| .. |
|
abacas
|
Update versions key in meta.yml for all modules (#787)
|
2021-10-03 08:20:26 +01:00 |
|
adapterremoval
|
Fix read indexing in AdapterRemoval module (#1051)
|
2021-11-10 12:21:12 +00:00 |
|
agrvate
|
Update agrvate version (#970)
|
2021-11-15 16:06:02 +01:00 |
|
allelecounter
|
Add cram support to Allelecounter module (#1013)
|
2021-11-02 17:00:25 +01:00 |
|
amps
|
Update versions key in meta.yml for all modules (#787)
|
2021-10-03 08:20:26 +01:00 |
|
arriba
|
Update versions key in meta.yml for all modules (#787)
|
2021-10-03 08:20:26 +01:00 |
|
artic
|
Update versions key in meta.yml for all modules (#787)
|
2021-10-03 08:20:26 +01:00 |
|
assemblyscan
|
add new assembly scan module (#971)
|
2021-10-29 10:01:23 +02:00 |
|
ataqv/ataqv
|
Add new module 'ataqv/ataqv' (#998)
|
2021-11-15 12:51:40 +00:00 |
|
bakta
|
add bakta module (#1085)
|
2021-11-21 12:17:25 +00:00 |
|
bamaligncleaner
|
Update versions key in meta.yml for all modules (#787)
|
2021-10-03 08:20:26 +01:00 |
|
bamtools/split
|
Update module: bamtools/split (#885)
|
2021-10-23 19:39:27 +01:00 |
|
bamutil/trimbam
|
Add bamutil/trimbam (#1060)
|
2021-11-15 16:44:12 +00:00 |
|
bandage/image
|
Backfill software licenses meta (#876)
|
2021-10-22 15:39:54 -07:00 |
|
bbmap
|
Add log to output from bbmap/align (#1050)
|
2021-11-10 10:27:52 +00:00 |
|
bcftools
|
Backfill software licenses meta (#876)
|
2021-10-22 15:39:54 -07:00 |
|
bedtools
|
Bedtools sort add extension choice input (#984)
|
2021-10-29 13:22:17 +01:00 |
|
bismark
|
Backfill software licenses meta (#876)
|
2021-10-22 15:39:54 -07:00 |
|
blast
|
Backfill software licenses meta (#876)
|
2021-10-22 15:39:54 -07:00 |
|
bowtie
|
Backfill software licenses meta (#876)
|
2021-10-22 15:39:54 -07:00 |
|
bowtie2
|
Backfill software licenses meta (#876)
|
2021-10-22 15:39:54 -07:00 |
|
bwa
|
Bwa index (#1040)
|
2021-11-15 11:26:01 +00:00 |
|
bwamem2
|
Backfill software licenses meta (#876)
|
2021-10-22 15:39:54 -07:00 |
|
bwameth
|
bwameth: Add touch command to fix problem with bwameth rejecting older files (#1037)
|
2021-11-06 16:05:04 +01:00 |
|
cat
|
Backfill software licenses meta (#876)
|
2021-10-22 15:39:54 -07:00 |
|
cellranger
|
new module cellranger mkref (#896)
|
2021-10-28 13:33:57 +02:00 |
|
checkm/lineagewf
|
New module: checkm/lineagewf (#899)
|
2021-10-26 21:54:10 +01:00 |
|
chromap
|
Update versions key in meta.yml for all modules (#787)
|
2021-10-03 08:20:26 +01:00 |
|
clonalframeml
|
add clonalframeml module (#974)
|
2021-11-15 19:43:53 +00:00 |
|
cmseq/polymut
|
Add new module: cmseq/polymut (#918)
|
2021-11-09 16:12:51 +01:00 |
|
cnvkit/batch
|
CNVkit: Make targets file optional when running in WGS mode (#1030)
|
2021-11-21 19:56:57 +00:00 |
|
