Matthias De Smet b1749445d7 fix output glob (#1551)		2022-04-22 12:50:17 +02:00
..
abacas
abricate
adapterremoval
adapterremovalfixprefix
agrvate
allelecounter
amplify/predict
amps
amrfinderplus
antismash/antismashlitedownloaddatabases
arriba
artic	Untar unzip meta (#1408)	2022-03-21 14:49:28 +01:00
ascat
assemblyscan
ataqv/ataqv
bakta
bamaligncleaner
bamcmp
bamtools
bamutil/trimbam
bandage/image
bbmap
bcftools
bclconvert
bedtools
biobambam
biscuit
bismark
blast	Update all modules to new NF DSL2 syntax (#1099)	2021-11-26 07:58:40 +00:00
bowtie
bowtie2
bracken/bracken
bwa
bwamem2
bwameth
cat	Update cat module (#1469)	2022-03-31 13:42:44 +02:00
cellranger
centrifuge
checkm/lineagewf
chromap
clonalframeml
cmseq/polymut
cnvkit/batch
cnvpytor
controlfreec
cooler
csvtk
custom
cutadapt
damageprofiler
dastool
dedup
deeparg
deeptools
deepvariant
delly/call
diamond	Fix formatting in yaml files, add yamllint config (#1279)	2022-02-15 11:15:27 +00:00
dragmap
dragonflye
dshbio
ectyper
elprep
emmtyper
ensemblvep
expansionhunter
faqcs
fargene
fastani
fastp
fastqc
fastqscan	Update all modules to new NF DSL2 syntax (#1099)	2021-11-26 07:58:40 +00:00
fasttree
fgbio
filtlong
flash
freebayes
gatk4
genmap
genrich
gffread
glnexus
graphmap2
gstama
gtdbtk/classifywf
gubbins
gunc
gunzip
hamronization
hicap
hifiasm
hisat2
hmmcopy
hmmer
homer
hpsuissero
ichorcna
idr
imputeme/vcftoprs
iqtree
ismapper
isoseq3	Fix formatting in yaml files, add yamllint config (#1279)	2022-02-15 11:15:27 +00:00
ivar
jupyternotebook
kaiju
kallisto/index
kallistobustools
khmer/normalizebymedian
kleborate
kraken2/kraken2
krona
last
leehom
legsta
lima
lissero
lofreq
macrel/contigs
macs2/callpeak
mafft
malt
maltextract
manta
mapdamage2
mash
mashtree
maxbin2
medaka
megahit
megan/rma2info
meningotype
metabat2
metaphlan3
methyldackel
minia
miniasm	Change syntax from task.ext.suffix to tast.ext.prefix in all modules (#1110)	2021-12-02 12:39:55 +00:00
minimap2
mlst
mobsuite/recon
mosdepth
msisensor
msisensorpro
mtnucratio
multiqc
mummer
muscle
nanolyse
nanoplot
ncbigenomedownload
nextclade
ngmaster
ngscheckmate/ncm
nucmer
optitype
pairix
pairtools
panaroo/run
pangolin
paraclu
pbbam/pbmerge
pbccs
peddy
phantompeakqualtools
phyloflash
picard
pirate
plasmidid
plink
plink2	implement plink2/score module (#1259)	2022-03-07 13:02:40 -05:00
pmdtools/filter
porechop
preseq
prinseqplusplus
prodigal
prokka
pycoqc
pydamage
qcat
qualimap
quast
racon
rapidnj
rasusa
raven
raxmlng
rgi/main
rmarkdownnotebook
roary	Update test.yml (#1419)	2022-03-19 15:06:21 +00:00
rsem
rseqc
salmon
samblaster
samtools
scoary
seacr/callpeak
seqkit
seqsero2
seqtk
sequenzautils
seqwish/induce
shovill
sistr
snapaligner
snpdists
snpeff
snpsift/split
snpsites
sourmash/sketch
spades
spatyper
sratools
ssuissero
stadeniolib/scramble
staphopiasccmec
star
stranger
strelka
stringtie
subread/featurecounts
svdb
tabix
tbprofiler/profile
tiddit
transdecoder
trimgalore
ucsc
ultra/pipeline
umitools
unicycler
untar
unzip
variantbam
vcfanno	Untar unzip meta (#1408)	2022-03-21 14:49:28 +01:00
vcflib/vcfuniq
vcftools
yara