Code

ASCC multi-assembly re-write#65

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DLBPointon merged 126 commits intodevsanger-tol/ascc:devfrom dp24_version_1sanger-tol/ascc:dp24_version_1Copy head branch name to clipboardJan 17, 2025

+13,770-3,404

Commits

Commits on Nov 12, 2024

• Updates as part of Version 1 rewrite

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• Updates as part of Version 1 rewrite

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• Updates as part of Version 1 rewrite

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Commits on Nov 13, 2024

• Updates from rewrite to main repo

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• Updates from rewite

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• Updating test case and CICD

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• Updates from Eeriks docs branch

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• Roll back a couple of things

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• Formatting updates

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• Newline

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• Updates for CICD - addition of the modules.json

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• Updates for CICD

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• Updates for CICD

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• Updates for CICD

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Commits on Nov 14, 2024

• Adding a test function to parse nextflow version and resouce requirements

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• Adding a test function to parse nextflow version and resouce requirements

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• Adding a test function to parse nextflow version and resouce requirements

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• Adding a test function to parse nextflow version and resouce requirements

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• Adding a test function to parse nextflow version and resouce requirements

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• Adding a test function to parse nextflow version and resouce requirements

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• Updates

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• Updates

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• Adding a GitHub test yaml

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Commits on Nov 15, 2024

• Pinning verison of nf-core and bug fixes

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• Pinning verison of nf-core and bug fixes

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Commits on Nov 18, 2024

• Update min nextflow version to test on

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Commits on Nov 20, 2024

• updates

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Commits on Nov 21, 2024

• Updating modules and fixing blast_lineage bug

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• Updating modules and fixing blast_lineage bug

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• Fixing CI data

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• Fixing CI data

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• Fixing CI data

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• Fixing CI data

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• Fixing CI data

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Commits on Nov 26, 2024

• Updating biopython+numpy images built with anaconda to biopython wo anaconda

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• Linting YML was broken

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• Pre Commit linting

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• Pre Commit linting

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• Pre Commit linting

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• Pre Commit linting

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• Pre Commit linting

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• Re-add pipeline download

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• Re-add pipeline download

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• Forgot to point it to the github_testing folder

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• Forgot to point it to the github_testing folder

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Commits on Nov 27, 2024

• Updating notes in the pipeline and removed the BTK_YAML arg from the github_test.yaml

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Commits on Nov 28, 2024

• Using realpath so we don't have to pass the bam around like a wally

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Commits on Nov 29, 2024

• Updates to pipeline

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• Uncomment out the organellar workflow

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• Lint

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• revert blast makeblastdb to original

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• Updated to fix organellar BTK issue

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Commits on Dec 2, 2024

• Removing local busco dataset call

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Commits on Dec 5, 2024

• Updates

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• Updating setup-nextflow from 1 to 2

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Commits on Dec 9, 2024

• Updates

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Commits on Dec 12, 2024

• Adding functionality for gzipped input

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• Adding functionality for gzipped input

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• Updates

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• Citation for sanger-tol-btk

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• Note for further updates

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Commits on Jan 10, 2025

• Adding Unzip function

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• Update linting workflow

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• Updating CICD and modules

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Commits on Jan 13, 2025

• Fix to control race conditions in runs with larger genomes

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• Making sure that the barcodes subworkflow works

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• Adding test file

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• Correcting cicd

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• Correcting path for pacbio_adaptors.fa

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• Debugging the tests

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• Debugging the test - Adding artifacts

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Commits on Jan 14, 2025

• Correcting use of channel.of to channel.frompath where appropriate

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Commits on Jan 15, 2025

• resourceParams is for overriding hpc configs!

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• Updating resource requirements in test.config

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• Trying to pin down a GitHub actions error

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• Trying to pin down a GitHub actions error

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• Trying to pin down a GitHub actions error

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• Truncating pipeline to ID failure

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• Truncating pipeline to ID failure

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• Truncating pipeline to ID failure

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• Truncating pipeline to ID failure

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• Truncating pipeline to ID failure

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• Truncating pipeline to ID failure

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• Truncating pipeline to ID failure

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• Truncating pipeline to ID failure

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• Truncating pipeline to ID failure

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• Truncating pipeline to ID failure

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• Truncating pipeline to ID failure

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• Truncating pipeline to ID failure

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• Truncating pipeline to ID failure

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• Truncating pipeline to ID failure

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• Truncating pipeline to ID failure

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• Truncating pipeline to ID failure

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• Wrong

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• Uncommenting subworkflows to test and correcting multiple downloads from artifacts

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• Uncommenting subworkflows to test and correcting multiple downloads from artifacts

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• Uncommenting subworkflows to test and correcting multiple downloads from artifacts

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• Uncommenting subworkflows to test and correcting multiple downloads from artifacts

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• Uncommenting subworkflows to test and correcting multiple downloads from artifacts

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• Uncommenting subworkflows to test and correcting multiple downloads from artifacts

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• Uncommenting subworkflows to test and correcting multiple downloads from artifacts

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• Uncommenting subworkflows to test and correcting multiple downloads from artifacts

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• Uncommenting subworkflows to test and correcting multiple downloads from artifacts

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• Uncommenting subworkflows to test and correcting multiple downloads from artifacts

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• Uncommenting subworkflows to test and correcting multiple downloads from artifacts

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Commits on Jan 16, 2025

• Fixed the blast issue locally

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• Fixed the blast issue locally

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• Fixed the blast issue locally

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• Linting NF-CORE

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• Changes to allow genomic_only runs

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• Adding new param

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• Adding VecScreen file

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Commits on Jan 17, 2025

• Changes to control EVERY subworklow and skip essentials if needed in rare cases

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• Changes to control EVERY subworklow and skip essentials if needed in rare cases

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• Changes to control EVERY subworklow and skip essentials if needed in rare cases

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• If your running without essentials, then don't do it on the organelles

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• Adding the paper

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• Adding the paper

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• Adding the paper - linting riles

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• Adding the paper - linting rules

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• Adding Eeriks changes to Usage

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• Template rules

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• Changes requested by Eerik

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• Changes requested by Eerik

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• Usage.md now properly updates

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• LINTING

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