cooler
|
Cooler cload (#634)
|
2021-11-15 21:43:55 +00:00 |
|
csvtk
|
Added new module csvtk/split (#1014)
|
2021-11-15 18:29:55 +00:00 |
|
custom
|
Add module get_chrom_sizes (#1063)
|
2021-11-15 19:22:12 +00:00 |
|
cutadapt
|
Backfill software licenses meta (#876)
|
2021-10-22 15:39:54 -07:00 |
|
damageprofiler
|
fix: reduce number of required input files for damage profiler (#612)
|
2021-10-20 10:02:30 +02:00 |
|
dastool
|
Add new module: Das Tool (#1004)
|
2021-11-19 08:33:29 +01:00 |
|
dedup
|
Add module: dedup (#907)
|
2021-10-28 12:10:21 +02:00 |
|
deeptools
|
Update versions key in meta.yml for all modules (#787)
|
2021-10-03 08:20:26 +01:00 |
|
delly/call
|
Backfill software licenses meta (#876)
|
2021-10-22 15:39:54 -07:00 |
|
diamond
|
Update versions key in meta.yml for all modules (#787)
|
2021-10-03 08:20:26 +01:00 |
|
dragonflye
|
Update versions key in meta.yml for all modules (#787)
|
2021-10-03 08:20:26 +01:00 |
|
dshbio
|
Update dsh-bio to 2.0.6. (#1075)
|
2021-11-16 11:37:27 +00:00 |
|
ectyper
|
add ectyper module (#948)
|
2021-11-21 12:14:02 +00:00 |
|
emmtyper
|
add emmtyper module (#1028)
|
2021-11-08 20:43:15 +01:00 |
|
ensemblvep
|
Backfill software licenses meta (#876)
|
2021-10-22 15:39:54 -07:00 |
|
expansionhunter
|
Backfill software licenses meta (#876)
|
2021-10-22 15:39:54 -07:00 |
|
fargene
|
new module fargene (#1068)
|
2021-11-15 16:42:48 +00:00 |
|
fastani
|
Update versions key in meta.yml for all modules (#787)
|
2021-10-03 08:20:26 +01:00 |
|
fastp
|
Backfill software licenses meta (#876)
|
2021-10-22 15:39:54 -07:00 |
|
fastqc
|
Backfill software licenses meta (#876)
|
2021-10-22 15:39:54 -07:00 |
|
fastqscan
|
add module for fastq-scan (#935)
|
2021-11-15 15:41:36 +01:00 |
|
fasttree
|
Update versions key in meta.yml for all modules (#787)
|
2021-10-03 08:20:26 +01:00 |
|
fgbio
|
Fgbio group reads by umi (#952)
|
2021-10-29 14:00:54 +02:00 |
|
filtlong
|
add filtlong (#919)
|
2021-10-27 17:00:11 +02:00 |
|
flash
|
Update versions key in meta.yml for all modules (#787)
|
2021-10-03 08:20:26 +01:00 |
|
freebayes
|
Merge freebayes subtools (#1015)
|
2021-11-03 11:22:06 +01:00 |
|
gatk4
|
Update in GATK4 variantfiltration: Added vcf_index to vcf tuple; output to vcf.gz format. (#1083)
|
2021-11-18 21:47:40 +01:00 |
|
genmap
|
Backfill software licenses meta (#876)
|
2021-10-22 15:39:54 -07:00 |
|
genrich
|
Refactor genrich to avoid params in main (#981)
|
2021-10-29 16:37:39 +02:00 |
|
gffread
|
Update versions key in meta.yml for all modules (#787)
|
2021-10-03 08:20:26 +01:00 |
|
glnexus
|
Backfill software licenses meta (#876)
|
2021-10-22 15:39:54 -07:00 |
|
graphmap2
|
Backfill software licenses meta (#876)
|
2021-10-22 15:39:54 -07:00 |
|
gstama
|
