| .. |
|
abacas
|
|
|
|
abricate
|
Prettier (#1405)
|
2022-03-18 14:27:50 +01:00 |
|
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
|
fix incorrect yaml formatting. (#1264)
|
2022-04-14 13:35:01 +02:00 |
|
amplify/predict
|
add module AMPlify (#1498)
|
2022-04-20 11:53:26 +02:00 |
|
amps
|
|
|
|
amrfinderplus
|
Prettier (#1405)
|
2022-03-18 14:27:50 +01:00 |
|
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
|
Prettier (#1405)
|
2022-03-18 14:27:50 +01:00 |
|
assemblyscan
|
|
|
|
ataqv/ataqv
|
|
|
|
bakta
|
update bakta to latest version (v1.4.0) (#1428)
|
2022-03-24 10:49:17 -06:00 |
|
bamaligncleaner
|
|
|
|
bamcmp
|
|
|
|
bamtools
|
Merge remote-tracking branch 'origin' into motus_profile
|
2022-05-05 09:41:13 -04:00 |
|
bamutil/trimbam
|
|
|
|
bandage/image
|
|
|
|
bbmap
|
Samtools version update (#1507)
|
2022-04-11 14:26:28 +02:00 |
|
bcftools
|
add stub to modules used in raredisease pipeline (#1206)
|
2022-03-28 17:48:39 +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
|
Prettier (#1405)
|
2022-03-18 14:27:50 +01:00 |
|
bismark
|
|
|
|
blast
|
|
|
|
bowtie
|
Samtools version update (#1507)
|
2022-04-11 14:26:28 +02:00 |
|
bowtie2
|
add sort option to bowtie2
|
2022-05-13 15:26:41 +02:00 |
|
bracken/bracken
|
Add bracken (#1423)
|
2022-03-22 16:40:21 +01:00 |
|
busco
|
Update meta.yml
|
2022-05-06 11:56:43 +00:00 |
|
bwa
|
feat: remove read_group which should be set up with task.ext.args (#1521)
|
2022-04-13 14:30:34 +02:00 |
|
bwamem2
|
feat: remove read_group which should be set up with task.ext.args (#1521)
|
2022-04-13 14:30:34 +02:00 |
|
bwameth
|
|
|
|
cat
|
Replace vanilla Linux Biocontainer with Ubuntu (#1557)
|
2022-04-22 14:50:07 +01:00 |
|
cellranger
|
Prettier (#1405)
|
2022-03-18 14:27:50 +01:00 |
|
centrifuge
|
Add centrifuge_kreport module (#1514)
|
2022-04-13 15:33:51 +02:00 |
|
checkm/lineagewf
|
|
|
|
chromap
|
Samtools version update (#1507)
|
2022-04-11 14:26:28 +02:00 |
|
clonalframeml
|
|
|
|
cmseq/polymut
|
|
|
|
cnvkit
|
Merge branch 'master' into cnvkit_reference
|
2022-05-24 08:03:44 +02:00 |
|
cnvpytor
|
remove prefix def in callcnvs
|
2022-05-06 10:56:58 +02:00 |
|
controlfreec
|
Fix Controlfreec: Add stub runs to test single sample input & make conda work with R scripts (#1504)
|
2022-04-08 11:43:40 +02:00 |
|
cooler
|
|
|
|
csvtk
|
Prettier (#1405)
|
2022-03-18 14:27:50 +01:00 |
|
custom
|
refactor: rename module
|
2022-05-11 17:33:45 +02:00 |
|
cutadapt
|
|
|
|
damageprofiler
|
|
|
|
dastool
|
DASTool output channels update (#1489)
|
2022-04-04 13:31:36 +02:00 |
|
dedup
|
|
|
|
deeparg
|
Deeparg singularity container fix 2 (#1406)
|
2022-03-18 16:21:55 +01:00 |
|
deeptools
|
style(deeptools): Indent script (#1439)
|
2022-03-24 19:44:31 +00:00 |
|
deepvariant
|
Revert recent changes made to some of the modules (#1463)
|
2022-03-30 20:21:06 +02:00 |
|
delly/call
|
|
|
|
diamond
|
Merge remote-tracking branch 'origin' into motus_profile
|
2022-05-05 09:41:13 -04:00 |
|
dragmap
|
feat: remove read_group which should be set up with task.ext.args (#1521)
|
2022-04-13 14:30:34 +02:00 |
|
dragonflye
|
Update dragonflye to latest version (#1442)
|
