nf-core_modules/tests/modules
FriederikeHanssen 950700bcdc
Update samtools version (#1361)
* Update samtools version

* update checksums
2022-02-28 23:13:11 +01:00
..
abacas
abricate add module for abricate (#1280) 2022-02-18 18:00:21 -07:00
adapterremoval
agrvate
allelecounter
amps
amrfinderplus add amrfinderplus module (#1284) 2022-02-19 23:02:23 +00:00
arriba
artic Patch fix artic/minion and ivar/variants modules (#1326) 2022-02-18 17:36:09 +00:00
assemblyscan
ataqv/ataqv Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
bakta
bamaligncleaner
bamcmp bamcmp (#1244) 2022-02-02 16:38:41 +00:00
bamtools
bamutil/trimbam
bandage/image
bbmap Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
bcftools bcftools/annotate follow up corrections (#1359) 2022-02-28 10:16:29 -05:00
bedtools
biobambam/bammarkduplicates2 First version of the biobambam/bammarkduplicates2 module (#1247) 2022-02-14 16:30:48 +00:00
bismark
blast
bowtie
bowtie2
bwa Update samtools version (#1361) 2022-02-28 23:13:11 +01:00
bwamem2
bwameth Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
cat
cellranger
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
cmseq/polymut
cnvkit/batch
controlfreec add controlfreec (#1333) 2022-02-28 19:08:58 +01:00
cooler
csvtk
custom
cutadapt
damageprofiler
dastool Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
dedup
deeparg
deeptools Add deeptools bamcoverage (#1316) 2022-02-18 09:35:41 +01:00
deepvariant
delly/call
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
dshbio
ectyper Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
emmtyper
ensemblvep
expansionhunter
faqcs Faqcs (#1339) 2022-02-23 16:30:22 +01:00
fargene
fastani
fastp
fastqc
fastqscan
fasttree
fgbio
filtlong
flash
freebayes
gatk4 Gatk4 selectvariants (#1346) 2022-02-24 09:51:48 +01:00
genmap
genrich
gffread
glnexus
graphmap2
gstama
gtdbtk/classifywf
gubbins
gunc
gunzip
hicap
hifiasm
hisat2
hmmcopy
hmmer feat: add hmmsearch module and tests (#1273) 2022-02-23 15:32:33 +01:00
homer
hpsuissero add module for hpsuisero (#1331) 2022-02-27 17:58:35 -07:00
ichorcna New module: ichorCNA (#1182) 2022-02-11 16:56:13 +01:00
idr
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
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
kallisto/index
kallistobustools
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
last
leehom
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
macs2/callpeak
mafft Add MAFFT module (#1351) 2022-02-28 00:40:24 -07:00
malt Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
maltextract
manta
mapdamage2
mash
mashtree
maxbin2
medaka Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
megahit
meningotype
metabat2
metaphlan3 Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
methyldackel
minia
miniasm
minimap2 Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
mlst
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
msisensorpro
mtnucratio
multiqc
mummer
muscle
nanolyse
nanoplot Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
ncbigenomedownload
nextclade
ngmaster
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
pairtools
pangolin Bump Pangolin version to 3.1.20 (#1296) 2022-02-15 10:46:20 +00:00
paraclu
pbbam/pbmerge
pbccs Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
peddy
phyloflash
picard update args & convert to bam (#1355) 2022-02-25 11:06:39 -07:00
pirate Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
plasmidid
plink
plink2
pmdtools/filter
porechop
preseq/lcextrap
prodigal
prokka
pycoqc
pydamage
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
racon
rapidnj
rasusa
raven
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
roary Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
rsem
rseqc
salmon
samblaster
samtools update samtools version to 1.15 (#1358) 2022-02-28 12:42:29 +01:00
scoary
seacr/callpeak Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
seqkit Seqkit pair (#1348) 2022-02-24 15:07:35 +01:00
seqsero2 Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
seqtk Seqtk seq (#1340) 2022-02-23 17:02:51 +01:00
sequenzautils
seqwish/induce
shovill
sistr add module for sistr (#1323) 2022-02-18 17:33:48 -07:00
snpdists
snpeff
snpsift/split
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
sratools
ssuissero add module for ssuisero (#1329) 2022-02-27 20:04:03 -07:00
staphopiasccmec
star
strelka
stringtie
subread/featurecounts
svdb update svdb merge (#1274) 2022-02-24 09:49:30 +01:00
tabix
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
unicycler
untar
unzip
variantbam
vcfanno refactored vcfanno (#1266) 2022-02-21 11:49:21 +01:00
vcflib/vcfuniq
vcftools
yara