Update: gstama/collapse (#1057)
|
2021-11-11 14:57:55 +00:00 |
|
gtdbtk/classifywf
|
Add gtdbtk/classifywf module (#765)
|
2021-10-05 21:23:01 +01:00 |
|
gubbins
|
Backfill software licenses meta (#876)
|
2021-10-22 15:39:54 -07:00 |
|
gunc
|
New module: gunc run (+ gunc downloaddb) (#880)
|
2021-11-03 17:01:23 +01:00 |
|
gunzip
|
update: gunzip to include meta input tuple (#1082)
|
2021-11-21 12:41:03 +00:00 |
|
hicap
|
[fix] hicap module allow optional outputs (#937)
|
2021-11-16 09:23:07 +00:00 |
|
hifiasm
|
Update versions key in meta.yml for all modules (#787)
|
2021-10-03 08:20:26 +01:00 |
|
hisat2
|
Update versions key in meta.yml for all modules (#787)
|
2021-10-03 08:20:26 +01:00 |
|
hmmcopy
|
readcounter module for hmmcopy (#1001)
|
2021-11-02 11:01:13 +00:00 |
|
hmmer/hmmalign
|
Backfill software licenses meta (#876)
|
2021-10-22 15:39:54 -07:00 |
|
homer
|
Backfill software licenses meta (#876)
|
2021-10-22 15:39:54 -07:00 |
|
idr
|
Add IDR module (#908)
|
2021-10-30 10:52:13 +02:00 |
|
imputeme/vcftoprs
|
Imputeme (#882)
|
2021-11-05 10:25:54 +01:00 |
|
iqtree
|
Update versions key in meta.yml for all modules (#787)
|
2021-10-03 08:20:26 +01:00 |
|
ismapper
|
Backfill software licenses meta (#876)
|
2021-10-22 15:39:54 -07:00 |
|
isoseq3
|
Backfill software licenses meta (#876)
|
2021-10-22 15:39:54 -07:00 |
|
ivar
|
Backfill software licenses meta (#876)
|
2021-10-22 15:39:54 -07:00 |
|
jupyternotebook
|
Notebook modules (#617)
|
2021-10-24 20:51:56 +02:00 |
|
kallisto/index
|
Backfill software licenses meta (#876)
|
2021-10-22 15:39:54 -07:00 |
|
kallistobustools
|
Update versions key in meta.yml for all modules (#787)
|
2021-10-03 08:20:26 +01:00 |
|
khmer/normalizebymedian
|
Khmer normalizebymedian (#985)
|
2021-10-29 13:23:34 +02:00 |
|
kleborate
|
Update versions key in meta.yml for all modules (#787)
|
2021-10-03 08:20:26 +01:00 |
|
kraken2/kraken2
|
Backfill software licenses meta (#876)
|
2021-10-22 15:39:54 -07:00 |
|
kronatools
|
add Kronatools KTImportTaxonomy (#928)
|
2021-11-15 17:40:46 +00:00 |
|
last
|
Update versions key in meta.yml for all modules (#787)
|
2021-10-03 08:20:26 +01:00 |
|
leehom
|
Add leehom module (#1052)
|
2021-11-15 15:26:06 +01:00 |
|
lib
|
Bulk update modules to use versions.yml (#739)
|
2021-09-27 09:41:24 +01:00 |
|
lima
|
Backfill software licenses meta (#876)
|
2021-10-22 15:39:54 -07:00 |
|
lissero
|
add lissero module (#1026)
|
2021-11-08 20:52:07 +01:00 |
|
lofreq
|
Update versions key in meta.yml for all modules (#787)
|
2021-10-03 08:20:26 +01:00 |
|
macs2/callpeak
|
Macs2 calllpeak (#1038)
|
2021-11-15 18:17:40 +01:00 |
|
malt
|
Update versions key in meta.yml for all modules (#787)
|
2021-10-03 08:20:26 +01:00 |
|
maltextract
|
