.. |
abacas
|
Fix formatting in yaml files, add yamllint config (#1279)
|
2022-02-15 11:15:27 +00:00 |
abricate
|
|
|
adapterremoval
|
Refactor adapterremoval (#1491)
|
2022-04-04 21:40:35 +02:00 |
adapterremovalfixprefix
|
Add AdapterRemovalFixPrefix (#1424)
|
2022-03-21 11:26:12 +01:00 |
agrvate
|
|
|
allelecounter
|
|
|
amplify/predict
|
add module AMPlify (#1498)
|
2022-04-20 11:53:26 +02:00 |
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
|
Patch fix artic/minion and ivar/variants modules (#1326)
|
2022-02-18 17:36:09 +00:00 |
ascat
|
|
|
assemblyscan
|
|
|
ataqv/ataqv
|
Fix formatting in yaml files, add yamllint config (#1279)
|
2022-02-15 11:15:27 +00:00 |
bakta
|
|
|
bamaligncleaner
|
|
|
bamcmp
|
Fix formatting in yaml files, add yamllint config (#1279)
|
2022-02-15 11:15:27 +00:00 |
bamtools
|
Merge remote-tracking branch 'origin' into motus_profile
|
2022-05-05 09:41:13 -04:00 |
bamutil/trimbam
|
|
|
bandage/image
|
|
|
bbmap
|
|
|
bcftools
|
update description
|
2022-05-24 16:17:15 +02:00 |
bclconvert
|
Module/bclconvert (#1485)
|
2022-04-21 15:39:22 +02:00 |
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
|
Fix formatting in yaml files, add yamllint config (#1279)
|
2022-02-15 11:15:27 +00:00 |
cat
|
|
|
cellranger
|
Prettier (#1405)
|
2022-03-18 14:27:50 +01:00 |
centrifuge
|
|
|
checkm/lineagewf
|
|
|
chromap
|
|
|
clonalframeml
|
|
|
cmseq/polymut
|
|
|
cnvkit
|
missing meta.id changed
|
2022-05-24 14:59:52 +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
|
Fix formatting in yaml files, add yamllint config (#1279)
|
2022-02-15 11:15:27 +00:00 |
damageprofiler
|
|
|
dastool
|
|
|
dedup
|
|
|
deeparg
|
|
|
deeptools
|
|
|
deepvariant
|
|
|
delly/call
|
Fix formatting in yaml files, add yamllint config (#1279)
|
2022-02-15 11:15:27 +00:00 |
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
|
Merge remote-tracking branch 'origin' into motus_profile
|
2022-05-05 09:41:13 -04:00 |
expansionhunter
|
add stub to modules used in raredisease pipeline (#1206)
|
2022-03-28 17:48:39 +02:00 |
faqcs
|
Prettier (#1405)
|
2022-03-18 14:27:50 +01:00 |
fargene
|
Fix formatting in yaml files, add yamllint config (#1279)
|
2022-02-15 11:15:27 +00:00 |
fastani
|
|
|
fastp
|
|
|
fastqc
|
add stub to modules used in raredisease pipeline (#1206)
|
2022-03-28 17:48:39 +02:00 |
fastqscan
|
|
|
fasttree
|
|
|
fgbio
|
|
|
filtlong
|
Fix formatting in yaml files, add yamllint config (#1279)
|
2022-02-15 11:15:27 +00:00 |
flash
|
|
|
freebayes
|
|
|
gamma/gamma
|
updating paths in test.yml
|
2022-05-24 16:27:00 -04:00 |
gatk4
|
rm unnecessary spark_user
|
2022-05-25 16:38:48 +02:00 |
genmap
|
|
|
genomescope2
|
Update outputs and test data set
|
2022-05-11 10:42:17 +00:00 |
genrich
|
Fix formatting in yaml files, add yamllint config (#1279)
|
2022-02-15 11:15:27 +00:00 |
gffread
|
Fix formatting in yaml files, add yamllint config (#1279)
|
2022-02-15 11:15:27 +00:00 |
glnexus
|
add stub to modules used in raredisease pipeline (#1206)
|