2022-03-24 14:56:32 -04:00 |
|
dshbio
|
Update dsh-bio to version 2.0.8. (#1483)
|
2022-04-09 11:13:47 -05:00 |
|
ectyper
|
|
|
|
elprep
|
Merge remote-tracking branch 'origin' into motus_profile
|
2022-05-05 09:41:13 -04:00 |
|
emmtyper
|
|
|
|
ensemblvep
|
update ensemblvep and snpeff modules
|
2022-05-05 12:57:14 +02:00 |
|
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
|
|
|
|
fastani
|
|
|
|
fastp
|
|
|
|
fastqc
|
add stub to modules used in raredisease pipeline (#1206)
|
2022-03-28 17:48:39 +02:00 |
|
fastqscan
|
|
|
|
fasttree
|
|
|
|
fgbio
|
|
|
|
filtlong
|
|
|
|
flash
|
|
|
|
freebayes
|
|
|
|
gamma
|
new module: GAMMA (#1532)
|
2022-04-23 10:12:06 -04:00 |
|
gatk4
|
fix version
|
2022-05-23 12:15:33 +02:00 |
|
genmap
|
|
|
|
genomescope2
|
Update outputs and test data set
|
2022-05-11 10:42:17 +00:00 |
|
genrich
|
|
|
|
gffread
|
|
|
|
glnexus
|
add stub to modules used in raredisease pipeline (#1206)
|
2022-03-28 17:48:39 +02:00 |
|
graphmap2
|
|
|
|
gstama
|
New Module: gstama/polyacleanup (#1468)
|
2022-03-31 09:11:51 -04:00 |
|
gtdbtk/classifywf
|
|
|
|
gubbins
|
|
|
|
gunc
|
|
|
|
gunzip
|
Replace vanilla Linux Biocontainer with Ubuntu (#1557)
|
2022-04-22 14:50:07 +01:00 |
|
hamronization
|
Prettier (#1405)
|
2022-03-18 14:27:50 +01:00 |
|
happy
|
Merge remote-tracking branch 'origin' into motus_profile
|
2022-05-05 09:41:13 -04:00 |
|
hicap
|
|
|
|
hifiasm
|
|
|
|
hisat2
|
Samtools version update (#1507)
|
2022-04-11 14:26:28 +02:00 |
|
hmmcopy
|
|
|
|
hmmer
|
Prettier (#1405)
|
2022-03-18 14:27:50 +01:00 |
|
hmtnote
|
Update main.nf
|
2022-05-16 15:20:15 +00:00 |
|
homer
|
Fix homer/maketagdirectory output collision (#1456)
|
2022-03-27 03:17:42 +00:00 |
|
hpsuissero
|
Prettier (#1405)
|
2022-03-18 14:27:50 +01:00 |
|
ichorcna
|
Prettier (#1405)
|
2022-03-18 14:27:50 +01:00 |
|
idr
|
|
|
|
imputeme/vcftoprs
|
|
|
|
iqtree
|
|
|
|
ismapper
|
|
|
|
isoseq3
|
|
|
|
ivar
|
|
|
|
jupyternotebook
|
|
|
|
kaiju
|
Kaiju2table module (#1545)
|
2022-04-22 11:26:30 +02:00 |
|
kallisto/index
|
|
|
|
kallistobustools
|
|
|
|
khmer/normalizebymedian
|
|
|
|
kleborate
|
|
|
|
kraken2/kraken2
|
update to kraken2: breaking change - output channels renamed (#1525)
|
2022-04-21 14:33:59 +02:00 |
|
krona
|
Merge remote-tracking branch 'origin' into motus_profile
|
2022-05-05 09:41:13 -04:00 |
|
last
|
|
|
|
leehom
|
Fix: Leehom meta output channel descriptions (#1356)
|
2022-02-27 14:35:47 +01:00 |
|
legsta
|
Prettier (#1405)
|
2022-03-18 14:27:50 +01:00 |
|
lima
|
|
|
|
lissero
|
|
|
|
lofreq
|
|
|
|
macrel/contigs
|
|
|
|
macs2/callpeak
|
Prettier (#1405)
|
2022-03-18 14:27:50 +01:00 |
|
mafft
|
Prettier (#1405)
|
2022-03-18 14:27:50 +01:00 |
|
malt
|
Add missing $prefix definition for MALT_RUN (#1373)
|
2022-03-03 17:58:04 +01:00 |
|
maltextract
|
|
|
|
manta
|
Revert manta changes (#1518)
|
2022-04-12 10:40:06 +02:00 |
|
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
|
|
|
|
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
|
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
|
Prettier (#1405)
|
2022-03-18 14:27:50 +01:00 |
|
mosdepth
|
|
|
|
motus
|
fix the typo in motus_profile.
