coproid - DSL2 conversion

Changed: - DSL2 rewrite - fastp replaced AdapterRemoval for read quality trimming/merging. - sam2lca is now used for computing the endogenous host DNA quantity, instead of custom python scripts, allowing for handling more flexibly test host genomes. - Pipeline reporting is now performed using Quarto, instead of Jupyter notebook - Minor JSON schema updates New: - aDNA damage testing using PyDamage - Interactive plots in report - Unit testing of most modules in the pipeline.

- Nextflow
Published by MeriamOs about 1 year ago

coproid - nf-core coproID v.1.1.1

This is a patch release

What's Changed

• Add pipeline schema
• Update environment to fix broken dependancies by @maxibor in https://github.com/nf-core/coproid/pull/50

Full Changelog: https://github.com/nf-core/coproid/compare/1.1...1.1.1

- Nextflow
Published by maxibor over 3 years ago

coproid - coproID v1.1 - Langley Panda

Changes since version 1.0

• Update mapped basepair count to be quicker and include it in report #14
• Remove outdated scripts #14
• Update logo to match font #13
• Update Sourcepredict to version 0.4 and reflect new parameters in coproID #19 e4afca7 c2d4164
• Changed bedtools bamtofastq to samtools fastq e4afca7
• Fixed column names in report (PC* to DIM* ) e4afca7
• Update README to inlude Zenodo badge, Quick start, contributor section, and tools references. 9874ae8 e85988b
• Update documentation bedfdde
• Update Nextflow minimum version to 19.04.0 44999fd
• Update travis for more recent nextflow requirements 1e3e454
• Adapt coproID to nf-core tools 1.8 release #21
• Add social preview image #22
• Fix Kraken2 segmentation error #26
• Update to nf-core tools 1.9 release, and doc for new version of sphinx #27
• coproID is now published in PeerJ

- Nextflow
Published by maxibor about 6 years ago

coproid - coproID v1.0 - Dioptre Walrus

coproID release 1.0

coproID is a pipeline I originally developped outside of nf-core to perform the host identification of archaelogical faeces using endogenous DNA content and machine learning on microbiome compositon. I adapted it to nf-core recently, following the hackaton in Tubingen.

coproID contains both published external softwares, homecooked package (sourcepredict), as well as custom python scripts.

Improvements over coproID version 0.6

• Support for 3 organism comparison
• Adding sourcepredict
• Updating reports to have interactive plotting
• Updated to use Kraken2 instead of Kraken1
• Adding docker

Adaptions to port to nf-core

• Major redefinition of the channels creation to adapt to iGenomes and profiles
• Added and adapted all the nf-core boilerplate code for support of configs and containers
• Improved documentation

- Nextflow
Published by maxibor about 7 years ago