.. |
abacas
|
Fix formatting in yaml files, add yamllint config (#1279)
|
2022-02-15 11:15:27 +00:00 |
abricate
|
Set process label to process_single for modules with no task.cpus usage (#2076)
|
2022-09-19 11:54:47 +02:00 |
adapterremoval
|
Refactor adapterremoval (#1491)
|
2022-04-04 21:40:35 +02:00 |
adapterremovalfixprefix
|
Set process label to process_single for modules with no task.cpus usage (#2076)
|
2022-09-19 11:54:47 +02:00 |
agrvate
|
Fix formatting in yaml files, add yamllint config (#1279)
|
2022-02-15 11:15:27 +00:00 |
allelecounter
|
fix incorrect yaml formatting. (#1264)
|
2022-04-14 13:35:01 +02:00 |
ampir
|
Set process label to process_single for modules with no task.cpus usage (#2076)
|
2022-09-19 11:54:47 +02:00 |
amplify/predict
|
Set process label to process_single for modules with no task.cpus usage (#2076)
|
2022-09-19 11:54:47 +02:00 |
amps
|
Fix formatting in yaml files, add yamllint config (#1279)
|
2022-02-15 11:15:27 +00:00 |
amrfinderplus
|
Set process label to process_single for modules with no task.cpus usage (#2076)
|
2022-09-19 11:54:47 +02:00 |
angsd/docounts
|
Add: ANGSD_DOCOUNTS (#2044)
|
2022-09-27 13:21:44 +02:00 |
antismash
|
Set process label to process_single for modules with no task.cpus usage (#2076)
|
2022-09-19 11:54:47 +02:00 |
ariba
|
|
|
arriba
|
Update Arriba to 2.3.0 (#1827)
|
2022-06-29 14:39:13 +02:00 |
artic
|
|
|
ascat
|
Added output files to ASCAT (#1820)
|
2022-06-28 14:45:57 +02:00 |
assemblyscan
|
Fix formatting in yaml files, add yamllint config (#1279)
|
2022-02-15 11:15:27 +00:00 |
ataqv
|
|
|
atlas
|
|
|
bakta
|
|
|
bamaligncleaner
|
|
|
bamcmp
|
|
|
bamtools
|
Adding module bamtools stats (#2104)
|
2022-09-27 06:24:43 +01:00 |
bamutil/trimbam
|
Set process label to process_single for modules with no task.cpus usage (#2076)
|
2022-09-19 11:54:47 +02:00 |
bandage/image
|
|
|
bases2fastq
|
Add bases2fastq (#2054)
|
2022-09-15 13:50:33 +00:00 |
bbmap
|
|
|
bcftools
|
Fix bcftools/stats module (#1953)
|
2022-09-21 16:10:38 +02:00 |
bcl2fastq
|
Module/bcl2fastq (#1883)
|
2022-07-14 13:18:21 +02:00 |
bclconvert
|
Bump bcl-convert version (#2077)
|
2022-09-16 14:34:52 +02:00 |
bedtools
|
Set process label to process_single for modules with no task.cpus usage (#2076)
|
2022-09-19 11:54:47 +02:00 |
biobambam
|
|
|
biscuit
|
|
|
bismark
|
|
|
blast
|
Add blast/tblastn module (#2092)
|
2022-09-26 17:43:41 +02:00 |
bowtie
|
|
|
bowtie2
|
|
|
bracken
|
|
|
busco
|
|
|
bwa
|
Set process label to process_single for modules with no task.cpus usage (#2076)
|
2022-09-19 11:54:47 +02:00 |
bwamem2
|
Set process label to process_single for modules with no task.cpus usage (#2076)
|
2022-09-19 11:54:47 +02:00 |
bwameth
|
|
|
cat
|
cat/fastq: update conditional (#2085)
|
2022-09-20 14:46:01 +02:00 |
cellranger
|
Fixes incorrectly quoted tags (#2113)
|
2022-09-27 20:37:56 +01:00 |
centrifuge
|
Set process label to process_single for modules with no task.cpus usage (#2076)
|
2022-09-19 11:54:47 +02:00 |
checkm/lineagewf
|
|
|
chromap
|
|
|
clonalframeml
|
|
|
cmseq/polymut
|
|
|
cnvkit
|
|
|
cnvpytor
|
|
|
controlfreec
|
|
|
cooler
|
|
