Nicolas Vannieuwkerke 81fff7384d small fix and typo		2022-06-09 15:08:02 +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	update arriba module	2022-05-09 14:55:59 +02:00
artic
ascat
assemblyscan
ataqv/ataqv
bakta
bamaligncleaner
bamcmp
bamtools	Merge branch 'master' into bamtools/convert/remove_TODO	2022-05-30 17:36:36 +01:00
bamutil/trimbam
bandage/image
bbmap
bcftools	fix test	2022-06-08 14:48:16 +02:00
bclconvert
bedtools	added bedtools split	2022-05-17 14:24:32 +02:00
biobambam	replace regex with fixed extensions	2022-05-17 09:54:06 +02:00
biscuit
bismark
blast
bowtie
bowtie2	add sort option to bowtie2	2022-05-13 15:26:41 +02:00
bracken/bracken
busco	Update meta.yml	2022-05-06 11:56:43 +00:00
bwa
bwamem2
bwameth
cat
cellranger
centrifuge
checkm/lineagewf
chromap
clonalframeml
cmseq/polymut
cnvkit	added fasta_fai as input + changed if statements	2022-06-02 12:57:50 +02:00
cnvpytor	remove prefix def in callcnvs	2022-05-06 10:56:58 +02:00
controlfreec
cooler
csvtk
custom	refactor: rename module	2022-05-11 17:33:45 +02:00
cutadapt
damageprofiler
dastool
dedup
deeparg
deeptools	changed container + add cram2bam conversion	2022-06-02 10:38:05 +02:00
deepvariant
delly/call
diamond	Merge remote-tracking branch 'origin' into motus_profile	2022-05-05 09:41:13 -04:00
dragmap
dragonflye
dshbio
ectyper
elprep	Merge remote-tracking branch 'origin' into motus_profile	2022-05-05 09:41:13 -04:00
emmtyper
ensemblvep	add optional fasta argument to ensemblvep	2022-06-09 11:45:27 +02:00
expansionhunter
faqcs
fargene
fastani
fastp
fastqc
fastqscan
fasttree
fgbio
filtlong	Actually add the changes	2022-05-31 15:49:57 +02:00
flash
freebayes
gamma/gamma	updating paths in test.yml	2022-05-24 16:27:00 -04:00
gatk	Apply suggestions from code review	2022-06-09 08:33:37 +02:00
gatk4	small fix and typo	2022-06-09 15:08:02 +02:00
genmap
genomescope2	Update outputs and test data set	2022-05-11 10:42:17 +00:00
genrich
gffread
glnexus
graphmap2
gstama
gtdbtk/classifywf
gubbins
gunc
gunzip
hamronization
happy	Merge remote-tracking branch 'origin' into motus_profile	2022-05-05 09:41:13 -04:00
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	Add module kat hist	2022-05-06 07:54:10 +00:00
khmer/normalizebymedian
kleborate
kraken2/kraken2
krona	Merge remote-tracking branch 'origin' into motus_profile	2022-05-05 09:41:13 -04:00
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	ran prettier	2022-05-16 14:30:40 +02:00
md5sum	fix software definitions	2022-05-06 11:07:05 +02:00
medaka
megahit
megan/rma2info
meningotype
meryl	Merge branch 'master' into meryl_unionsum	2022-05-09 16:16:08 +02:00
metabat2
metaphlan3	Merge remote-tracking branch 'origin' into motus_profile	2022-05-05 09:41:13 -04:00
methyldackel
minia
miniasm
minimap2	Merge remote-tracking branch 'origin' into motus_profile	2022-05-05 09:41:13 -04:00
mlst
mobsuite/recon
mosdepth	Update main.nf	2022-05-25 19:42:15 +01:00
motus	fix the typo in motus_profile.	2022-05-12 09:20:32 -04:00
msisensor
msisensorpro
mtnucratio
multiqc	Update modules/multiqc/main.nf	2022-06-08 14:41:10 +02:00
mummer
muscle
nanolyse
nanoplot
ncbigenomedownload
nextclade
ngmaster
ngscheckmate/ncm
nucmer
optitype
pairix
pairtools
panaroo/run
pangolin
paraclu
pbbam/pbmerge
pbccs
peddy
phantompeakqualtools
phyloflash
picard	bump picard versions	2022-05-30 10:15:40 +02:00
pirate
plasmidid
plink
plink2
pmdtools/filter
porechop
preseq
prinseqplusplus	Add PRINSEQPLUSPLUS (#1481)	2022-04-03 16:06:22 +02:00
prodigal
prokka
pycoqc
pydamage
qcat
qualimap
quast
racon
rapidnj
rasusa
raven
raxmlng
rgi/main
rhocall/annotate	fix versions.yaml	2022-06-07 14:43:35 +02:00
rmarkdownnotebook
roary
rsem
rseqc
rtgtools/vcfeval	Added memory allocation to VCFeval	2022-05-13 10:03:20 +02:00
salmon
samblaster
samtools	rename aligned to alignment	2022-05-09 16:07:49 +02:00
scoary
seacr/callpeak
seqkit
seqsero2
seqtk
sequenzautils
seqwish/induce
shasum	fix software definitions	2022-05-06 11:07:05 +02:00
shigatyper	Merge remote-tracking branch 'origin' into motus_profile	2022-05-05 09:41:13 -04:00
shovill
sistr
slimfastq	Merge remote-tracking branch 'origin' into motus_profile	2022-05-05 09:41:13 -04:00
snapaligner	merge snapaligner modes into one	2022-05-06 14:10:44 +02:00
snippy/run	Update main.nf	2022-06-03 13:05:43 -06:00
snpdists
snpeff	Merge remote-tracking branch 'origin' into motus_profile	2022-05-05 09:41:13 -04:00
snpsift/split
snpsites
sortmerna
sourmash/sketch
spades
spatyper
sratools	refactor: move files to custom section	2022-05-11 17:33:45 +02:00
srst2/srst2	Merge remote-tracking branch 'origin' into motus_profile	2022-05-05 09:41:13 -04:00
ssuissero
stadeniolib/scramble
staphopiasccmec
star	Bump container version for STAR to 2.7.10a	2022-05-27 11:35:04 +01:00
stranger
strelka
stringtie
subread/featurecounts
svdb	update svdb version	2022-05-06 00:18:16 +02:00
tabix	Merge remote-tracking branch 'origin' into motus_profile	2022-05-05 09:41:13 -04:00
tbprofiler/profile
tiddit	fix path to symbolic links	2022-06-08 11:46:45 +02:00
transdecoder
trimgalore
ucsc
ultra/pipeline
umitools	Update umitools/dedup module to make --output-stats optional	2022-05-23 22:31:09 +01:00
unicycler
untar	fix untar output dir	2022-06-02 11:09:55 +02:00
unzip
vardictjava	Merge remote-tracking branch 'origin' into motus_profile	2022-05-05 09:41:13 -04:00
variantbam
vcfanno
vcflib/vcfuniq
vcftools
vsearch/usearchglobal	Merge branch 'vsearch_usearch_global' of https://github.com/jtangrot/nf-core_modules into vsearch_usearch_global	2022-05-30 13:05:00 +02:00
yara