..
abacas
Update all modules to new NF DSL2 syntax ( #1099 )
2021-11-26 07:58:40 +00:00
abricate
add module for abricate ( #1280 )
2022-02-18 18:00:21 -07:00
adapterremoval
Update all modules to new NF DSL2 syntax ( #1099 )
2021-11-26 07:58:40 +00:00
agrvate
Update all modules to new NF DSL2 syntax ( #1099 )
2021-11-26 07:58:40 +00:00
allelecounter
Update all modules to new NF DSL2 syntax ( #1099 )
2021-11-26 07:58:40 +00:00
amps
Update all modules to new NF DSL2 syntax ( #1099 )
2021-11-26 07:58:40 +00:00
arriba
Update all modules to new NF DSL2 syntax ( #1099 )
2021-11-26 07:58:40 +00:00
artic
Patch fix artic/minion and ivar/variants modules ( #1326 )
2022-02-18 17:36:09 +00:00
assemblyscan
Update all modules to new NF DSL2 syntax ( #1099 )
2021-11-26 07:58:40 +00:00
ataqv /ataqv
Fix formatting in yaml files, add yamllint config ( #1279 )
2022-02-15 11:15:27 +00:00
bakta
Update all modules to new NF DSL2 syntax ( #1099 )
2021-11-26 07:58:40 +00:00
bamaligncleaner
Update all modules to new NF DSL2 syntax ( #1099 )
2021-11-26 07:58:40 +00:00
bamcmp
bamcmp ( #1244 )
2022-02-02 16:38:41 +00:00
bamtools
New module: bamtools/convert ( #1219 )
2022-01-28 09:58:25 +00:00
bamutil /trimbam
Update all modules to new NF DSL2 syntax ( #1099 )
2021-11-26 07:58:40 +00:00
bandage /image
Update all modules to new NF DSL2 syntax ( #1099 )
2021-11-26 07:58:40 +00:00
bbmap
Fix formatting in yaml files, add yamllint config ( #1279 )
2022-02-15 11:15:27 +00:00
bcftools
Bump versions for Pangolin and Nextclade ( #1255 )
2022-02-02 15:19:46 +00:00
bedtools
Change syntax from task.ext.suffix to tast.ext.prefix in all modules ( #1110 )
2021-12-02 12:39:55 +00:00
biobambam /bammarkduplicates2
First version of the biobambam/bammarkduplicates2 module ( #1247 )
2022-02-14 16:30:48 +00:00
bismark
Update all modules to new NF DSL2 syntax ( #1099 )
2021-11-26 07:58:40 +00:00
blast
Update all modules to new NF DSL2 syntax ( #1099 )
2021-11-26 07:58:40 +00:00
bowtie
Update all modules to new NF DSL2 syntax ( #1099 )
2021-11-26 07:58:40 +00:00
bowtie2
Bump software versions for viralrecon modules ( #1198 )
2022-01-07 17:52:39 +00:00
bwa
Add new boolean sort_bam as input to be able to chose between sort and view in bwamem and bwamem2mem ( #1125 )
2021-12-08 14:31:27 +00:00
bwamem2
Add new boolean sort_bam as input to be able to chose between sort and view in bwamem and bwamem2mem ( #1125 )
2021-12-08 14:31:27 +00:00
bwameth
Fix formatting in yaml files, add yamllint config ( #1279 )
2022-02-15 11:15:27 +00:00
cat
Editing the CAT/CAT module to handle single files ( #1196 )
2022-01-06 16:41:36 +00:00
cellranger
Add bcl2fastq2 to cellranger dockerfile ( #1115 )
2022-01-25 19:58:22 +01:00
checkm /lineagewf
Fix formatting in yaml files, add yamllint config ( #1279 )
2022-02-15 11:15:27 +00:00
chromap
Fix formatting in yaml files, add yamllint config ( #1279 )
2022-02-15 11:15:27 +00:00
clonalframeml
Update all modules to new NF DSL2 syntax ( #1099 )
2021-11-26 07:58:40 +00:00
cmseq /polymut
Update all modules to new NF DSL2 syntax ( #1099 )