|
csvtk
|
|
|
custom
|
Fix broken Quast module and bump MultiQC version in dumpsoftwareversions (#2108)
|
2022-09-27 09:35:52 +01:00 |
cutadapt
|
|
|
damageprofiler
|
Set process label to process_single for modules with no task.cpus usage (#2076)
|
2022-09-19 11:54:47 +02:00 |
dastool
|
Set process label to process_single for modules with no task.cpus usage (#2076)
|
2022-09-19 11:54:47 +02:00 |
dedup
|
Set process label to process_single for modules with no task.cpus usage (#2076)
|
2022-09-19 11:54:47 +02:00 |
deeparg
|
Set process label to process_single for modules with no task.cpus usage (#2076)
|
2022-09-19 11:54:47 +02:00 |
deepbgc
|
Set process label to process_single for modules with no task.cpus usage (#2076)
|
2022-09-19 11:54:47 +02:00 |
deeptools
|
|
|
deepvariant
|
Deepvariant - Update main.nf (#2110)
|
2022-09-27 15:34:10 +02:00 |
delly/call
|
updated the version of delly (#2105)
|
2022-09-27 08:57:36 +02:00 |
diamond
|
|
|
dragmap
|
|
|
dragonflye
|
|
|
dshbio
|
Update dsh-bio to 2.1 (#2100)
|
2022-09-26 10:41:33 +01:00 |
ectyper
|
|
|
eido
|
Fixes incorrectly quoted tags (#2113)
|
2022-09-27 20:37:56 +01:00 |
elprep
|
|
|
emmtyper
|
|
|
ensemblvep
|
|
|
entrezdirect
|
Set process label to process_single for modules with no task.cpus usage (#2076)
|
2022-09-19 11:54:47 +02:00 |
epang
|
Make epang output meta with the jplace channel (#2073)
|
2022-09-16 10:22:50 +02:00 |
expansionhunter
|
|
|
faqcs
|
Prettier (#1405)
|
2022-03-18 14:27:50 +01:00 |
fargene
|
Add HAMRONIZATION/FARGENE and updates all HARMONIZATION tools to 1.1.1 (#2107)
|
2022-09-27 15:32:18 +02:00 |
fastani
|
|
|
fastawindows
|
|
|
fastk
|
|
|
fastp
|
Fix duplicated input in single-end fastp command (#2034)
|
2022-09-09 11:08:52 +02:00 |
fastqc
|
|
|
fastqscan
|
|
|
fasttree
|
Fix formatting in yaml files, add yamllint config (#1279)
|
2022-02-15 11:15:27 +00:00 |
ffq
|
|
|
fgbio
|
|
|
filtlong
|
|
|
flash
|
|
|
flye
|
|
|
fq/lint
|
|
|
freebayes
|
|
|
gamma/gamma
|
|
|
gappa
|
Adding gappa/examineheattree (#2084)
|
2022-09-22 15:51:25 +02:00 |
gatk
|
Set process label to process_single for modules with no task.cpus usage (#2076)
|
2022-09-19 11:54:47 +02:00 |
gatk4
|
new module gatk4/printsvevidence (#2103)
|
2022-09-27 08:30:16 +02:00 |
gecco/run
|
|
|
genescopefk
|
|
|
genmap
|
Fixes incorrectly quoted tags (#2113)
|
2022-09-27 20:37:56 +01:00 |
genmod
|
|
|
genomescope2
|
Update outputs and test data set
|
2022-05-11 10:42:17 +00:00 |
genotyphi/parse
|
add module for mykrobe predict and genotyphi parse (#1818)
|
2022-09-26 15:18:04 +01:00 |
genrich
|
|
|
gffread
|
|
|
glimpse/chunk
|
|
|
glnexus
|
|
|
goat/taxonsearch
|
2012 bug related to species input in goattaxonsearch module (#2099)
|
2022-09-23 10:58:40 -06:00 |
graphmap2
|
Fix formatting in yaml files, add yamllint config (#1279)
|
2022-02-15 11:15:27 +00:00 |
gstama
|
|
|
gtdbtk/classifywf
|
|
|
gubbins
|
|
|
gunc
|
Fixes incorrectly quoted tags (#2113)
|
2022-09-27 20:37:56 +01:00 |
gunzip
|
Set process label to process_single for modules with no task.cpus usage (#2076)
|
2022-09-19 11:54:47 +02:00 |
gvcftools/extractvariants
|
|
|
