SusiJo 810564deca Merge branch 'master' into gatk_spark		2022-05-31 15:24:58 +02:00
..
abacas
abricate
adapterremoval
adapterremovalfixprefix
agrvate
allelecounter
amplify/predict
amps
amrfinderplus
antismash	Apply suggestions from code review	2022-05-12 15:28:19 +02:00
arriba
artic
ascat
assemblyscan
ataqv/ataqv
bakta
bamaligncleaner
bamcmp
bamtools
bamutil/trimbam
bandage/image
bbmap
bcftools	fix lint error	2022-05-23 12:59:48 +02:00
bclconvert
bedtools	added bedtools split	2022-05-17 14:24:32 +02:00
biobambam	fix config	2022-05-17 09:09:19 +02:00
biscuit
bismark
blast
bowtie
bowtie2	add PE sorted test	2022-05-13 19:16:50 +02:00
bracken/bracken
busco
bwa
bwamem2
bwameth
cat
cellranger
centrifuge
checkm/lineagewf
chromap
clonalframeml
cmseq/polymut
cnvkit	missing meta.id changed	2022-05-24 14:59:52 +02:00
cnvpytor
controlfreec
cooler
csvtk
custom	tests: add missing paths to config	2022-05-11 18:17:27 +02:00
cutadapt
damageprofiler
dastool
dedup
deeparg
deeptools
deepvariant
delly/call
diamond
dragmap
dragonflye
dshbio
ectyper
elprep
emmtyper
ensemblvep
expansionhunter
faqcs
fargene
fastani
fastp
fastqc
fastqscan
fasttree	Update all modules to new NF DSL2 syntax (#1099)	2021-11-26 07:58:40 +00:00
fgbio
filtlong	Switch from md5sum to string due to conda flakiness	2022-05-31 14:45:41 +02:00
flash
freebayes
gamma/gamma	fixed test.yml	2022-05-24 19:27:09 -04:00
gatk4	adjusted newlines	2022-05-31 14:54:39 +02:00
genmap
genomescope2	Update tests/modules/genomescope2/test.yml	2022-05-13 11:27:42 +02:00
genrich
gffread
glnexus
graphmap2
gstama
gtdbtk/classifywf
gubbins
gunc
gunzip
hamronization
happy
hicap
hifiasm
hisat2
hmmcopy
hmmer
hmtnote	Update main.nf	2022-05-16 15:20:15 +00:00
homer
hpsuissero
ichorcna
idr
imputeme/vcftoprs
iqtree
ismapper
isoseq3
ivar
jupyternotebook
kaiju
kallisto/index
kallistobustools
kat/hist	Update tests/modules/kat/hist/test.yml	2022-05-23 08:51:49 +02:00
khmer/normalizebymedian
kleborate
kraken2/kraken2
krona
last
leehom
legsta
lima
lissero
lofreq
macrel/contigs
macs2/callpeak
mafft
malt
maltextract
manta
mapdamage2
mash	Patch mash screen	2022-05-25 12:29:14 +00:00
mashtree
maxbin2
maxquant/lfq
md5sum
medaka
megahit
megan/rma2info
meningotype
meryl	Merge branch 'master' into meryl_unionsum	2022-05-09 16:16:08 +02:00
metabat2
metaphlan3
methyldackel
minia
miniasm
minimap2
mlst
mobsuite/recon
mosdepth	Update main.nf	2022-05-25 19:38:12 +01:00
motus	Update tests/modules/motus/profile/test.yml	2022-05-12 20:55:54 +01:00
msisensor
msisensorpro
mtnucratio
multiqc
mummer
muscle	Update all modules to new NF DSL2 syntax (#1099)	2021-11-26 07:58:40 +00:00
nanolyse
nanoplot	Fix formatting in yaml files, add yamllint config (#1279)	2022-02-15 11:15:27 +00:00
ncbigenomedownload
nextclade
ngmaster
ngscheckmate/ncm
nucmer
optitype
pairix
pairtools
panaroo/run
pangolin
paraclu
pbbam/pbmerge
pbccs
peddy
phantompeakqualtools
phyloflash
picard	fix tests (again)	2022-05-22 06:54:09 +02:00
pirate
plasmidid
plink
plink2
pmdtools/filter
porechop
preseq
prinseqplusplus
prodigal
prokka
pycoqc
pydamage
qcat
qualimap
quast
racon
rapidnj
rasusa
raven
raxmlng
rgi/main
rmarkdownnotebook
roary
rsem
rseqc
rtgtools/vcfeval	Small update on the output channels	2022-05-10 12:34:52 +02:00
salmon
samblaster
samtools
scoary
seacr/callpeak
seqkit
seqsero2
seqtk
sequenzautils
seqwish/induce
shasum
shigatyper
shovill
sistr
slimfastq
snapaligner
snpdists
snpeff
snpsift/split
snpsites
sourmash/sketch
spades	Update all modules to new NF DSL2 syntax (#1099)	2021-11-26 07:58:40 +00:00
spatyper
sratools	refactor: move files to custom section	2022-05-11 17:33:45 +02:00
srst2/srst2
ssuissero
stadeniolib/scramble
staphopiasccmec
star	Fix tests	2022-05-27 12:14:10 +01:00
stranger
strelka
stringtie
subread/featurecounts
svdb
tabix
tbprofiler/profile
tiddit
transdecoder
trimgalore
ucsc
ultra/pipeline
umitools	Fix Conda tests	2022-05-23 22:39:12 +01:00
unicycler
untar
unzip
vardictjava
variantbam
vcfanno
vcflib/vcfuniq
vcftools
vsearch/usearchglobal	prettier	2022-05-30 13:35:12 +02:00
yara