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Commits on Aug 12, 2024

• specify how to install nextflow and java without conda

  eikematthias

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Commits on Aug 8, 2024

• now mentioning the profile medcluster

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• Merge branch 'master' into docs

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• Merge branch 'master' into interleaved

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Commits on Jul 12, 2024

• Listing salmon database parameter in usage page

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Commits on Jul 4, 2024

• minimal executable example in quickstart

  eikematthias

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• Updating the docs for SRA quick start and how to create a config file

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Commits on Mar 21, 2024

• Extended documentation

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Commits on Mar 5, 2024

• Updated sylph workflow for usage with google cloud batch. Fixed typos in usage docu. Removal of conditional time limit until it's fixed.

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• Fix typos

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Commits on Feb 29, 2024

• update usage docs

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Commits on Feb 21, 2024

• adding magscot parameters to enable custom bin refinement

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Commits on Jan 30, 2024

• adding docs, error handling for maxbin2 changed

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Commits on Dec 1, 2023

• adding a workflow for the tool sylth. sylth will need a externally prepared database to function.

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Commits on Nov 30, 2023

• removing help and header from main.nf to lib, adding first tests for validity of salmon database

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Commits on Nov 20, 2023

• edits to docs

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Commits on Nov 8, 2023

• further edits on installation and quickstart docs

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Commits on Oct 26, 2023

• changing README structure, updating usage docs

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Commits on Sep 26, 2023

• binner revamp, added semibin, freely choose which binner to use

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Commits on Sep 19, 2023

• co-assembly now possible, additional merged abundance table for magscot refined bins

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Commits on Aug 9, 2023

• implemented per sample check if single-end or not for sra input

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Commits on Jun 9, 2023

• first version of salmon workflow

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Commits on May 17, 2023

• Merge remote-tracking branch 'origin/master' into dev

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Commits on May 16, 2023

• include checkm bin quality table as output, optional outputs for assembly and metaphlan to prevent error crashing if one sample does not contain contigs of needed size threshold, checkm is now skip…

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Commits on Apr 28, 2023

• renamed Repository to TOFU-MAaPO

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• metagenomic-workflows is now TOFU-MAaPO

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• Merge branch 'master' into dev

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Commits on Apr 12, 2023

• updated usage and installation docs, updated process tags, cleaned configs, etc

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Commits on Apr 4, 2023

• adding docs for installation and custom config, fixing updating metaphlan and humann processes to create dir if not yet present

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Commits on Mar 20, 2023

• 1.3.1

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• updated usage docs, updated configs for kiel medcluster, misc cleaning

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Commits on Mar 8, 2023

• updating usage docs and more publishing standardization

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Commits on Dec 14, 2022

• 1.3.1

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• misc changes to assembly module, adding metaphlan merge-script, adjusting configs

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Commits on Nov 2, 2022

• Version 1.3 Extended Genome Assembly (#8)

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