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nf-core/eager: Changelog

All notable changes to this project will be documented in this file.

The format is based on Keep a Changelog and this project adheres to Semantic Versioning.

[Unpublished / Dev Branch]

`Fixed`

#110 - Fix for MultiQC Missing Second FastQC report

[2.0.3] - 2018-12-09

`Added`

#80 - BWA Index file handling
#77 - Lots of documentation updates by @jfy133
#81 - Renaming of certain BAM options
#92 - Complete restructure of BAM options

`Fixed`

#84 - Fix for Samtools index issues
#96 - Fix for MarkDuplicates issues found by @nilesh-tawari

Other

Added Slack button to repository readme

[2.0.2] - 2018-11-03

`Changed`

#70 - Uninitialized readPaths warning removed

`Added`

#73 - Travis CI Testing of Conda Environment added

`Fixed`

#72 - iconv Issue with R in conda environment

[2.0.1] - 2018-11-02

`Fixed`

#69 - FastQC issues with conda environments

[2.0.0] "Kaufbeuren" - 2018-10-17

Initial release of nf-core/eager:

`Added`

FastQC read quality control
(Optional) Read complexity filtering with FastP
Read merging and clipping using AdapterRemoval v2
Mapping using BWA / BWA Mem or CircularMapper
Library Complexity Estimation with Preseq
Conversion and Filtering of BAM files using Samtools
Damage assessment via DamageProfiler, additional filtering using PMDTools
Duplication removal via DeDup
BAM Clipping with BamUtil for UDGhalf protocols
QualiMap BAM quality control analysis

Furthermore, this already creates an interactive report using MultiQC, which will be upgraded in V2.1 "Ulm" to contain more aDNA specific metrics.

⚡