Code

Nf test#69

Code

Merged

AmstlerStephan merged 77 commits intodevgenepi/umi-pipeline-nf:devfrom nf-testgenepi/umi-pipeline-nf:nf-testCopy head branch name to clipboardJun 20, 2024

+72,809-92

Commits

Commits on Mar 6, 2024

• Update README.md

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• adapt README

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• add credits to original python scripts

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• Add citation file

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• add name of ONT repository

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• Merge pull request #63 from genepi/add_credits

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• adapt citation

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• remove repository citation

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• adapt citation

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• adapt citation

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• Adapt citation file

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• adapt citation

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• adapt config files

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• adapt test.config

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• reduce initial polish cluster resources

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• prepare release

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• Merge pull request #64 from genepi/Adapt-Dockerfile

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• convert to 0.2.0

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• Update test.config

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• Update custom.config

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• Update nextflow.config

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• Update README.md

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• Update README.md

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Commits on Mar 7, 2024

• init nf-test

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• add gitignore

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• adapt config files to use nf-test

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• move test data

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• adapt test.config

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• move testing data

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• add data and tests for the cluster filtering and reformating

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• add further tests for reformat filter cluster

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• add snapshot to test main workflow

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• no snapshots for workflows

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• move testing data

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• Merge branch 'nf-test' of https://github.com/genepi/umi-pipeline-nf into nf-test

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Commits on Mar 8, 2024

• adapt freebayes variant calling flags

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• Update README.md

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• Merge branch 'main' of https://github.com/genepi/umi-pipeline-nf into main

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• adjust freebayes process

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• prepare release 0.2.1

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Commits on Mar 11, 2024

• adapt module structure

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• adapt module paths in main workflow

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• add test data for variant calling

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• Add variant calling test data

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• Add test cases

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• Add freebayes test cases

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• Add tests for all variant callers

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• a

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• adapt lofreq parameters to have no minimal coverage

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• remove typo

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Commits on Mar 12, 2024

• Add fastq test files for merge input

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• Add tests and snapshot for merge_fastq

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• add test data for mapping

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• add tests for consensus and final consensus reads

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• Create test cases for split_reads

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Commits on Mar 15, 2024

• prepare tests for split reads process

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• prepare tests for umi detection

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• Add tests for clustering

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• remove params snippet

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• add tests for cluster polishing

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• add tests for cluster reformatting using

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Commits on Jun 17, 2024

• Add CI tests for nf-test

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• Update ci-tests.yml

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• Adapt docker file path

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• Merge branch 'nf-test' of https://github.com/genepi/umi-pipeline-nf into nf-test

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Commits on Jun 18, 2024

• updated testing paramaters for faster execution

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• Updated test cases

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• Updated local nf-test to v0.9.0 and updated snapshots

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• Merge pull request #67 from genepi/main

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• specify minimap2 version

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• test using existing release container

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• remove docker initiation

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• Temporarily remove snapshots of miniminap2

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Commits on Jun 19, 2024

• adapt testing for merging fastq files

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Commits on Jun 20, 2024

• Adapt java version and update snapshots

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• java is installed in docker, obsolete to install it additionally

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• Resolving merge_fastq tests

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