Update versions key in meta.yml for all modules (#787)
|
2021-10-03 08:20:26 +01:00 |
|
manta
|
Update to allow cram + update needed to use the gatk4 modules in sarek (#976)
|
2021-10-29 13:01:05 +02:00 |
|
mapdamage2
|
Add new module Mapdamage2 (#975)
|
2021-11-09 14:05:23 +01:00 |
|
mash/sketch
|
Update versions key in meta.yml for all modules (#787)
|
2021-10-03 08:20:26 +01:00 |
|
mashtree
|
add mashtree module (#767)
|
2021-10-05 21:27:30 +01:00 |
|
maxbin2
|
New module: maxbin2 (#895)
|
2021-10-26 22:07:33 +01:00 |
|
medaka
|
Add Medaka module (#992)
|
2021-11-15 17:26:37 +00:00 |
|
megahit
|
Add MEGAHIT (#810)
|
2021-10-12 16:06:06 +01:00 |
|
meningotype
|
add meningotype module (#1022)
|
2021-11-06 16:44:26 +01:00 |
|
metabat2
|
New module: metabat2 (#875)
|
2021-11-08 21:08:26 +01:00 |
|
metaphlan3
|
Update versions key in meta.yml for all modules (#787)
|
2021-10-03 08:20:26 +01:00 |
|
methyldackel
|
Backfill software licenses meta (#876)
|
2021-10-22 15:39:54 -07:00 |
|
minia
|
Backfill software licenses meta (#876)
|
2021-10-22 15:39:54 -07:00 |
|
miniasm
|
Add Miniasm module (#962)
|
2021-11-15 17:50:56 +00:00 |
|
minimap2
|
Backfill software licenses meta (#876)
|
2021-10-22 15:39:54 -07:00 |
|
mlst
|
added classic mlst module (#742)
|
2021-10-05 20:49:46 +01:00 |
|
mosdepth
|
Backfill software licenses meta (#876)
|
2021-10-22 15:39:54 -07:00 |
|
msisensor
|
Update versions key in meta.yml for all modules (#787)
|
2021-10-03 08:20:26 +01:00 |
|
mtnucratio
|
Mtnucratio (#986)
|
2021-10-29 15:02:02 +02:00 |
|
multiqc
|
Backfill software licenses meta (#876)
|
2021-10-22 15:39:54 -07:00 |
|
mummer
|
Initial commit mummer module (#940)
|
2021-11-15 16:53:41 +01:00 |
|
muscle
|
Update versions key in meta.yml for all modules (#787)
|
2021-10-03 08:20:26 +01:00 |
|
nanolyse
|
Backfill software licenses meta (#876)
|
2021-10-22 15:39:54 -07:00 |
|
nanoplot
|
Backfill software licenses meta (#876)
|
2021-10-22 15:39:54 -07:00 |
|
ncbigenomedownload
|
add ncbi-genome-download module (#980)
|
2021-11-15 18:32:53 +00:00 |
|
nextclade
|
Update versions key in meta.yml for all modules (#787)
|
2021-10-03 08:20:26 +01:00 |
|
ngmaster
|
add ngmaster module (#1024)
|
2021-11-10 11:25:50 -07:00 |
|
nucmer
|
add new nucmer module (#945)
|
2021-11-15 22:05:34 +00:00 |
|
optitype
|
Backfill software licenses meta (#876)
|
2021-10-22 15:39:54 -07:00 |
|
pairix
|
Update versions key in meta.yml for all modules (#787)
|
2021-10-03 08:20:26 +01:00 |
|
pairtools
|
Update versions key in meta.yml for all modules (#787)
|
2021-10-03 08:20:26 +01:00 |
|
pangolin
|
Backfill software licenses meta (#876)
|
2021-10-22 15:39:54 -07:00 |
|
paraclu
|
add paraclu (#909)
|
2021-10-27 15:48:49 +02:00 |
|
pbbam/pbmerge