hamronization
|
Add HAMRONIZATION/FARGENE and updates all HARMONIZATION tools to 1.1.1 (#2107)
|
2022-09-27 15:32:18 +02:00 |
haplocheck
|
|
|
haplogrep2/classify
|
|
|
happy
|
|
|
hicap
|
|
|
hifiasm
|
|
|
hisat2
|
|
|
hmmcopy
|
Fixes incorrectly quoted tags (#2113)
|
2022-09-27 20:37:56 +01:00 |
hmmer
|
Fixes incorrectly quoted tags (#2113)
|
2022-09-27 20:37:56 +01:00 |
hmtnote
|
|
|
homer
|
|
|
hpsuissero
|
|
|
ichorcna
|
|
|
idr
|
|
|
imputeme/vcftoprs
|
|
|
instrain/profile
|
|
|
iqtree
|
|
|
ismapper
|
|
|
isoseq3
|
|
|
ivar
|
|
|
jupyternotebook
|
|
|
kaiju
|
Set process label to process_single for modules with no task.cpus usage (#2076)
|
2022-09-19 11:54:47 +02:00 |
kallisto/index
|
|
|
kallistobustools
|
|
|
kat/hist
|
|
|
khmer
|
|
|
kleborate
|
|
|
kraken2/kraken2
|
|
|
krakentools
|
Set process label to process_single for modules with no task.cpus usage (#2076)
|
2022-09-19 11:54:47 +02:00 |
krona
|
Set process label to process_single for modules with no task.cpus usage (#2076)
|
2022-09-19 11:54:47 +02:00 |
last
|
|
|
leehom
|
|
|
legsta
|
|
|
lima
|
|
|
lissero
|
|
|
lofreq
|
|
|
macrel/contigs
|
|
|
macs2/callpeak
|
|
|
mafft
|
|
|
malt
|
|
|
maltextract
|
|
|
manta
|
|
|
mapdamage2
|
Set process label to process_single for modules with no task.cpus usage (#2076)
|
2022-09-19 11:54:47 +02:00 |
mash
|
|
|
mashtree
|
|
|
maxbin2
|
|
|
maxquant/lfq
|
|
|
mcroni
|
|
|
md5sum
|
Set process label to process_single for modules with no task.cpus usage (#2076)
|
2022-09-19 11:54:47 +02:00 |
medaka
|
|
|
megahit
|
|
|
megan
|
Set process label to process_single for modules with no task.cpus usage (#2076)
|
2022-09-19 11:54:47 +02:00 |
meningotype
|
|
|
merqury
|
|
|
merquryfk
|
|
|
meryl
|
|
|
metabat2
|
|
|
metaphlan3
|
|
|
methyldackel
|
|
|
minia
|
|
|
miniasm
|
|
|
minimap2
|
|
|
mlst
|
Add args to mlst (#1962)
|
2022-09-26 15:48:35 +01:00 |
mobsuite/recon
|
|
|
mosdepth
|
|
|
motus
|
Set process label to process_single for modules with no task.cpus usage (#2076)
|
2022-09-19 11:54:47 +02:00 |
msisensor
|
|
|
msisensor2
|
Fixes incorrectly quoted tags (#2113)
|
2022-09-27 20:37:56 +01:00 |
msisensorpro
|
|
|
mtnucratio
|
Set process label to process_single for modules with no task.cpus usage (#2076)
|
2022-09-19 11:54:47 +02:00 |
multiqc
|
Set process label to process_single for modules with no task.cpus usage (#2076)
|
2022-09-19 11:54:47 +02:00 |
multivcfanalyzer
|
Fixes incorrectly quoted tags (#2113)
|
2022-09-27 20:37:56 +01:00 |
mummer
|
|
|
muscle
|
Set process label to process_single for modules with no task.cpus usage (#2076)
|
2022-09-19 11:54:47 +02:00 |
mykrobe/predict
|
add module for mykrobe predict and genotyphi parse (#1818)
|
2022-09-26 15:18:04 +01:00 |
nanolyse
|
|
|
nanoplot
|
|
|
ncbigenomedownload
|
|
|
nextclade
|
|
|
nextgenmap
|
New Module: NextGenMap (#1938)
|
2022-09-27 20:44:47 +01:00 |
ngmaster
|
|
|
ngscheckmate/ncm
|
|
|
nucmer
|
|
|
optitype
|
|
|
pairix
|
|
|
pairtools
|
|
|
panaroo/run
|
|
|
pangolin
|
|
|
paraclu
|
|
|
pasty
|
|
|
pbbam/pbmerge
|
|
|
pbccs
|
|
|
pbptyper
|
|
|
pear
|
|
|
peddy
|
|
|
phantompeakqualtools
|
|
|
phyloflash
