Sarek 3.1 - Rapaätno

What's Changed

• Back to business on dev by @maxulysse in #762
• Update subway map by @FriederikeHanssen in #766
• Dev deepvariant by @maxulysse in #768
• Fix gatk4 cnnscorevariants by @maxulysse in #770
• add logo for Danish National Genome Center by @maxulysse in #774
• update to new modules syntax + patch on non-up to date modules by @maxulysse in #771
• nf core template merge 2.6 by @maxulysse in #773
• AWS outdir paths were mixed up by @FriederikeHanssen in #777
• Add this years posters by @FriederikeHanssen in #775
• use chr length file by default since cf is otherwise not working by @FriederikeHanssen in #783
• No scatter on full size tests to avoid issues with in or output files randomly not staged by @FriederikeHanssen in #782
• Updated docs of bcftools stats variant depth by @SusiJo in #788
• ci: Move tmpdir to ~ by @emiller88 in #791
• Fix somatic test with mutect2 by @SusiJo in #790
• Md cram by @FriederikeHanssen in #735
• don't annotate gvcfs by @FriederikeHanssen in #793
• Don't publish unzip files by @FriederikeHanssen in #794
• Update ci.yml by @maxulysse in #796
• Update all subworkflows name by @maxulysse in #784
• Fix sample header error when starting from bams by @FriederikeHanssen in #807
• More complete CI by @maxulysse in #806
• add rgid, to separate sample info by @FriederikeHanssen in #814
• Fix validation of input when launching from website by @FriederikeHanssen in #813
• collect cnvkit reference to not be consumed by @FriederikeHanssen in #817
• prioritze test conf for mutect in tests by @FriederikeHanssen in #815
• Use putIfAbsent by @FriederikeHanssen in #821
• add speed up parameters for genomicsdb by @FriederikeHanssen in #827
• Add option for cnvkit to provide external Cnn reference by @FriederikeHanssen in #825
• add more docs about scatter/gather by @FriederikeHanssen in #820
• Fix bug with no variantcalling when starting from step recalibration Issue 763 by @FriederikeHanssen in #828
• Update modules & tool versions by @FriederikeHanssen in #822
• Get ride of copyTo to enable s3 buckets in different regiosn by @maxulysse in #839
• remove cf len file from config by @FriederikeHanssen in #841
• increase samtools stats memory by @FriederikeHanssen in #842

Full Changelog: 3.0.2...3.1