nf-core/exoseq issues and pull requests

#40 - Difference of pipelines

Issue - State: open - Opened by kokyriakidis over 5 years ago - 2 comments

#39 - Prepare for nf-core sync

Issue - State: open - Opened by sven1103 about 6 years ago

#38 - remove duplicate help + fix some alignment

Pull Request - State: closed - Opened by maxulysse over 6 years ago - 1 comment

#37 - update dependencies

Pull Request - State: closed - Opened by maxulysse over 6 years ago

#36 - Update Dependencies

Issue - State: closed - Opened by apeltzer over 6 years ago

#35 - Singularity Support

Issue - State: open - Opened by apeltzer over 6 years ago

#34 - Add Travis CI Testing to ExoSeq

Pull Request - State: open - Opened by apeltzer over 6 years ago - 1 comment

#33 - Trimgalore fuse fastqc

Pull Request - State: closed - Opened by apeltzer over 6 years ago - 1 comment

#32 - Include Switch to skip GenotypeGVCFs ?

Issue - State: open - Opened by apeltzer over 6 years ago

#31 - Merge Mapping BAM and Samtools sort

Pull Request - State: closed - Opened by apeltzer over 6 years ago

#30 - Replaced old $process syntax withName syntax

Pull Request - State: closed - Opened by apeltzer over 6 years ago

#29 - AWSbatch profiles added

Pull Request - State: closed - Opened by apeltzer over 6 years ago

#28 - Get rid of $processName stuff and use withname syntax

Issue - State: closed - Opened by apeltzer over 6 years ago - 1 comment

#27 - Add AWSBatch Profiles

Issue - State: closed - Opened by apeltzer over 6 years ago
Labels: enhancement

#26 - Add a DOI on first release

Issue - State: open - Opened by apeltzer over 6 years ago
Labels: enhancement

#25 - Removed problematic local executor specification

Pull Request - State: closed - Opened by alneberg over 6 years ago - 6 comments

#24 - Update gitter channel with the exoseq one

Pull Request - State: closed - Opened by maxulysse over 6 years ago - 1 comment

#23 - Parallelization for Haplotypecaller

Issue - State: closed - Opened by veeravalli over 6 years ago - 3 comments
Labels: wontfix

#22 - Configuration - nest assemblies and references

Issue - State: closed - Opened by marchoeppner over 6 years ago - 1 comment

#21 - Split MultiQC output into fastq, library and sample

Issue - State: open - Opened by marchoeppner over 6 years ago

#20 - Enable multi-lane support

Issue - State: open - Opened by marchoeppner over 6 years ago - 4 comments

#19 - Add HSMetrics

Issue - State: open - Opened by marchoeppner over 6 years ago

#18 - Switch to a CSV/TSV based input

Issue - State: open - Opened by marchoeppner over 6 years ago - 6 comments

#17 - Remove support for genome processing

Issue - State: closed - Opened by marchoeppner over 6 years ago - 2 comments

#16 - Merge BWA and Samtools steps

Issue - State: closed - Opened by marchoeppner over 6 years ago - 1 comment
Labels: WIP

#15 - Move FastQC into trimGalore

Issue - State: closed - Opened by marchoeppner over 6 years ago - 2 comments

#14 - Make CRAM default alignment format

Issue - State: closed - Opened by marchoeppner over 6 years ago - 2 comments

#13 - Travis Tests for ExoSeq

Pull Request - State: closed - Opened by apeltzer over 6 years ago - 1 comment
Labels: WIP

#12 - Software versions in single process

Pull Request - State: closed - Opened by apeltzer over 6 years ago - 1 comment

#11 - Get it all nextflowy

Pull Request - State: closed - Opened by apeltzer over 6 years ago

#10 - Evaluate / Integrate Googles DeepVariant Caller?

Issue - State: closed - Opened by apeltzer over 6 years ago - 2 comments

#9 - Joint Discovery merge with main script

Issue - State: open - Opened by apeltzer over 6 years ago - 2 comments

#8 - Collect software versions in a single process

Issue - State: closed - Opened by apeltzer over 6 years ago

#7 - Move kits to a base params definition, similar to igenomes

Issue - State: closed - Opened by apeltzer over 6 years ago - 3 comments

#6 - Automatically check Reference Files are compatible

Issue - State: closed - Opened by apeltzer over 6 years ago - 1 comment

#5 - Provide additional nf script for preparing Exome-Kit files

Issue - State: open - Opened by apeltzer over 6 years ago

#4 - Add Travis Tests for ExoSeq

Issue - State: open - Opened by apeltzer over 6 years ago

#3 - Support for mixed capture methods

Issue - State: open - Opened by apeltzer over 6 years ago

#2 - Updated Documentation

Pull Request - State: closed - Opened by apeltzer over 6 years ago

#1 - Some changes to follow more nf-core rules in NGI-ExoSeq

Pull Request - State: closed - Opened by ewels over 6 years ago - 1 comment

GitHub / nf-core/exoseq issues and pull requests