2021-11-26 07:58:40 +00:00
cnvkit /batch
Update all modules to new NF DSL2 syntax ( #1099 )
2021-11-26 07:58:40 +00:00
cooler
Update all modules to new NF DSL2 syntax ( #1099 )
2021-11-26 07:58:40 +00:00
csvtk
Update all modules to new NF DSL2 syntax ( #1099 )
2021-11-26 07:58:40 +00:00
custom
Update all modules to new NF DSL2 syntax ( #1099 )
2021-11-26 07:58:40 +00:00
cutadapt
Update all modules to new NF DSL2 syntax ( #1099 )
2021-11-26 07:58:40 +00:00
damageprofiler
Update all modules to new NF DSL2 syntax ( #1099 )
2021-11-26 07:58:40 +00:00
dastool
Fix formatting in yaml files, add yamllint config ( #1279 )
2022-02-15 11:15:27 +00:00
dedup
Update all modules to new NF DSL2 syntax ( #1099 )
2021-11-26 07:58:40 +00:00
deeparg
Add deeparg ( #1234 )
2022-01-26 15:19:16 +01:00
deeptools
Add deeptools bamcoverage ( #1316 )
2022-02-18 09:35:41 +01:00
deepvariant
Update version & add intervals usage ( #1214 )
2022-01-17 16:40:31 +01:00
delly /call
Update all modules to new NF DSL2 syntax ( #1099 )
2021-11-26 07:58:40 +00:00
diamond
Fix formatting in yaml files, add yamllint config ( #1279 )
2022-02-15 11:15:27 +00:00
dragmap
Fix formatting in yaml files, add yamllint config ( #1279 )
2022-02-15 11:15:27 +00:00
dragonflye
Update all modules to new NF DSL2 syntax ( #1099 )
2021-11-26 07:58:40 +00:00
dshbio
Update dsh-bio to version 2.0.7, add support for compressed GFA 1.0 format ( #1207 )
2022-01-17 09:24:40 +00:00
ectyper
Fix formatting in yaml files, add yamllint config ( #1279 )
2022-02-15 11:15:27 +00:00
emmtyper
Update all modules to new NF DSL2 syntax ( #1099 )
2021-11-26 07:58:40 +00:00
ensemblvep
greatly simplify syntax ( #1121 )
2021-12-07 11:18:12 +01:00
expansionhunter
Update all modules to new NF DSL2 syntax ( #1099 )
2021-11-26 07:58:40 +00:00
fargene
takes gunzip out of fargene main.nf ( #1090 )
2021-11-29 14:32:23 +01:00
fastani
Update all modules to new NF DSL2 syntax ( #1099 )
2021-11-26 07:58:40 +00:00
fastp
Bump software versions for viralrecon modules ( #1198 )
2022-01-07 17:52:39 +00:00
fastqc
Update all modules to new NF DSL2 syntax ( #1099 )
2021-11-26 07:58:40 +00:00
fastqscan
Update all modules to new NF DSL2 syntax ( #1099 )
2021-11-26 07:58:40 +00:00
fasttree
Update all modules to new NF DSL2 syntax ( #1099 )
2021-11-26 07:58:40 +00:00
fgbio
Added UMI sub-workflow ( #1098 )
2021-12-09 11:16:40 +01:00
filtlong
Update all modules to new NF DSL2 syntax ( #1099 )
2021-11-26 07:58:40 +00:00
flash
Update all modules to new NF DSL2 syntax ( #1099 )
2021-11-26 07:58:40 +00:00
freebayes
Update intervals ( #1278 )
2022-02-10 10:34:22 +01:00
gatk4
add mergemutectstats ( #1314 )
2022-02-18 09:38:55 +01:00
genmap
Update all modules to new NF DSL2 syntax ( #1099 )
2021-11-26 07:58:40 +00:00
genrich
Update all modules to new NF DSL2 syntax ( #1099 )
2021-11-26 07:58:40 +00:00
gffread
Replace remaining task.ext.suffix with task.ext.prefix ( #1117 )
2021-12-07 15:00:43 +01:00
glnexus
Update all modules to new NF DSL2 syntax ( #1099 )
2021-11-26 07:58:40 +00:00
graphmap2
