fluffy_hematology_wgs v1.1.0

Features

• add multiqc rna config (59612f7)
• add new copy result files to seperate folder (265f836)
• add sample order to multiqc general stats (c92267c)
• add xlsx file with snvs (223d9cf)
• additional Manta output file that does not filter for disease type (31e84e8)
• adds peddy to MultiQC report (6ab071e)
• adds peddy to MultiQC report (c40fd6c)
• adds peddy to MultiQC report (8b69390)
• Arriba produces pdf output (2dee8d7)
• cnvkit highlights genes in chromosome scatter plots (c5b50dd)
• dux4-igh rna fusioncatcher count added (5099d48)
• GATK implemented (229e649)
• html report (72c559e)
• html report (cc30051)
• intial commit for cnv summary table (62c6d53)
• Manta filters ins del dup on length (c7eb206)
• Manta output on indels and duplications (5ab34a2)
• merged in T-only and RNA pipelines (0eb36b0)
• mosdepth shows 15x (4da17a1)
• mosdepth thresholds (58da543)
• Peddy implemented (df22206)
• remove neutral calls and highlight low conf (efd61f4)
• search DUX4 fusion in t and upgrade fusioncatcher results to hg38 (ddc4c66)
• star to multiqc_r (4432f3e)
• star to multiqc_r (ae2ba1a)
• svdb and gatk (6514f2a)
• svdb and gatk (74976f8)
• svdb running (701e98c)
• vcf filtering on tm exons (05cdc78)

Bug Fixes

• add back conda vars in common create rule (b67bd42)
• add env for cp results (643c4b7)
• add missing container and conda envs (b01edfd)
• Add TN to filenames (473fcf0)
• added output json and removed imagemagick requirement (80946a8)
• added path (a4ba402)
• adjusted bugs in Manta (7e5f331)
• adjusted paths in test config (fae6b1d)
• can handle not annotated variants now (0f8ea9d)
• changed according to reviews (c4c707e)
• cnvkit highlights (2eb8523)
• cnvkit_to_table.py (5826f69)
• dry run (32bffa9)
• dry run schema fix (ab5577d)
• filtering version upgrade (f70c81d)
• fix spelling in cnvkit table (73118fd)
• fix spelling on putput (68b8da4)
• header row changed (9920264)
• Manta filtering fixed (8a34e15)
• MultiQC DNA running now (bfa5b51)
• multiqc fix naming and inputfiles (a1e3ef3)
• multiqc replacename parameter fixed (2629d56)
• prealignment update (18ddcb2)
• protected space fixed (0652d41)
• removed double command for cnv_scatter (de84855)
• replace total seq(samtools) with total reads (picard) (3fe896d)
• run samtools stats w/o bed to get correct total reads in multiqc (bb4d1d4)
• runs and creates all wanted output (f9a8daa)
• set requirments so they work on marvin at least (da277e2)
• testing config fixed (4b2b383)
• testing config fixed (7f99e2b)
• testing config missing property added ([441e58c](https://www.github.com/clinical-genomics-uppsala/fluffy_hematology_wgs/commit/441e58cac7d262803c7b84...