Code

Many additions#48

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DLBPointon merged 120 commits intodevsanger-tol/ascc:devfrom dp24_btk_datasetssanger-tol/ascc:dp24_btk_datasetsCopy head branch name to clipboardSep 11, 2024

+3,523-384

Commits

Commits on Apr 5, 2024

• initial work on the merge modules

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• Updates to the create_btk_dataset process

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• Updates to the create_btk_dataset process

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• Adding Diamond Blast subworkflow

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• Added the UNIPROT diamond blast subworkflow

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• Typo

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Commits on Apr 8, 2024

• additions to scripts and a rewrite

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• Adding and updating modules

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• Adding more modules

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• Updating the modules conf for the diamond blastx

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Commits on Apr 17, 2024

• updates to modules

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• Update to config

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Commits on Apr 18, 2024

• Addition of the V2 python scripts

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• Modifications for malformed channels

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• Updated

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• Updated

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• Addition of a V2 python script

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• updates for merge BTK datasets

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• Remove ls -lh and unnecessary args

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Commits on Apr 19, 2024

• Addition of the trimNs subworkflow

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• Addition of the trimNs subworkflow

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• Addition of the trimNs subworkflow

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• Addition of the trimNs subworkflow

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• Addition of the ascc merge tables module

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• module which was missing from the diamond subworkflow, required to generate the hits file

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• Updates to the modules

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• Updating modules config

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• Addition of a new module to generate the hits file

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• Addition of re-written scripts

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• Addition of re-written scripts

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• addition of ascc merge tables script

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• Skeleton module for the sanger-tol_btk module/pipeline

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• Adding the expected values for the sanger-tol-blobltoolkit pipeline/module

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• adding args

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• Adding IN-DEVELOPMENT banner

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• Merge branch 'dev' into dp24_btk_datasets

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• linting fix

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• Prettier Fix

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• Adding skeleton module

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• Formatting and EditorConfig linting

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• updating container

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• removed

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• formatting

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Commits on Apr 23, 2024

• Updating from sanger-tol containers to public more suitable ones

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• spelling

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Commits on Apr 30, 2024

• modified: modules/local/autofiltering.nf

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• new file: bin/abnormal_contamination_check.py

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Commits on May 9, 2024

• Updates

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• Updats

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• Adding the sanger tol btk pipeline

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  010f7c9

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• Fix the script

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• Add the script for generating the samplesheet

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• Adding the module for abnormal checks

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• Updates to add contam check

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• Updates to add contam check

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• Updates to add contam check

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Commits on May 13, 2024

• Updates to all

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• Updates to all

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• Updates to all

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• Updates to all

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Commits on May 23, 2024

• Updates

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• Updates

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Commits on May 28, 2024

• Fixing the autofilter, wrong file was being passed and booling the output was incomplete -- fixed

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Commits on Jun 11, 2024

• Updates

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Commits on Jun 20, 2024

• Updates

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Commits on Jun 25, 2024

• Fixes that were stopping the pipeline completing

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Commits on Jun 27, 2024

• Update for ea

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• Update to use the sorted bam file for generate_samplesheet

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• Update to use the sorted bam file for generate_samplesheet

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• Update to use the sorted bam file for generate_samplesheet

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• Input Channel lacked meta and so failed the input check

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• Updates to channel paths and channels for modules

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Commits on Jul 3, 2024

• Update based on work of ea12

  

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  authored and

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• Update to command

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• Linting fix

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• Updates - fixed errpr in test.yaml

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Commits on Jul 5, 2024

• Updates for testing

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• Updates for testing

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• Adding https rather than http

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• add file exist arg to linting

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• add file exist arg to linting

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• add file exist arg to linting

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• add file exist arg to linting

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  8e111e1

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Commits on Jul 8, 2024

• Correct treeval to ascc

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Commits on Jul 9, 2024

• correction

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Commits on Jul 10, 2024

• Update workflow

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• Update test.yaml

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• Updates to Workflows

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Commits on Jul 12, 2024

• Updates, changes to flags and ci to allow for turning off btk

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Commits on Jul 18, 2024

• Fixing reviewer comments

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• Fixed Variable name for cicd

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Commits on Jul 25, 2024

• Adding version output and stubs

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Commits on Jul 26, 2024

• updates and version outputs

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• Adding Merge Tables - spelling error - tuple error

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Commits on Aug 6, 2024

• Updates to spelling, name corrections to match OLD_ASCC

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• Adding include_exclude checker

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• Removed extra script and renamed V2

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• Updates to check

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Commits on Aug 7, 2024

• ea10 edits to dp24_btk_datasets_branch

  

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• 07.08.2024 edits

  

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• ran linting with black

  

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• Updating the version of BTK, spelling and bug fixes

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• Merge branch 'dp24_btk_datasets' into dp24_btk_datasets_ea10_edits2

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• Merge pull request #55 from sanger-tol/dp24_btk_datasets_ea10_edits2

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Commits on Aug 8, 2024

• Addition of new scripts to filter and double check data

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• Adding new scripts for filtering and double checking data #56

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• Updates for #56

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• Updates for #56

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• Updates closes #56 and additions to the output.md file

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• Prettier linting

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Commits on Aug 9, 2024

• Update to the sanger-tol module to remove the yaml flag which is now depreciated

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• closes #57 filters the output to that directly needed for analysis

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• Addition of 2/3 indicator files needed for integration into the current sanger automation workflows

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• Addition of 2/3 indicator files needed for integration into the current sanger automation workflows

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• Addition of indicator files, these are saved to the main outdir

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• Addition of indicator files, these are saved to the main outdir

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• Addition of indicator files, these are saved to the main outdir

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• Addition of indicator files, these are saved to the main outdir

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Commits on Aug 14, 2024

• Adding 13 subworkflow images

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• minor update

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