Update all modules to new NF DSL2 syntax ( #1099 )
2021-11-26 07:58:40 +00:00
gstama
Change syntax from task.ext.suffix to tast.ext.prefix in all modules ( #1110 )
2021-12-02 12:39:55 +00:00
gtdbtk /classifywf
Update all modules to new NF DSL2 syntax ( #1099 )
2021-11-26 07:58:40 +00:00
gubbins
Update all modules to new NF DSL2 syntax ( #1099 )
2021-11-26 07:58:40 +00:00
gunc
Update all modules to new NF DSL2 syntax ( #1099 )
2021-11-26 07:58:40 +00:00
gunzip
Update all modules to new NF DSL2 syntax ( #1099 )
2021-11-26 07:58:40 +00:00
hicap
Update all modules to new NF DSL2 syntax ( #1099 )
2021-11-26 07:58:40 +00:00
hifiasm
Update all modules to new NF DSL2 syntax ( #1099 )
2021-11-26 07:58:40 +00:00
hisat2
Update all modules to new NF DSL2 syntax ( #1099 )
2021-11-26 07:58:40 +00:00
hmmcopy
hmmcopy/mapCounter ( #1175 )
2021-12-17 15:39:50 +00:00
hmmer /hmmalign
Fix test data paths for hmmer/hmmalign ( #1272 )
2022-02-10 13:14:44 +01:00
homer
Update all modules to new NF DSL2 syntax ( #1099 )
2021-11-26 07:58:40 +00:00
ichorcna
New module: ichorCNA ( #1182 )
2022-02-11 16:56:13 +01:00
idr
Update all modules to new NF DSL2 syntax ( #1099 )
2021-11-26 07:58:40 +00:00
imputeme /vcftoprs
Fix formatting in yaml files, add yamllint config ( #1279 )
2022-02-15 11:15:27 +00:00
iqtree
Fix formatting in yaml files, add yamllint config ( #1279 )
2022-02-15 11:15:27 +00:00
ismapper
Update all modules to new NF DSL2 syntax ( #1099 )
2021-11-26 07:58:40 +00:00
isoseq3
Fix formatting in yaml files, add yamllint config ( #1279 )
2022-02-15 11:15:27 +00:00
ivar
Patch fix artic/minion and ivar/variants modules ( #1326 )
2022-02-18 17:36:09 +00:00
jupyternotebook
Update all modules to new NF DSL2 syntax ( #1099 )
2021-11-26 07:58:40 +00:00
kallisto /index
Update all modules to new NF DSL2 syntax ( #1099 )
2021-11-26 07:58:40 +00:00
kallistobustools
Update all modules to new NF DSL2 syntax ( #1099 )
2021-11-26 07:58:40 +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
Update all modules to new NF DSL2 syntax ( #1099 )
2021-11-26 07:58:40 +00:00
krona
Update all modules to new NF DSL2 syntax ( #1099 )
2021-11-26 07:58:40 +00:00
last
Change syntax from task.ext.suffix to tast.ext.prefix in all modules ( #1110 )
2021-12-02 12:39:55 +00:00
leehom
Update all modules to new NF DSL2 syntax ( #1099 )
2021-11-26 07:58:40 +00:00
legsta
add module for legsta ( #1319 )
2022-02-18 17:42:18 -07:00
lima
Fix formatting in yaml files, add yamllint config ( #1279 )
2022-02-15 11:15:27 +00:00
lissero
Fix formatting in yaml files, add yamllint config ( #1279 )
2022-02-15 11:15:27 +00:00
lofreq
Fix formatting in yaml files, add yamllint config ( #1279 )
2022-02-15 11:15:27 +00:00
macrel /contigs
Add new module macrel/contigs ( #1109 )
2021-12-09 13:17:50 +01:00
macs2 /callpeak
Update all modules to new NF DSL2 syntax ( #1099 )
2021-11-26 07:58:40 +00:00
malt
Fix formatting in yaml files, add yamllint config ( #1279 )
2022-02-15 11:15:27 +00:00
maltextract
Update all modules to new NF DSL2 syntax ( #1099 )
2021-11-26 07:58:40 +00:00
manta
