millironx/nf-core_modules
1
0
Fork 0
mirror of https://github.com/MillironX/nf-core_modules.git synced 2024-12-22 02:58:17 +00:00
Code Issues Releases Packages Activity
nf-core_modules/modules
History
nickhsmith 8717792135
include intervals_index (#1308) 
* include intervals_index

In order to run the GATK `GenotypeGVCFs` tool with an interval file (such as a .bed file) you need to have the corresponding index file. Otherwise you get the following error message
```
A USER ERROR has occurred: An index is required but was not found for file genome.bed.gz: work/6c/541fce2dc670597f62a571c72288c6/genome.bed.gz. Support for unindexed block-compressed files has been temporarily disabled. Try running IndexFeatureFile on the input.
```

including the index file fixes this problem

* Update meta.yml
2022-02-16 18:35:09 +01:00
..
abacas Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
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
arriba Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
artic Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +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 Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
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 Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
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
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 formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
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 include intervals_index (#1308) 2022-02-16 18:35:09 +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/hmmalign Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
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 Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +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
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
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 Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
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 Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
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
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 Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +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 rename (#1304) 2022-02-16 17:28:08 +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
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 Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
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 Add when: block (#1261) 2022-02-04 09:53:32 +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