[2.0.7] - 2019-06-10

apeltzer released this 10 Jun 20:15

· 2537 commits to master since this release

b8d3dec

[2.0.7] - 2019-06-10

`Added`

#189 - Outputing unmapped reads in a fastq files with the --strip_input_fastq flag
#186 - Make FastQC skipping [possible]
/(#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
#220 - Added post-mapping filtering statistics module and corresponding MultiQC statistics #217

`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 sa]mtools view first
#221 - Fix BWA Index not being reused by multiple samples

`Dependencies`

Added DeDup v0.12.5 (json support)
Added mtnucratio v0.5 (json support)
Updated Picard 2.18.27 -> 2.20.2
Updated GATK 4.1.0.0 -> 4.1.2.0
Updated damageprofiler 0.4.4 -> 0.4.5
Updated r-rmarkdown 1.11 -> 1.12
Updated fastp 0.19.7 -> 0.20.0
Updated qualimap 2.2.2b -> 2.2.2c

Assets 2