Release fluffy_hematology_wgs v1.1.0 · clinical-genomics-uppsala/fluffy_hematology_wgs

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)

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)
type included (aa9ef7e)
typo found in Snakefile (26654df)
update multiqc sample order to use pedegree names (1a19652)
update order of multiqc inputfiles so Fold80 is from HSMetrics not wgs metrics (bb8d5fb)

add log thresholds and ploidy to cnvkit table (a798609)
adjusted for new cluster (779b5eb)
Manta now filters anything that did not PASS all filters (5832c8d)
priority now for parabricks fq2bam (584ed9e)
prority to fusioncatcher (6db152a)

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