|
2022-05-12 09:20:32 -04:00 |
|
msisensor
|
|
|
|
msisensorpro
|
Prettier (#1405)
|
2022-03-18 14:27:50 +01:00 |
|
mtnucratio
|
|
|
|
multiqc
|
add stub to modules used in raredisease pipeline (#1206)
|
2022-03-28 17:48:39 +02:00 |
|
mummer
|
|
|
|
muscle
|
|
|
|
nanolyse
|
|
|
|
nanoplot
|
|
|
|
ncbigenomedownload
|
|
|
|
nextclade
|
|
|
|
ngmaster
|
|
|
|
ngscheckmate/ncm
|
Prettier (#1405)
|
2022-03-18 14:27:50 +01:00 |
|
nucmer
|
|
|
|
optitype
|
Add BAM indexes as input for optitype module. (#1388)
|
2022-03-15 17:02:40 +01:00 |
|
pairix
|
|
|
|
pairtools
|
|
|
|
panaroo/run
|
add module for panaroo, fix pirate tests (#1444)
|
2022-03-24 20:11:04 -06:00 |
|
pangolin
|
|
|
|
paraclu
|
|
|
|
pbbam/pbmerge
|
|
|
|
pbccs
|
|
|
|
peddy
|
|
|
|
phantompeakqualtools
|
Allow to pass arguments to the phantompeakqualtools script itself (#1562)
|
2022-04-25 19:07:43 +02:00 |
|
phyloflash
|
|
|
|
picard
|
revert wgsmetrics'
|
2022-05-22 06:44:17 +02:00 |
|
pirate
|
add module for panaroo, fix pirate tests (#1444)
|
2022-03-24 20:11:04 -06:00 |
|
plasmidid
|
|
|
|
plink
|
|
|
|
plink2
|
Prettier (#1405)
|
2022-03-18 14:27:50 +01:00 |
|
pmdtools/filter
|
|
|
|
porechop
|
|
|
|
preseq
|
Split preseq lcextrap and ccurve (#1440)
|
2022-03-25 17:11:40 +00:00 |
|
prinseqplusplus
|
Add PRINSEQPLUSPLUS (#1481)
|
2022-04-03 16:06:22 +02:00 |
|
prodigal
|
|
|
|
prokka
|
|
|
|
pycoqc
|
|
|
|
pydamage
|
Update PyDamage module (#1467)
|
2022-03-31 09:18:18 -04:00 |
|
qcat
|
|
|
|
qualimap
|
Samtools version update (#1507)
|
2022-04-11 14:26:28 +02:00 |
|
quast
|
|
|
|
racon
|
|
|
|
rapidnj
|
|
|
|
rasusa
|
|
|
|
raven
|
|
|
|
raxmlng
|
|
|
|
rgi/main
|
Prettier (#1405)
|
2022-03-18 14:27:50 +01:00 |
|
rmarkdownnotebook
|
|
|
|
roary
|
|
|
|
rsem
|
Bump STAR version to 2.7.10a for RSEM modules (#1573)
|
2022-04-27 19:21:26 +01:00 |
|
rseqc
|
Change label for rseqc/tin to process_high (#1327)
|
2022-02-21 13:26:51 +00:00 |
|
rtgtools/vcfeval
|
Added memory allocation to VCFeval
|
2022-05-13 10:03:20 +02:00 |
|
salmon
|
|
|
|
samblaster
|
Samtools version update (#1507)
|
2022-04-11 14:26:28 +02:00 |
|
samtools
|
rename aligned to alignment
|
2022-05-09 16:07:49 +02:00 |
|
scoary
|
|
|
|
seacr/callpeak
|
|
|
|
seqkit
|
feat: add module for seqkit stats (#1466)
|
2022-03-30 23:01:17 +02:00 |
|
seqsero2
|
|
|
|
seqtk
|
Prettier (#1405)
|
2022-03-18 14:27:50 +01:00 |
|
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
|
Prettier (#1405)
|
2022-03-18 14:27:50 +01:00 |
|
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
|
|
|
|
snpeff
|
Merge remote-tracking branch 'origin' into motus_profile
|
2022-05-05 09:41:13 -04:00 |
|
snpsift/split
|
|
|
|
snpsites
|
|
|
|
sortmerna
|
|
|
|
sourmash/sketch
|
Prettier (#1405)
|
2022-03-18 14:27:50 +01:00 |
|
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
|
Prettier (#1405)
|
2022-03-18 14:27:50 +01:00 |
|
stadeniolib/scramble
|
new tool: staden_io_lib (#1499)
|
2022-04-08 09:54:15 -04:00 |
|
staphopiasccmec
|
|
|
|
star
|
Samtools version update (#1507)
|
2022-04-11 14:26:28 +02:00 |
|
stranger
|
add stubs for stranger (#1543)
|
2022-04-22 10:10:43 +02:00 |
|
strelka
|
|
|
|
stringtie
|
Rename process from STRINGTIE to STRINGTIE_STRINGTIE (#1546)
|
2022-04-22 15:13:06 +01:00 |
|
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 tiddit/sv (#1580)
|
2022-04-28 14:06:38 +02:00 |
|
transdecoder
|
|
|
|
trimgalore
|
Add Trimgalore output for unpaired reads (#1568)
|
2022-04-26 19:15:24 +01:00 |
|
ucsc
|
add stub to modules used in raredisease pipeline (#1206)
|
2022-03-28 17:48:39 +02:00 |
|
ultra/pipeline
|
|
|
|
umitools
|
Add outputs for umitools dedup summary stats (#1422)
|
2022-03-18 20:21:41 +00:00 |
|
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
|
Merge remote-tracking branch 'origin' into motus_profile
|
2022-05-05 09:41:13 -04:00 |
|
variantbam
|
|
|
|
vcfanno
|
add stub to modules used in raredisease pipeline (#1206)
|
2022-03-28 17:48:39 +02:00 |
|
vcflib/vcfuniq
|
|
|
|
vcftools
|
|
|
|
yara
|
Samtools version update (#1507)
|
2022-04-11 14:26:28 +02:00 |
