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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[Unpublished Version / DEV]

`Added`

#189 - Outputing unmapped reads in a fastq files with the --strip_input_fastq flag
#186 - Make FastQC skipping [possible] /(nf-core#182)
Merged in nf-core/tools release V1.6 template changes
A lot more automated tests using Travis CI
Don't ignore DamageProfiler errors anymore

`Fixed`

#152 - DamageProfiler errors won't crash entire pipeline anymore
#176 - Increase runtime for DamageProfiler on large reference genomes
#172 - DamageProfiler errors won't crash entire pipeline anymore
#174 - Publish DeDup files properly
#196 - Fix reference issues
#196 - Fix issues with PE data being mapped incompletely
#200 - Fix minor issue with some typos
#210 - Fix PMDTools encoding issue from samtools calmd generated files by running through samtools view first

`Dependencies`

Added DeDup v0.12.5 (json support)
Added mtnucratio v0.5 (json support)
Updated Picard 2.18.27 -> 2.19.0
Updated GATK 4.1.0.0 -> 4.1.1.1
Updated damageprofiler 0.4.4 -> 0.4.5
Updated r-rmarkdown 1.11 -> 1.12

[2.0.6] - 2019-03-05

`Added`

#152 - Clarified --complexity_filter flag to be specifically for poly G trimming.
#155 - Added Dedup log to output folders
#159 - Added Possibility to skip AdapterRemoval, skip merging, skip trimming fixing #64,#137 - thanks to @maxibor, @jfy133

`Fixed`

#151 - Fixed [post-deduplication step errors](nf-core#128
#147 - Fix Samtools Index for large references
#145 - Added Picard Memory Handling fix

`Dependencies`

Picard Tools 2.18.23 -> 2.18.27
GATK 4.0.12.0 -> 4.1.0.0
FastP 0.19.6 -> 0.19.7

[2.0.5] - 2019-01-28

`Added`

#127 - Added a second testcase for testing the pipeline properly
#129 - Support BAM files as input format
#131 - Support different reference genome file extensions

`Fixed`

#128 - Fixed reference genome handling errors

`Dependencies`

Picard Tools 2.18.21 -> 2.18.23
R-Markdown 1.10 -> 1.11
FastP 0.19.5 -> 0.19.6

[2.0.4] - 2019-01-09

`Added`

#111 - Allow Zipped FastA reference input
#113 - All files are now staged via channels, which is considered best practice by Nextflow
#114 - Add proper runtime defaults for multiple processes
#118 - Add centralized configs handling by https://github.com/nf-core/configs
#115 - Add DamageProfiler MultiQC support
#122 - Add pulling from Dockerhub again

`Fixed`

#110 - Fix for MultiQC Missing Second FastQC report
#112 - Remove redundant UDG options

[2.0.3] - 2018-12-12

`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.

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