Code

Adds modules nextflow pseudocode#79

Code

Merged

cgpu merged 40 commits intodevsheynkman-lab/Long-Read-Proteogenomics:devfrom adds-modules-nextflow-pseudocodesheynkman-lab/Long-Read-Proteogenomics:adds-modules-nextflow-pseudocodeCopy head branch name to clipboardNov 24, 2020

+177-9

Commits

Commits on Nov 7, 2020

• Adds nf-core template for nextflow pips

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• Absorbs dev latest changes

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• Cleans up template main.nf and adds swag cli message

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• Updates nextflow.config

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• Adds Dockerfile and env yaml updates

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• Removes redundant files from assets

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• Deleted nf schema json

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• Removes redundant configs

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• Updates README with template structure

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• Updates docs/

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• Updates repo name in changelog

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• Updates template test.config

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• Adds bin folder and template wrapper R script

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• Adds pbccs in env.yml

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• Changes the location of pipeline info, logs

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• Adds .github folder

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• Merge branch 'adds-nextflow-boilerplate' of https://github.com/sheynkman-lab/Long-Read-Proteogenomics into adds-nextflow-boilerplate

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• Removes redendant files from GH actions

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• Updates CONTRIBUTING.md

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• Updates ISSUE_TEMPLATE

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• Update PULL_REQUEST_TEMPLATE.md

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• Removes AWS tests

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• Adds misspelling test

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• Removes linting.yml

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  91ea8d9

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• Corrects typo

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• Removes igenomes config

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• Merge branch 'adds-nextflow-boilerplate' of https://github.com/sheynkman-lab/Long-Read-Proteogenomics into adds-nextflow-boilerplate

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Commits on Nov 8, 2020

• Fixes typos caught by review-dog

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• Adds tentative LICENSE

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• Adds environment.yml with pandas, numpy, biopython

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• Adds CCS process

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• Adds pbbam (required for ccs --chunk subsequent routine)

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• Adds pbindex, ccs processes (w/ parallel --chunks)

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Commits on Nov 9, 2020

• Removes redundant bai (pbi is needed)

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• Adds temp process mock ccs and flag for testing

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Commits on Nov 24, 2020

• Absorbs latest changes from dev

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  e860d54

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• Corrects typo caught by reviewdog gh-action

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• Typo fix

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• Deletes commented out section

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• Makes the section note more informative

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