|
Backfill software licenses meta (#876)
|
2021-10-22 15:39:54 -07:00 |
|
pbccs
|
Update module: pbccs (#1018)
|
2021-11-11 14:19:26 +00:00 |
|
peddy
|
Peddy nf core2 2dev0 (#1048)
|
2021-11-21 20:14:09 +00:00 |
|
phantompeakqualtools
|
Remove def software lines and emit versions channel as plural (#780)
|
2021-10-01 14:04:56 +01:00 |
|
phyloflash
|
Add phyloflash module (#786)
|
2021-11-21 19:43:58 +00:00 |
|
picard
|
Fix picard markduplicates (#1084)
|
2021-11-18 21:54:14 +01:00 |
|
pirate
|
add pirate module (#777)
|
2021-10-05 22:28:25 +01:00 |
|
plasmidid
|
Update versions key in meta.yml for all modules (#787)
|
2021-10-03 08:20:26 +01:00 |
|
plink
|
Implement plink/extract module (#901)
|
2021-11-09 14:03:13 +00:00 |
|
plink2/vcf
|
New module: plink2/vcf (#1006)
|
2021-11-15 13:55:18 +00:00 |
|
pmdtools/filter
|
add new module pmdtools/filter #847 (#963)
|
2021-11-13 15:09:14 +00:00 |
|
porechop
|
add porechop module (#914)
|
2021-10-28 13:21:36 +02:00 |
|
preseq/lcextrap
|
Update versions key in meta.yml for all modules (#787)
|
2021-10-03 08:20:26 +01:00 |
|
prodigal
|
Update versions key in meta.yml for all modules (#787)
|
2021-10-03 08:20:26 +01:00 |
|
prokka
|
Update versions key in meta.yml for all modules (#787)
|
2021-10-03 08:20:26 +01:00 |
|
pycoqc
|
Update versions key in meta.yml for all modules (#787)
|
2021-10-03 08:20:26 +01:00 |
|
pydamage
|
Update versions key in meta.yml for all modules (#787)
|
2021-10-03 08:20:26 +01:00 |
|
qcat
|
Backfill software licenses meta (#876)
|
2021-10-22 15:39:54 -07:00 |
|
qualimap
|
Backfill software licenses meta (#876)
|
2021-10-22 15:39:54 -07:00 |
|
quast
|
Backfill software licenses meta (#876)
|
2021-10-22 15:39:54 -07:00 |
|
racon
|
Add Racon module to nf-core/modules (#949)
|
2021-10-29 13:33:38 +01:00 |
|
rapidnj
|
Update versions key in meta.yml for all modules (#787)
|
2021-10-03 08:20:26 +01:00 |
|
rasusa
|
Update versions key in meta.yml for all modules (#787)
|
2021-10-03 08:20:26 +01:00 |
|
raxmlng
|
Update versions key in meta.yml for all modules (#787)
|
2021-10-03 08:20:26 +01:00 |
|
rmarkdownnotebook
|
Notebook modules (#617)
|
2021-10-24 20:51:56 +02:00 |
|
roary
|
add roary module (#776)
|
2021-10-05 22:08:47 +01:00 |
|
rsem
|
Backfill software licenses meta (#876)
|
2021-10-22 15:39:54 -07:00 |
|
rseqc
|
Backfill software licenses meta (#876)
|
2021-10-22 15:39:54 -07:00 |
|
salmon
|
Backfill software licenses meta (#876)
|
2021-10-22 15:39:54 -07:00 |
|
samblaster
|
New module: Samblaster (#954)
|
2021-11-04 18:18:56 +01:00 |
|
samtools
|
Add thread option to samtools modules (#1069)
|
2021-11-18 22:24:47 +01:00 |
|
scoary
|
add scoary module (#1034)
|
2021-11-06 16:34:39 +01:00 |
|
seacr/callpeak
|