2022-03-28 17:48:39 +02:00 |
graphmap2
|
|
|
gstama
|
|
|
gtdbtk/classifywf
|
Fix formatting in yaml files, add yamllint config (#1279)
|
2022-02-15 11:15:27 +00:00 |
gubbins
|
Fix formatting in yaml files, add yamllint config (#1279)
|
2022-02-15 11:15:27 +00:00 |
gunc
|
|
|
gunzip
|
|
|
hamronization
|
|
|
happy
|
Merge remote-tracking branch 'origin' into motus_profile
|
2022-05-05 09:41:13 -04:00 |
hicap
|
Fix formatting in yaml files, add yamllint config (#1279)
|
2022-02-15 11:15:27 +00:00 |
hifiasm
|
|
|
hisat2
|
|
|
hmmcopy
|
|
|
hmmer
|
|
|
hmtnote
|
Update main.nf
|
2022-05-16 15:20:15 +00:00 |
homer
|
|
|
hpsuissero
|
Prettier (#1405)
|
2022-03-18 14:27:50 +01:00 |
ichorcna
|
|
|
idr
|
Fix formatting in yaml files, add yamllint config (#1279)
|
2022-02-15 11:15:27 +00:00 |
imputeme/vcftoprs
|
|
|
iqtree
|
Fix formatting in yaml files, add yamllint config (#1279)
|
2022-02-15 11:15:27 +00:00 |
ismapper
|
|
|
isoseq3
|
|
|
ivar
|
|
|
jupyternotebook
|
Add when: block (#1261)
|
2022-02-04 09:53:32 +01:00 |
kaiju
|
|
|
kallisto/index
|
|
|
kallistobustools
|
|
|
kat/hist
|
Add module kat hist
|
2022-05-06 07:54:10 +00:00 |
khmer/normalizebymedian
|
Fix formatting in yaml files, add yamllint config (#1279)
|
2022-02-15 11:15:27 +00:00 |
kleborate
|
Fix formatting in yaml files, add yamllint config (#1279)
|
2022-02-15 11:15:27 +00:00 |
kraken2/kraken2
|
|
|
krona
|
integrating suggestions from PR comments, including recovery of tests for kronadb and more detailed explanation of input database in yml file
|
2022-05-05 13:51:41 +02:00 |
last
|
|
|
leehom
|
Fix: Leehom meta output channel descriptions (#1356)
|
2022-02-27 14:35:47 +01:00 |
legsta
|
|
|
lima
|
|
|
lissero
|
|
|
lofreq
|
|
|
macrel/contigs
|
|
|
macs2/callpeak
|
Prettier (#1405)
|
2022-03-18 14:27:50 +01:00 |
mafft
|
|
|
malt
|
|
|
maltextract
|
|
|
manta
|
|
|
mapdamage2
|
|
|
mash
|
Add mash screen
|
2022-05-20 13:23:11 +00:00 |
mashtree
|
Fix formatting in yaml files, add yamllint config (#1279)
|
2022-02-15 11:15:27 +00:00 |
maxbin2
|
Fix for Maxbin2 emitting input files (#1376)
|
2022-03-08 15:56:23 +01:00 |
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
|
Fix formatting in yaml files, add yamllint config (#1279)
|
2022-02-15 11:15:27 +00:00 |
megahit
|
|
|
megan/rma2info
|
Add MEGAN/RMA2INFO (#1513)
|
2022-04-12 08:35:36 +02:00 |
meningotype
|
Fix formatting in yaml files, add yamllint config (#1279)
|
2022-02-15 11:15:27 +00:00 |
meryl
|
Merge branch 'master' into meryl_unionsum
|
2022-05-09 16:16:08 +02:00 |
metabat2
|
|
|
metaphlan3
|
Add additional handling of fq.gz file name suffix
|
2022-05-02 14:16:12 +02:00 |
methyldackel
|
|
|
minia
|
|
|
miniasm
|
|
|
minimap2
|
Merge remote-tracking branch 'origin' into motus_profile
|
2022-05-05 09:41:13 -04:00 |
mlst
|
Fix formatting in yaml files, add yamllint config (#1279)
|
2022-02-15 11:15:27 +00:00 |
mobsuite/recon
|
|
|
mosdepth
|
Update modules/mosdepth/main.nf
|
2022-05-24 13:45:52 +02:00 |
motus
|
fix the typo in motus_profile.
