Ramprasad Neethiraj fd5f6f5f4f Revert recent changes made to some of the modules (#1463) ... * revert changes to modules * fix tests * fix kraken2 * fix untar * fix cat * add blank lines * fix typo		2022-03-30 20:21:06 +02:00
..
abacas
abricate
adapterremoval
adapterremovalfixprefix
agrvate
allelecounter
amps
amrfinderplus
arriba
artic
ascat
assemblyscan
ataqv/ataqv
bakta
bamaligncleaner
bamcmp
bamtools
bamutil/trimbam
bandage/image
bbmap
bcftools
bedtools
biobambam/bammarkduplicates2
biscuit
bismark
blast
bowtie
bowtie2
bracken/bracken
bwa
bwamem2
bwameth
cat	Revert recent changes made to some of the modules (#1463)	2022-03-30 20:21:06 +02:00
cellranger
centrifuge
checkm/lineagewf
chromap
clonalframeml
cmseq/polymut
cnvkit/batch
cnvpytor
controlfreec
cooler
csvtk
custom
cutadapt
damageprofiler
dastool
dedup
deeparg
deeptools
deepvariant	Revert recent changes made to some of the modules (#1463)	2022-03-30 20:21:06 +02:00
delly/call
diamond
dragmap
dragonflye
dshbio
ectyper
emmtyper
ensemblvep
expansionhunter
faqcs
fargene
fastani
fastp
fastqc
fastqscan
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
ivar
jupyternotebook
kaiju/kaiju
kallisto/index
kallistobustools
khmer/normalizebymedian
kleborate
kraken2/kraken2
krona
last
leehom
legsta
lima
lissero
lofreq
macrel/contigs
macs2/callpeak
mafft
malt
maltextract
manta	Revert recent changes made to some of the modules (#1463)	2022-03-30 20:21:06 +02:00
mapdamage2
mash
mashtree
maxbin2
medaka
megahit	Fix formatting in yaml files, add yamllint config (#1279)	2022-02-15 11:15:27 +00:00
meningotype
metabat2
metaphlan3
methyldackel
minia
miniasm
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
pmdtools/filter
porechop
preseq
prodigal
prokka
pycoqc
pydamage
qcat
qualimap
quast
racon
rapidnj
rasusa
raven
raxmlng
rgi/main
rmarkdownnotebook
roary
rsem
rseqc
salmon
samblaster
samtools
scoary
seacr/callpeak
seqkit
seqsero2
seqtk
sequenzautils
seqwish/induce
shovill
sistr
snpdists
snpeff
snpsift/split
snpsites
sortmerna
sourmash/sketch
spades
spatyper
sratools
ssuissero
staphopiasccmec
star
stranger
strelka
stringtie
subread/featurecounts
svdb
tabix
tbprofiler/profile
tiddit	Revert recent changes made to some of the modules (#1463)	2022-03-30 20:21:06 +02:00
transdecoder
trimgalore
ucsc
ultra/pipeline
umitools
unicycler
untar
unzip
variantbam
vcfanno
vcflib/vcfuniq
vcftools
yara