Backfill software licenses meta (#876)
|
2021-10-22 15:39:54 -07:00 |
|
seqkit/split2
|
Backfill software licenses meta (#876)
|
2021-10-22 15:39:54 -07:00 |
|
seqsero2
|
add seqsero2 module (#1016)
|
2021-11-04 07:49:30 +00:00 |
|
seqtk
|
New module seqtk/mergepe (#951)
|
2021-10-28 16:53:33 +02:00 |
|
sequenzautils
|
Backfill software licenses meta (#876)
|
2021-10-22 15:39:54 -07:00 |
|
seqwish/induce
|
Backfill software licenses meta (#876)
|
2021-10-22 15:39:54 -07:00 |
|
shovill
|
Update versions key in meta.yml for all modules (#787)
|
2021-10-03 08:20:26 +01:00 |
|
snpdists
|
Update versions key in meta.yml for all modules (#787)
|
2021-10-03 08:20:26 +01:00 |
|
snpeff
|
Backfill software licenses meta (#876)
|
2021-10-22 15:39:54 -07:00 |
|
snpsites
|
Backfill software licenses meta (#876)
|
2021-10-22 15:39:54 -07:00 |
|
sortmerna
|
Fix sortmerna docker container pointer (#791)
|
2021-10-05 12:05:37 +02:00 |
|
spades
|
Change Spades input (#1039)
|
2021-11-15 11:53:07 +00:00 |
|
spatyper
|
Update main.nf (#938)
|
2021-11-15 15:47:41 +01:00 |
|
sratools
|
Backfill software licenses meta (#876)
|
2021-10-22 15:39:54 -07:00 |
|
staphopiasccmec
|
Update versions key in meta.yml for all modules (#787)
|
2021-10-03 08:20:26 +01:00 |
|
star
|
Backfill software licenses meta (#876)
|
2021-10-22 15:39:54 -07:00 |
|
strelka
|
Update to allow cram + update needed to use the gatk4 modules in sarek (#976)
|
2021-10-29 13:01:05 +02:00 |
|
stringtie
|
Backfill software licenses meta (#876)
|
2021-10-22 15:39:54 -07:00 |
|
subread/featurecounts
|
Update versions key in meta.yml for all modules (#787)
|
2021-10-03 08:20:26 +01:00 |
|
tabix
|
Backfill software licenses meta (#876)
|
2021-10-22 15:39:54 -07:00 |
|
tbprofiler/profile
|
add module for tbprofiler (#947)
|
2021-11-15 15:35:55 +01:00 |
|
tiddit
|
Backfill software licenses meta (#876)
|
2021-10-22 15:39:54 -07:00 |
|
trimgalore
|
Backfill software licenses meta (#876)
|
2021-10-22 15:39:54 -07:00 |
|
ucsc
|
New module: ucsc/liftover (#868)
|
2021-10-21 18:04:15 +02:00 |
|
ultra/pipeline
|
Update: uLTRA (#1081)
|
2021-11-21 13:00:53 +00:00 |
|
umitools
|
added meta.yml for umitools (#860)
|
2021-10-23 17:30:10 +01:00 |
|
unicycler
|
Unicycler with long read input (#1041)
|
2021-11-15 11:48:56 +00:00 |
|
untar
|
Backfill software licenses meta (#876)
|
2021-10-22 15:39:54 -07:00 |
|
unzip
|
Backfill software licenses meta (#876)
|
2021-10-22 15:39:54 -07:00 |
|
variantbam
|
Backfill software licenses meta (#876)
|
2021-10-22 15:39:54 -07:00 |
|
vcftools
|
Update versions key in meta.yml for all modules (#787)
|
2021-10-03 08:20:26 +01:00 |
|
yara
|
Update versions key in meta.yml for all modules (#787)
|
2021-10-03 08:20:26 +01:00 |
45985ff6f0