|
2022-05-12 09:20:32 -04:00 |
msisensor
|
|
|
msisensorpro
|
|
|
mtnucratio
|
Fix formatting in yaml files, add yamllint config (#1279)
|
2022-02-15 11:15:27 +00:00 |
multiqc
|
|
|
mummer
|
|
|
muscle
|
|
|
nanolyse
|
Fix formatting in yaml files, add yamllint config (#1279)
|
2022-02-15 11:15:27 +00:00 |
nanoplot
|
Fix formatting in yaml files, add yamllint config (#1279)
|
2022-02-15 11:15:27 +00:00 |
ncbigenomedownload
|
Fix formatting in yaml files, add yamllint config (#1279)
|
2022-02-15 11:15:27 +00:00 |
nextclade
|
|
|
ngmaster
|
Fix formatting in yaml files, add yamllint config (#1279)
|
2022-02-15 11:15:27 +00:00 |
ngscheckmate/ncm
|
Prettier (#1405)
|
2022-03-18 14:27:50 +01:00 |
nucmer
|
|
|
optitype
|
|
|
pairix
|
|
|
pairtools
|
|
|
panaroo/run
|
add module for panaroo, fix pirate tests (#1444)
|
2022-03-24 20:11:04 -06:00 |
pangolin
|
|
|
paraclu
|
Fix formatting in yaml files, add yamllint config (#1279)
|
2022-02-15 11:15:27 +00:00 |
pbbam/pbmerge
|
|
|
pbccs
|
Fix formatting in yaml files, add yamllint config (#1279)
|
2022-02-15 11:15:27 +00:00 |
peddy
|
Fix formatting in yaml files, add yamllint config (#1279)
|
2022-02-15 11:15:27 +00:00 |
phantompeakqualtools
|
|
|
phyloflash
|
Fix formatting in yaml files, add yamllint config (#1279)
|
2022-02-15 11:15:27 +00:00 |
picard
|
revert wgsmetrics'
|
2022-05-22 06:44:17 +02:00 |
pirate
|
|
|
plasmidid
|
|
|
plink
|
Fix formatting in yaml files, add yamllint config (#1279)
|
2022-02-15 11:15:27 +00:00 |
plink2
|
|
|
pmdtools/filter
|
Fix formatting in yaml files, add yamllint config (#1279)
|
2022-02-15 11:15:27 +00:00 |
porechop
|
|
|
preseq
|
|
|
prinseqplusplus
|
|
|
prodigal
|
|
|
prokka
|
|
|
pycoqc
|
Fix formatting in yaml files, add yamllint config (#1279)
|
2022-02-15 11:15:27 +00:00 |
pydamage
|
|
|
qcat
|
Fix formatting in yaml files, add yamllint config (#1279)
|
2022-02-15 11:15:27 +00:00 |
qualimap
|
|
|
quast
|
|
|
racon
|
Fix formatting in yaml files, add yamllint config (#1279)
|
2022-02-15 11:15:27 +00:00 |
rapidnj
|
Fix formatting in yaml files, add yamllint config (#1279)
|
2022-02-15 11:15:27 +00:00 |
rasusa
|
|
|
raven
|
|
|
raxmlng
|
|
|
rgi/main
|
Prettier (#1405)
|
2022-03-18 14:27:50 +01:00 |
rmarkdownnotebook
|
Add when: block (#1261)
|
2022-02-04 09:53:32 +01:00 |
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
|
Fix formatting in yaml files, add yamllint config (#1279)
|
2022-02-15 11:15:27 +00:00 |
seqkit
|
|
|
seqsero2
|
Fix formatting in yaml files, add yamllint config (#1279)
|
2022-02-15 11:15:27 +00:00 |
seqtk
|
Prettier (#1405)
|
2022-03-18 14:27:50 +01:00 |
sequenzautils
|
|
|
seqwish/induce
|
Fix formatting in yaml files, add yamllint config (#1279)
|
2022-02-15 11:15:27 +00:00 |
shasum
|
fix software definitions
|
2022-05-06 11:07:05 +02:00 |
shigatyper
|
Update modules/shigatyper/main.nf
|
2022-04-22 08:49:44 -06:00 |
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 |
snpdists
|
Fix formatting in yaml files, add yamllint config (#1279)
|
2022-02-15 11:15:27 +00:00 |
snpeff
|
Merge remote-tracking branch 'origin' into motus_profile
|
2022-05-05 09:41:13 -04:00 |
snpsift/split
|
Fix formatting in yaml files, add yamllint config (#1279)
|
2022-02-15 11:15:27 +00:00 |
snpsites
|
Fix formatting in yaml files, add yamllint config (#1279)
|
2022-02-15 11:15:27 +00:00 |
sortmerna
|
|
|
sourmash/sketch
|
|
|
spades
|
|
|
spatyper
|
Fix formatting in yaml files, add yamllint config (#1279)
|
2022-02-15 11:15:27 +00:00 |
sratools
|
refactor: move files to custom section
|
2022-05-11 17:33:45 +02:00 |
srst2/srst2
|
added tests
|
2022-05-02 11:30:19 -04:00 |
ssuissero
|
|
|
stadeniolib/scramble
|
new tool: staden_io_lib (#1499)
|
2022-04-08 09:54:15 -04:00 |
staphopiasccmec
|
|
|
star
|
|
|
stranger
|
add stubs for stranger (#1543)
|
2022-04-22 10:10:43 +02:00 |
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
|
Fix formatting in yaml files, add yamllint config (#1279)
|
2022-02-15 11:15:27 +00:00 |
tiddit
|
|
|
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
|
Replace vanilla Linux Biocontainer with Ubuntu (#1557)
|
2022-04-22 14:50:07 +01:00 |
unzip
|
Untar unzip meta (#1408)
|
2022-03-21 14:49:28 +01:00 |
vardictjava
|
Moved the BED file to the main tuple
|
2022-05-03 15:31:05 +02:00 |
variantbam
|
|
|
vcfanno
|
add stub to modules used in raredisease pipeline (#1206)
|
2022-03-28 17:48:39 +02:00 |
vcflib/vcfuniq
|
Fix formatting in yaml files, add yamllint config (#1279)
|
2022-02-15 11:15:27 +00:00 |
vcftools
|
|
|
yara
|
|
|