Concondancecheck 3.0.0

New Concondancecheck pipeline making use of Nextflow.

new automated
liftover if needed
Open array support
vcf support
cram/bam support

What's Changed

• Various small fixes for bin/ConcordanceCheck.sh by @pneerincx in #34
• first version of nf pipeline by @Gerbenvandervries in #33
• typo by @Gerbenvandervries in #35
• Major changes to dataflow of the pipeline, cram/bam support, extra logging to automated by @Gerbenvandervries in #36
• updated automation scripts, and bugfix fixed filenames. by @Gerbenvandervries in #37
• New version of ParseDarwinSamplesheet.sh script, finetuning concordance.sh, changed log location, lost of bugfixes by @Gerbenvandervries in #38
• made isilonmount location dependent on chaparone machine by @Gerbenvandervries in #39
• improve rsync command by @Gerbenvandervries in #40
• ignore project postfix by @Gerbenvandervries in #41
• bugfixes by @Gerbenvandervries in #42
• sort vcfs by @Gerbenvandervries in #43

New Contributors

• @Gerbenvandervries made their first contribution in #33

Full Changelog: 2.2.1...3.0.0

2.2.1

• concordanceCheck can now work with both .final.vcf.gz and GAVIN files.
• fixing ConcordanceCheck when vcf file is not gzipped

2.2.0

Merge pull request #27 from RoanKanninga/master

fixing location from where sbatch is running
changed sampleId in outputfile

ConcordanceCheck 2.1.0

replacing old way of processing concordance samplesheets

Concordance Check 2.0.0

Re-implemented Concordance Check in separate repo. (Previous version was included in NGS_Automated)