Code

Substantial rewrite of the pipeline#32

Code

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robomics merged 54 commits intomainrobomics/call_tad_cliques:mainfrom rewriterobomics/call_tad_cliques:rewriteCopy head branch name to clipboardJun 7, 2024

+2,296-868

Commits

Commits on May 30, 2024

• Add subworkflow to validate samplesheets

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• Add subworkflow to process TADs

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• Add subworkflow to run NCHG

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• Refactor

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• Add subworkflow to run call TAD cliques

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• Update main.nf and nextflow.config

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• Add new Dockerfiles

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• Update env.yml

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• Remove unnecessary import

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• Update base config

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• Remove debug code

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• Update dependabot

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• Update CI

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• Merge branch 'main' into rewrite

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• Merge branch 'main' into rewrite

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• Update container uris in nextflow.config

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• Bugfix

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• Bugfix

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• Merge branch 'main' into rewrite

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• Add missing tag

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• Merge branch 'main' into rewrite

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Commits on May 31, 2024

• Debugging

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• Debugging

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• Remove debug code

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• Speed up CI

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• Bugfix

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• Fail CI on test dataset cache miss

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• Update NCHG Dockerfile

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• Update test config

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• Merge branch 'main' into rewrite

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Commits on Jun 3, 2024

• Update apply_normalization.py

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• Update plot_maximal_clique_sizes.py

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• Update NCHG subworkflow

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• Update cliques workflow

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• Bugfix

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• Bugfix

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Commits on Jun 4, 2024

• Bugfix

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• Merge branch 'main' into rewrite

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• Update nextflow.config

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• Add label process_very_high

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• Let call_cliques.py run for longer

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• Refactor

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• Support specifying different cutoffs for cis and trans cliques

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• Merge branch 'main' into rewrite

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• Update CI

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• Bugfix

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• Bugfix

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Commits on Jun 5, 2024

• Bugfix

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• Update cliques workflow

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Commits on Jun 6, 2024

• Output NCHG expected values

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Commits on Jun 7, 2024

• Bugfix

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• Update plot_significant_interactions.py

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• Update README

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• Update nextflow.config

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