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Ensure POSTPROCESSVEPPANEL in output#311

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FerriolCalvet merged 4 commits intodevfrom
fix-storing
Jun 26, 2025
Merged

Ensure POSTPROCESSVEPPANEL in output#311
FerriolCalvet merged 4 commits intodevfrom
fix-storing

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@FerriolCalvet
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@FerriolCalvet FerriolCalvet commented Jun 25, 2025

  • Fix storing of POSTPROCESSVEPPANEL
  • Fix storing of mutabilities, only compressed, and avoid having it twice

@FerriolCalvet FerriolCalvet linked an issue Jun 25, 2025 that may be closed by this pull request
@FerriolCalvet FerriolCalvet requested a review from Copilot June 25, 2025 16:23
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Pull Request Overview

This PR ensures that the POSTPROCESSVEPPANEL outputs are exposed by the CREATE_PANELS workflow and published to the output directory. Key changes include:

  • Expose compact_panel_annotation and rich_panel_annotation from POSTPROCESSVEPPANEL in the main workflow.
  • Add publishDir configuration for POSTPROCESSVEPPANEL and MUTABILITY_BGZIPTABIX in modules.config.
  • Remove POSTPROCESS_VEP_ANNOTATION from the grouped withName block in modules.config.

Reviewed Changes

Copilot reviewed 2 out of 2 changed files in this pull request and generated no comments.

File Description
subworkflows/local/createpanels/main.nf Added postprocessed_panel and postprocessed_panel_rich outputs for POSTPROCESSVEPPANEL.
conf/modules.config Configured publishDir for POSTPROCESSVEPPANEL and MUTABILITY_BGZIPTABIX; updated the process group names.
Comments suppressed due to low confidence (2)

conf/modules.config:160

  • The glob pattern "{tsv}" will not match files with a .tsv extension. Consider using ".tsv" or "*.{tsv}" to correctly capture TSV files.
                pattern: "*{tsv}"

conf/modules.config:387

  • The glob pattern "{.gz|.tbi}" is not valid for matching .gz or .tbi files. Use a pattern like ".{gz,tbi}" or separate patterns for each extension.
                pattern: "*{.gz|.tbi}"

@FerriolCalvet
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tested and it works

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LGTM! 💯

@FerriolCalvet FerriolCalvet merged commit aae8f0b into dev Jun 26, 2025
@FerriolCalvet FerriolCalvet deleted the fix-storing branch June 26, 2025 08:49
FerriolCalvet added a commit that referenced this pull request Jul 28, 2025
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
* 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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