clean code
list inputs

* saturation data loading working

* gene saturation all tracks working with TP53

* tested additional complementary plots

missing:
- handle sample information input files
- handle reference datasets
- handle multiple genes

* update gene saturation inputs from pipeline

- not tested
- pending to decide creation of unique_splice_sites

* Squashed commit of the following:

commit 10c12aa
Author: FerriolCalvet <ferriolcalvet@gmail.com>
Date:   Thu Jul 24 12:35:40 2025 +0200

    update gnomAD threshold to 0.001

    - ignore errors in omega plot

commit 31e741e
Author: FerriolCalvet <ferriolcalvet@gmail.com>
Date:   Tue Jul 22 18:34:11 2025 +0200

    update description and fix broken link

commit 7b0fd9b
Merge: 72dc4d9 cb18adc
Author: Ferriol Calvet <38539786+FerriolCalvet@users.noreply.github.com>
Date:   Sun Jul 20 22:34:46 2025 +0200

    Merge pull request #315 from bbglab/dev

commit cb18adc
Author: FerriolCalvet <ferriolcalvet@gmail.com>
Date:   Sat Jul 19 12:40:39 2025 +0200

    fix bug in mut density & update omega container

commit 1b4a52d
Author: FerriolCalvet <ferriolcalvet@gmail.com>
Date:   Tue Jul 15 15:52:07 2025 +0200

    fix broken path for test_real

commit db6d640
Author: Ferriol Calvet <38539786+FerriolCalvet@users.noreply.github.com>
Date:   Fri Jul 11 15:50:45 2025 +0200

    Allow gene selection in consensus (#316)

    * update consensus building to filter genes

    - add consensus compliance param
    - add list of genes param
    - NOT tested

    * tested gene filter implementation

    - consensus panels implemented in polars
    - allowing subset for specific genes

commit b92c2b9
Author: FerriolCalvet <ferriolcalvet@gmail.com>
Date:   Thu Jul 10 23:56:47 2025 +0200

    add metro map

commit 11fb1c5
Author: FerriolCalvet <ferriolcalvet@gmail.com>
Date:   Thu Jul 10 08:25:31 2025 +0200

    update description in main README

commit 628f282
Author: Ferriol Calvet <38539786+FerriolCalvet@users.noreply.github.com>
Date:   Mon Jul 7 19:14:21 2025 +0200

    Add more complete docs (#306)

    * first doc update

    * update in usage documentation

    - list params
    - list structural parameters and files

    * backbone of output docs

    * update usage description with custom sets of mutations

    * fix headers

    * docs: Update usage with vep information

    * update output description

    * update order of usage information

    * update distribution of information in the docs

    * fix typo in docs/output.md
    * fix markdown linting

    * remove unnecessary validation params from config

    - REQUIRES TESTING

    * remove remaining references to download VEP cache

    * update dag format to mmd

    * update in usage

    * update documentation of file formatting and some params

    * add examples in file formatting docs

    * apply review comments

    * remove Nextflow parameters section

    * minor fix in nextflow.config

    ---------

    Co-authored-by: Miquel L. Grau <miguel.grau@irbbarcelona.org>

commit 72dc4d9
Author: FerriolCalvet <ferriolcalvet@gmail.com>
Date:   Mon Jul 7 15:53:47 2025 +0200

    temporary LICENSE definition

commit 14c5246
Author: Ferriol Calvet <38539786+FerriolCalvet@users.noreply.github.com>
Date:   Fri Jun 27 11:19:45 2025 +0200

    fix bug in panel_annotation (#313)

    reimplement it with click solved the problem
    - only_canonical boolean working
    - not tested

commit 764782a
Author: Ferriol Calvet <38539786+FerriolCalvet@users.noreply.github.com>
Date:   Thu Jun 26 23:23:05 2025 +0200

    Update mutation rate to mutation density (#307)

    * rename mutrate to mut density

    - reimplement with click
    - partial renaming
    - simplification of sample_name logic

    * full update of mutation rate to mutation density

    * define other_sample_SNP based on all VAF

    * update mutation density functions

    - clean code
    - add explanation on mutation density

    * apply review changes

commit aae8f0b
Author: Ferriol Calvet <38539786+FerriolCalvet@users.noreply.github.com>
Date:   Thu Jun 26 10:49:00 2025 +0200

    Ensure POSTPROCESSVEPPANEL in output (#311)

    * fix relative mutabilities output

    * explicitly define postprocessveppanel outdir

    * force outputting postprocesspanel

    * update storing fixes

commit dd25b9b
Merge: 05c80ee 26d5d9b
Author: Ferriol Calvet <38539786+FerriolCalvet@users.noreply.github.com>
Date:   Wed Jun 4 23:09:29 2025 +0200

    Merge pull request #303 from bbglab/dev

    First pre-release merge

commit 05c80ee
Merge: ea9a301 e06218a
Author: Ferriol Calvet <38539786+FerriolCalvet@users.noreply.github.com>
Date:   Tue Apr 29 10:30:23 2025 +0200

    Merge pull request #289 from bbglab/tmp-dev

    First release

commit e06218a
Merge: 7559d7f ea9a301
Author: Ferriol Calvet <38539786+FerriolCalvet@users.noreply.github.com>
Date:   Tue Apr 29 10:11:05 2025 +0200

    Merge branch 'main' into tmp-dev

commit ea9a301
Author: FerriolCalvet <ferriolcalvet@gmail.com>
Date:   Thu Jul 25 16:05:10 2024 +0200

    update schema

* update stacked plot needles

* minor fixes after merge

- NOT WORKING

* update linewidth and size

- add mutation types

* fix plot saturation within pipeline
- collect sitecomparisons
- remove reference to ddg. requires external
- fix input unique to keep header and minimal information
- tested and works

* fix o3d logs output

* plot multiple genes, not only TP53

* apply review suggestions

- temporary solution to domain information loading

* update domain definition and plotting

- subset domains to in_panel ones
- update domain name definition
- plotting modules works
- missing autoexons plot
- update signatures output

* - separate generation of depth per exon
- add general error handling to all plotting modules
- generate exons bedfile within panel

* batch update of exon definitions

- use correct exons definition
- update custom bedfile name
- not tested

* fix exons panel generation

* add error handling to omega plot
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