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* stop the execution if duplicates are found in annotation - add missing params to config - not tested * update somatic mutations filtering params definition * fix bug in JSON file creation\n-tested * add no_filter param * update HDP signature extraction outputs * publish all HDP generated files * update clean mutations with no_filter as well * fix one more bug * final bug fix now it all works * fix collection of filters in FILTER * fix merge * final fix tested and it works with and without filtering
- Add sample name column option to main function in deepcsa_maf2samplevcfs.py
FerriolCalvet
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Jun 4, 2025
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already tested several times
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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
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* 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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