update manta to enable jointcalling ( #1218 )
2022-02-10 10:37:31 +01:00
mapdamage2
Update all modules to new NF DSL2 syntax ( #1099 )
2021-11-26 07:58:40 +00:00
mash
add module for mash dist ( #1193 )
2022-01-04 17:29:49 +01:00
mashtree
Update all modules to new NF DSL2 syntax ( #1099 )
2021-11-26 07:58:40 +00:00
maxbin2
Update all modules to new NF DSL2 syntax ( #1099 )
2021-11-26 07:58:40 +00:00
medaka
Fix formatting in yaml files, add yamllint config ( #1279 )
2022-02-15 11:15:27 +00:00
megahit
Update all modules to new NF DSL2 syntax ( #1099 )
2021-11-26 07:58:40 +00:00
meningotype
Update all modules to new NF DSL2 syntax ( #1099 )
2021-11-26 07:58:40 +00:00
metabat2
Update metabat2 output channels and compression ( #1111 )
2021-12-09 15:00:32 +01:00
metaphlan3
Fix formatting in yaml files, add yamllint config ( #1279 )
2022-02-15 11:15:27 +00:00
methyldackel
Update all modules to new NF DSL2 syntax ( #1099 )
2021-11-26 07:58:40 +00:00
minia
Update all modules to new NF DSL2 syntax ( #1099 )
2021-11-26 07:58:40 +00:00
miniasm
Change syntax from task.ext.suffix to tast.ext.prefix in all modules ( #1110 )
2021-12-02 12:39:55 +00:00
minimap2
Fix formatting in yaml files, add yamllint config ( #1279 )
2022-02-15 11:15:27 +00:00
mlst
Update all modules to new NF DSL2 syntax ( #1099 )
2021-11-26 07:58:40 +00:00
mobsuite /recon
add mobsuite_recon module ( #1270 )
2022-02-18 17:52:38 -07:00
mosdepth
Update mosdepth ( #1256 )
2022-02-09 12:45:55 +00:00
msisensor
Update all modules to new NF DSL2 syntax ( #1099 )
2021-11-26 07:58:40 +00:00
msisensorpro
Add msisensorpro ( #1267 )
2022-02-09 21:05:49 +01:00
mtnucratio
Update all modules to new NF DSL2 syntax ( #1099 )
2021-11-26 07:58:40 +00:00
multiqc
Update all modules to new NF DSL2 syntax ( #1099 )
2021-11-26 07:58:40 +00:00
mummer
Update all modules to new NF DSL2 syntax ( #1099 )
2021-11-26 07:58:40 +00:00
muscle
Update all modules to new NF DSL2 syntax ( #1099 )
2021-11-26 07:58:40 +00:00
nanolyse
Change syntax from task.ext.suffix to tast.ext.prefix in all modules ( #1110 )
2021-12-02 12:39:55 +00:00
nanoplot
Fix formatting in yaml files, add yamllint config ( #1279 )
2022-02-15 11:15:27 +00:00
ncbigenomedownload
Update all modules to new NF DSL2 syntax ( #1099 )
2021-11-26 07:58:40 +00:00
nextclade
Bump Nextclade version to 1.10.1 ( #1236 )
2022-01-27 12:53:14 +00:00
ngmaster
Update all modules to new NF DSL2 syntax ( #1099 )
2021-11-26 07:58:40 +00:00
nucmer
Fix formatting in yaml files, add yamllint config ( #1279 )
2022-02-15 11:15:27 +00:00
optitype
Fix formatting in yaml files, add yamllint config ( #1279 )
2022-02-15 11:15:27 +00:00
pairix
Update all modules to new NF DSL2 syntax ( #1099 )
2021-11-26 07:58:40 +00:00
pairtools
Change syntax from task.ext.suffix to tast.ext.prefix in all modules ( #1110 )
2021-12-02 12:39:55 +00:00
pangolin
Bump Pangolin version to 3.1.20 ( #1296 )
2022-02-15 10:46:20 +00:00
paraclu
Update all modules to new NF DSL2 syntax ( #1099 )
2021-11-26 07:58:40 +00:00
pbbam /pbmerge
