millironx/nf-core_modules
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nf-core_modules/modules
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Ramprasad Neethiraj ee915a43e4
update svdb merge (#1274) 
* update svdb merge

* fix undefined variable error

* remove prio join in the script block

* fix error

* fix error again

* update tests and refactor
2022-02-24 09:49:30 +01:00
..
abacas Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
abricate add module for abricate (#1280) 2022-02-18 18:00:21 -07:00
adapterremoval Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
agrvate Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
allelecounter Add when: block (#1261) 2022-02-04 09:53:32 +01:00
amps Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
amrfinderplus add amrfinderplus module (#1284) 2022-02-19 23:02:23 +00:00
arriba Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
artic Patch fix artic/minion and ivar/variants modules (#1326) 2022-02-18 17:36:09 +00:00
assemblyscan Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
ataqv/ataqv Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
bakta Update Bakta module (#1257) 2022-02-17 08:59:31 -07:00
bamaligncleaner Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
bamcmp Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
bamtools Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
bamutil/trimbam Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
bandage/image Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
bbmap Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
bcftools Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
bedtools Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
biobambam/bammarkduplicates2 Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
bismark Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
blast Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
bowtie Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
bowtie2 Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
bwa Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
bwamem2 Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
bwameth Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
cat Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
cellranger Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
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 Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
cmseq/polymut Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
cnvkit/batch Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
cooler Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
csvtk Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
custom Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
cutadapt Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
damageprofiler Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
dastool Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
dedup Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
deeparg Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
deeptools Add deeptools bamcoverage (#1316) 2022-02-18 09:35:41 +01:00
deepvariant Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
delly/call Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +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 Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
dshbio Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
ectyper Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
emmtyper Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
ensemblvep Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
expansionhunter Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
faqcs Faqcs (#1339) 2022-02-23 16:30:22 +01:00
fargene Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
fastani Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
fastp fix fastp to allow exporting of only *.merged.fastq.gz (#1325) 2022-02-18 15:38:05 +01:00
fastqc Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
fastqscan Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
fasttree Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
fgbio Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
filtlong Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
flash Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
freebayes Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
gatk4 Gatk4 combinegvcfs (#1342) 2022-02-23 16:29:29 +01:00
genmap Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +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 Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
graphmap2 Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
gstama Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
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 Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
gunzip Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
hicap Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
hifiasm Add when: block (#1261) 2022-02-04 09:53:32 +01:00
hisat2 Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
hmmcopy Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
hmmer feat: add hmmsearch module and tests (#1273) 2022-02-23 15:32:33 +01:00
homer Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
ichorcna New module: ichorCNA (#1182) 2022-02-11 16:56:13 +01:00
idr Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
imputeme/vcftoprs Add when: block (#1261) 2022-02-04 09:53:32 +01:00
iqtree Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
ismapper Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +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 Add when: block (#1261) 2022-02-04 09:53:32 +01:00
kallisto/index Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
kallistobustools Add when: block (#1261) 2022-02-04 09:53:32 +01:00
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 Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
krona Add when: block (#1261) 2022-02-04 09:53:32 +01:00
last Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
leehom Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +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 Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
macs2/callpeak Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
malt Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
maltextract Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
manta Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
mapdamage2 Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
mash Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
mashtree Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
maxbin2 Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
medaka Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
megahit Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
meningotype Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
metabat2 Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
metaphlan3 Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
methyldackel Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
minia Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
miniasm Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
minimap2 Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
mlst Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
mobsuite/recon add mobsuite_recon module (#1270) 2022-02-18 17:52:38 -07:00
mosdepth Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
msisensor Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
msisensorpro Add msisensorpro (#1267) 2022-02-09 21:05:49 +01:00
mtnucratio Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
multiqc Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
mummer Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
muscle Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
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 Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
ngmaster Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +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 Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
pairtools Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
pangolin Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
paraclu Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
pbbam/pbmerge Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
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 Add when: block (#1261) 2022-02-04 09:53:32 +01:00
phyloflash Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
picard Picard addorreplacereadgroups (#1305) 2022-02-18 19:59:06 -07:00
pirate Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
plasmidid Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
plink Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
plink2 Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
pmdtools/filter Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
porechop Add when: block (#1261) 2022-02-04 09:53:32 +01:00
preseq/lcextrap Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
prodigal fix yml formatting (#1263) 2022-02-07 18:16:43 +01:00
prokka Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
pycoqc Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
pydamage Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +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 Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
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 Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
raven Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
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 Add when: block (#1261) 2022-02-04 09:53:32 +01:00
roary Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
rsem Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
rseqc Change label for rseqc/tin to process_high (#1327) 2022-02-21 13:26:51 +00:00
salmon Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
samblaster Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
samtools Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
scoary Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
seacr/callpeak Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
seqkit/split2 Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
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 Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
seqwish/induce Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
shovill Add when: block (#1261) 2022-02-04 09:53:32 +01:00
sistr add module for sistr (#1323) 2022-02-18 17:33:48 -07:00
snpdists Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
snpeff Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
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 Add when: block (#1261) 2022-02-04 09:53:32 +01:00
sourmash/sketch feat: add sourmash sketch (#1287) 2022-02-15 12:30:28 +01:00
spades Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
spatyper Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
sratools Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
staphopiasccmec Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
star Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
strelka Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
stringtie Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
subread/featurecounts Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
svdb update svdb merge (#1274) 2022-02-24 09:49:30 +01:00
tabix Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
tbprofiler/profile Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
tiddit Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
transdecoder Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
trimgalore Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
ucsc Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
ultra/pipeline Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
umitools Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
unicycler Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
untar Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
unzip Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
variantbam Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
vcfanno refactored vcfanno (#1266) 2022-02-21 11:49:21 +01:00
vcflib/vcfuniq Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
vcftools Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
yara Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00