nvnieuwk 49825425bb Update delly/call version (#1991) ... updated version + added tests		2022-09-02 10:08:41 +02:00
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abacas
abricate
adapterremoval
adapterremovalfixprefix
agrvate
allelecounter
ampir
amplify/predict
amps
amrfinderplus
antismash
ariba
arriba
artic
ascat
assemblyscan
ataqv
atlas
bakta
bamaligncleaner
bamcmp
bamtools
bamutil/trimbam
bandage/image
bbmap
bcftools
bcl2fastq
bclconvert
bedtools
biobambam
biscuit
bismark
blast
bowtie
bowtie2
bracken/bracken
busco
bwa
bwamem2
bwameth
cat
cellranger
centrifuge
checkm/lineagewf
chromap
clonalframeml
cmseq/polymut
cnvkit
cnvpytor
controlfreec
cooler
csvtk
custom
cutadapt
damageprofiler
dastool
dedup
deeparg
deeptools
deepvariant
delly/call
diamond
dragmap
dragonflye
dshbio
ectyper	Fix formatting in yaml files, add yamllint config (#1279)	2022-02-15 11:15:27 +00:00
elprep
emmtyper
ensemblvep
entrezdirect
expansionhunter
faqcs
fargene
fastani
fastk
fastp
fastqc
fastqscan
fasttree
ffq
fgbio
filtlong
flash	Fix formatting in yaml files, add yamllint config (#1279)	2022-02-15 11:15:27 +00:00
flye
fq/lint
freebayes
gamma/gamma
gatk
gatk4
gecco/run
genescopefk
genmap
genmod
genomescope2
genrich
gffread
glimpse/chunk
glnexus
goat/taxonsearch
graphmap2
gstama
gtdbtk/classifywf
gubbins
gunc
gunzip
gvcftools/extractvariants
hamronization
haplocheck
happy
hicap
hifiasm
hisat2
hmmcopy
hmmer
hmtnote	Update main.nf	2022-05-16 15:20:15 +00:00
homer
hpsuissero
ichorcna
idr
imputeme/vcftoprs
instrain/profile
iqtree
ismapper
isoseq3
ivar
jupyternotebook
kaiju
kallisto/index
kallistobustools
kat/hist
khmer
kleborate
kraken2/kraken2
krakentools/kreport2krona
krona
last
leehom
legsta
lima
lissero
lofreq	Fix formatting in yaml files, add yamllint config (#1279)	2022-02-15 11:15:27 +00:00
macrel/contigs
macs2/callpeak
mafft
malt	Update MALT to older version due to major bug in most recent version (#1796)	2022-06-20 08:20:22 +02:00
maltextract
manta
mapdamage2
mash
mashtree
maxbin2
maxquant/lfq
mcroni
md5sum
medaka
megahit
megan
meningotype
merqury
merquryfk
meryl
metabat2
metaphlan3
methyldackel
minia
miniasm
minimap2
mlst
mobsuite/recon
mosdepth
motus
msisensor
msisensorpro
mtnucratio
multiqc
multivcfanalyzer
mummer
muscle
nanolyse
nanoplot
ncbigenomedownload
nextclade
ngmaster
ngscheckmate/ncm
nucmer
optitype
pairix
pairtools
panaroo/run
pangolin
paraclu
pbbam/pbmerge
pbccs
pear
peddy
phantompeakqualtools
phyloflash
picard
pints/caller
pirate
plasmidfinder
plasmidid
plink
plink2
pmdtools/filter
porechop
preseq
prinseqplusplus
prodigal
prokka
pycoqc
pydamage
qcat
qualimap
quast
racon
rapidnj
rasusa
raven
raxmlng
rgi/main
rhocall/annotate
rmarkdownnotebook
roary
rsem
rseqc
rtgtools
salmon
samblaster
samtools
scoary
seacr/callpeak
seqkit
seqsero2
seqtk
sequenzautils
seqwish/induce
sexdeterrmine
shasum
shigatyper
shovill	Add when: block (#1261)	2022-02-04 09:53:32 +01:00
sistr
slimfastq
snapaligner
snippy/run
snpdists
snpeff
snpsift/split
snpsites
sortmerna
sourmash/sketch
spades
spatyper
sratools
srst2/srst2
ssuissero
stadeniolib/scramble
staphopiasccmec
star
stranger
strelka
stringtie
subread/featurecounts
svdb
tabix
tailfindr
tbprofiler/profile
tiddit
transdecoder
trimgalore
trimmomatic
ucsc
ultra
umitools
unicycler
untar
unzip
vardictjava
variantbam
vcf2db
vcf2maf
vcfanno
vcflib/vcfuniq
vcftools
vsearch/usearchglobal
yara