|
|
|
picard
|
|
|
pints/caller
|
|
|
pirate
|
|
|
plasmidfinder
|
|
|
plasmidid
|
|
|
plink
|
|
|
plink2
|
|
|
pmdtools/filter
|
|
|
porechop
|
|
|
preseq
|
Set process label to process_single for modules with no task.cpus usage (#2076)
|
2022-09-19 11:54:47 +02:00 |
prinseqplusplus
|
|
|
prodigal
|
Set process label to process_single for modules with no task.cpus usage (#2076)
|
2022-09-19 11:54:47 +02:00 |
prokka
|
|
|
pycoqc
|
|
|
pydamage
|
Set process label to process_single for modules with no task.cpus usage (#2076)
|
2022-09-19 11:54:47 +02:00 |
qcat
|
Fix formatting in yaml files, add yamllint config (#1279)
|
2022-02-15 11:15:27 +00:00 |
qualimap
|
Fix broken Quast module and bump MultiQC version in dumpsoftwareversions (#2108)
|
2022-09-27 09:35:52 +01:00 |
quast
|
|
|
racon
|
|
|
rapidnj
|
|
|
rasusa
|
Fix formatting in yaml files, add yamllint config (#1279)
|
2022-02-15 11:15:27 +00:00 |
raven
|
|
|
raxmlng
|
|
|
rgi/main
|
|
|
rhocall/annotate
|
|
|
rmarkdownnotebook
|
|
|
roary
|
|
|
rsem
|
|
|
rseqc
|
|
|
rtgtools
|
|
|
salmon
|
|
|
samblaster
|
|
|
samtools
|
Multithreaded samtools commands (#2080)
|
2022-09-26 17:44:36 +01:00 |
scoary
|
Fix formatting in yaml files, add yamllint config (#1279)
|
2022-02-15 11:15:27 +00:00 |
scramble
|
|
|
seacr/callpeak
|
|
|
seqkit
|
|
|
seqsero2
|
Fix formatting in yaml files, add yamllint config (#1279)
|
2022-02-15 11:15:27 +00:00 |
seqtk
|
Fixes incorrectly quoted tags (#2113)
|
2022-09-27 20:37:56 +01:00 |
sequenzautils
|
|
|
seqwish/induce
|
Bump seqwish/induce to v0.7.6 (#2083)
|
2022-09-26 17:01:21 +01:00 |
seroba/run
|
add module for seroba (#1816)
|
2022-09-26 16:06:08 +01:00 |
sexdeterrmine
|
Set process label to process_single for modules with no task.cpus usage (#2076)
|
2022-09-19 11:54:47 +02:00 |
shasum
|
|
|
shigatyper
|
|
|
shovill
|
|
|
sistr
|
|
|
slimfastq
|
|
|
snapaligner
|
|
|
snippy
|
|
|
snpdists
|
|
|
snpeff
|
|
|
snpsift/split
|
|
|
snpsites
|
|
|
somalier
|
Somalier relate (#2001)
|
2022-09-19 13:22:24 +02:00 |
sortmerna
|
|
|
sourmash/sketch
|
|
|
spades
|
|
|
spatyper
|
Fix formatting in yaml files, add yamllint config (#1279)
|
2022-02-15 11:15:27 +00:00 |
sratools
|
|
|
srst2/srst2
|
|
|
ssuissero
|
|
|
stadeniolib/scramble
|
|
|
staphopiasccmec
|
|
|
star
|
|
|
stranger
|
|
|
strelka
|
|
|
stringtie
|
Make stringtie/merge arguments configurable (#2049)
|
2022-09-26 14:26:53 +01:00 |
subread/featurecounts
|
|
|
svdb
|
|
|
svtk/standardize
|
|
|
tabix
|
Added an output channel for the gzi index (#2036)
|
2022-09-26 21:47:41 +02:00 |
tailfindr
|
|
|
tbprofiler/profile
|
|
|
tiddit
|
|
|
transdecoder
|
|
|
trimgalore
|
|
|
trimmomatic
|
|
|
ucsc
|
Set process label to process_single for modules with no task.cpus usage (#2076)
|
2022-09-19 11:54:47 +02:00 |
ultra
|
|
|
umitools
|
|
|
unicycler
|
|
|
untar
|
|
|
unzip
|
|
|
vardictjava
|
|
|
variantbam
|
|
|
vcf2db
|
|
|
vcf2maf
|
|
|
vcfanno
|
small changes to vcfanno (#1804)
|
2022-06-24 08:58:26 +02:00 |
vcflib/vcfuniq
|
|
|
vcftools
|
|
|
vsearch
|
New module: Vsearch sintax (#2094)
|
2022-09-26 14:45:01 +01:00 |
whamg
|
|
|
yara
|
|
|