Change syntax from task.ext.suffix to tast.ext.prefix in all modules ( #1110 )
2021-12-02 12:39:55 +00:00
pbccs
Fix formatting in yaml files, add yamllint config ( #1279 )
2022-02-15 11:15:27 +00:00
peddy
Update all modules to new NF DSL2 syntax ( #1099 )
2021-11-26 07:58:40 +00:00
phyloflash
Update all modules to new NF DSL2 syntax ( #1099 )
2021-11-26 07:58:40 +00:00
picard
Picard fixmateinformation ( #1315 )
2022-02-18 18:18:05 -07:00
pirate
Fix formatting in yaml files, add yamllint config ( #1279 )
2022-02-15 11:15:27 +00:00
plasmidid
Update all modules to new NF DSL2 syntax ( #1099 )
2021-11-26 07:58:40 +00:00
plink
Change syntax from task.ext.suffix to tast.ext.prefix in all modules ( #1110 )
2021-12-02 12:39:55 +00:00
plink2
New module: plink2/extract ( #1228 )
2022-02-03 10:42:56 +00:00
pmdtools /filter
Update all modules to new NF DSL2 syntax ( #1099 )
2021-11-26 07:58:40 +00:00
porechop
Change syntax from task.ext.suffix to tast.ext.prefix in all modules ( #1110 )
2021-12-02 12:39:55 +00:00
preseq /lcextrap
Update all modules to new NF DSL2 syntax ( #1099 )
2021-11-26 07:58:40 +00:00
prodigal
Update all modules to new NF DSL2 syntax ( #1099 )
2021-11-26 07:58:40 +00:00
prokka
Update all modules to new NF DSL2 syntax ( #1099 )
2021-11-26 07:58:40 +00:00
pycoqc
Update all modules to new NF DSL2 syntax ( #1099 )
2021-11-26 07:58:40 +00:00
pydamage
Update all modules to new NF DSL2 syntax ( #1099 )
2021-11-26 07:58:40 +00:00
qcat
Fix formatting in yaml files, add yamllint config ( #1279 )
2022-02-15 11:15:27 +00:00
qualimap
add qualimap with cram files + remove val from qualimap/bam, instead use empty list as everywhere else ( #1320 )
2022-02-18 09:43:53 +01:00
quast
Update all modules to new NF DSL2 syntax ( #1099 )
2021-11-26 07:58:40 +00:00
racon
Update all modules to new NF DSL2 syntax ( #1099 )
2021-11-26 07:58:40 +00:00
rapidnj
Update all modules to new NF DSL2 syntax ( #1099 )
2021-11-26 07:58:40 +00:00
rasusa
Change syntax from task.ext.suffix to tast.ext.prefix in all modules ( #1110 )
2021-12-02 12:39:55 +00:00
raven
Raven assembler ( #1087 )
2022-02-01 11:47:01 +01:00
raxmlng
Fix formatting in yaml files, add yamllint config ( #1279 )
2022-02-15 11:15:27 +00:00
rgi /main
add module for rgi ( #1321 )
2022-02-18 17:23:44 -07:00
rmarkdownnotebook
Update all modules to new NF DSL2 syntax ( #1099 )
2021-11-26 07:58:40 +00:00
roary
Fix formatting in yaml files, add yamllint config ( #1279 )
2022-02-15 11:15:27 +00:00
rsem
Update all modules to new NF DSL2 syntax ( #1099 )
2021-11-26 07:58:40 +00:00
rseqc
Provide BAI when running rseqc/tin ( #1177 )
2021-12-17 10:00:09 +00:00
salmon
Update all modules to new NF DSL2 syntax ( #1099 )
2021-11-26 07:58:40 +00:00
samblaster
Change syntax from task.ext.suffix to tast.ext.prefix in all modules ( #1110 )
2021-12-02 12:39:55 +00:00
samtools
Bump software versions for viralrecon modules ( #1198 )
2022-01-07 17:52:39 +00:00
scoary
Update all modules to new NF DSL2 syntax ( #1099 )
2021-11-26 07:58:40 +00:00
seacr /callpeak
Fix formatting in yaml files, add yamllint config ( #1279 )
2022-02-15 11:15:27 +00:00
seqkit /split2
Update version & prefix ( #1120 )
2021-12-07 10:22:32 +01:00
seqsero2
Fix formatting in yaml files, add yamllint config ( #1279 )
2022-02-15 11:15:27 +00:00
seqtk
Seqtk rename ( #1304 )
2022-02-16 17:28:08 +01:00
sequenzautils
Update all modules to new NF DSL2 syntax ( #1099 )
2021-11-26 07:58:40 +00:00
seqwish /induce
Update all modules to new NF DSL2 syntax ( #1099 )
2021-11-26 07:58:40 +00:00
shovill
Update all modules to new NF DSL2 syntax ( #1099 )
2021-11-26 07:58:40 +00:00
sistr
add module for sistr ( #1323 )
2022-02-18 17:33:48 -07:00
snpdists
Update all modules to new NF DSL2 syntax ( #1099 )
2021-11-26 07:58:40 +00:00
snpeff
greatly simplify syntax ( #1121 )
2021-12-07 11:18:12 +01:00
snpsift /split
Added new module snpsift/split ( #1031 )
2021-12-17 09:08:14 +01:00
snpsites
Fix formatting in yaml files, add yamllint config ( #1279 )
2022-02-15 11:15:27 +00:00
sourmash /sketch
feat: add sourmash sketch ( #1287 )
2022-02-15 12:30:28 +01:00
spades
Update all modules to new NF DSL2 syntax ( #1099 )
2021-11-26 07:58:40 +00:00
spatyper
Update all modules to new NF DSL2 syntax ( #1099 )
2021-11-26 07:58:40 +00:00
sratools
Update all modules to new NF DSL2 syntax ( #1099 )
2021-11-26 07:58:40 +00:00
staphopiasccmec
Update all modules to new NF DSL2 syntax ( #1099 )
2021-11-26 07:58:40 +00:00
star
Update all modules to new NF DSL2 syntax ( #1099 )
2021-11-26 07:58:40 +00:00
strelka
Update intervals ( #1278 )
2022-02-10 10:34:22 +01:00
stringtie
Update all modules to new NF DSL2 syntax ( #1099 )
2021-11-26 07:58:40 +00:00
subread /featurecounts
Update all modules to new NF DSL2 syntax ( #1099 )
2021-11-26 07:58:40 +00:00
svdb
Add svdb/merge ( #1233 )
2022-02-04 15:29:44 +01:00
tabix
Update all modules to new NF DSL2 syntax ( #1099 )
2021-11-26 07:58:40 +00:00
tbprofiler /profile
Fix formatting in yaml files, add yamllint config ( #1279 )
2022-02-15 11:15:27 +00:00
tiddit
Update all modules to new NF DSL2 syntax ( #1099 )
2021-11-26 07:58:40 +00:00
transdecoder
Transdecoder predict ( #1251 )
2022-02-02 09:46:07 +01:00
trimgalore
Update all modules to new NF DSL2 syntax ( #1099 )
2021-11-26 07:58:40 +00:00
ucsc
ucsc/wigtobigwig: add meta map ( #1199 )
2022-01-11 21:31:37 +00:00
ultra /pipeline
Change syntax from task.ext.suffix to tast.ext.prefix in all modules ( #1110 )
2021-12-02 12:39:55 +00:00
unicycler
Update all modules to new NF DSL2 syntax ( #1099 )
2021-11-26 07:58:40 +00:00
untar
Update all modules to new NF DSL2 syntax ( #1099 )
2021-11-26 07:58:40 +00:00
unzip
Update all modules to new NF DSL2 syntax ( #1099 )
2021-11-26 07:58:40 +00:00
variantbam
Update all modules to new NF DSL2 syntax ( #1099 )
2021-11-26 07:58:40 +00:00
vcfanno
New module/vcfanno ( #1204 )
2022-01-20 08:46:31 +00:00
vcflib /vcfuniq
Add new vcflib/vcfuniq module ( #1208 )
2022-01-14 18:18:11 +00:00
vcftools
Update all modules to new NF DSL2 syntax ( #1099 )
2021-11-26 07:58:40 +00:00
yara
Update all modules to new NF DSL2 syntax ( #1099 )
2021-11-26 07:58:40 +00:00
f655e5dea2