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nf-core_modules/modules
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Edmund Miller 27936729f2
Add samtools to homer/maketagdirectory to use bam files (#1437) 
* fix(homer): Update dependancies for maketagdirectory

Closes #1363

* test(homer): Add tests for bam usage

* style(homer): Rename meta test

* fix(homer): Update args order and add missing \\

* docs(homer): Add DESeq2 and edgeR

Co-authored-by: FriederikeHanssen <Friederike.hanssen@qbic.uni-tuebingen.de>

* test(homer): Update md5sum

* test(homer): bam => sam

* fix(homer): Use nextflow conda recipe instead of biocontainers with commas

Co-authored-by: FriederikeHanssen <Friederike.hanssen@qbic.uni-tuebingen.de>
2022-03-25 17:13:30 +00:00
..
abacas Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
abricate Prettier (#1405) 2022-03-18 14:27:50 +01:00
adapterremoval Prettier (#1405) 2022-03-18 14:27:50 +01:00
adapterremovalfixprefix Add AdapterRemovalFixPrefix (#1424) 2022-03-21 11:26:12 +01:00
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 Prettier (#1405) 2022-03-18 14:27:50 +01:00
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
ascat Prettier (#1405) 2022-03-18 14:27:50 +01:00
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 to latest version (v1.4.0) (#1428) 2022-03-24 10:49:17 -06:00
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 feat(bbmap): Initialize pileup module (#1441) 2022-03-24 17:38:24 -06:00
bcftools Prettier (#1405) 2022-03-18 14:27:50 +01:00
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
biscuit Prettier (#1405) 2022-03-18 14:27:50 +01:00
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
bracken/bracken Add bracken (#1423) 2022-03-22 16:40:21 +01:00
bwa Fix indentation in bwa/aln meta (#1392) 2022-03-15 06:22:44 +01:00
bwamem2 Update samtools version (#1361) 2022-02-28 23:13:11 +01:00
bwameth Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
cat CAT: Use meta map and supply output file name via modules.config (#1446) 2022-03-25 14:01:57 +01:00
cellranger Prettier (#1405) 2022-03-18 14:27:50 +01:00
centrifuge Add centrifuge module (#1410) 2022-03-18 15:39:27 +01:00
checkm/lineagewf Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
chromap Bump chromap version 0.2.0 (#1374) 2022-03-10 09:23:45 +01:00
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
cnvpytor Prettier (#1405) 2022-03-18 14:27:50 +01:00
controlfreec Prettier (#1405) 2022-03-18 14:27:50 +01:00
cooler Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
csvtk Prettier (#1405) 2022-03-18 14:27:50 +01:00
custom Update samtools version (#1361) 2022-02-28 23:13:11 +01:00
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 Deeparg singularity container fix 2 (#1406) 2022-03-18 16:21:55 +01:00
deeptools style(deeptools): Indent script (#1439) 2022-03-24 19:44:31 +00:00
deepvariant separate gvcf and vcf in output channels (#1371) 2022-03-03 11:54:07 +01:00
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 feat: add readgroup info + reorder samtools command line to mimic bwamem (#1447) 2022-03-25 11:26:47 +01:00
dragonflye Update dragonflye to latest version (#1442) 2022-03-24 14:56:32 -04:00
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 Prettier (#1405) 2022-03-18 14:27:50 +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 Prettier (#1405) 2022-03-18 14:27:50 +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
hamronization Prettier (#1405) 2022-03-18 14:27:50 +01:00
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 Prettier (#1405) 2022-03-18 14:27:50 +01:00
homer Add samtools to homer/maketagdirectory to use bam files (#1437) 2022-03-25 17:13:30 +00:00
hpsuissero Prettier (#1405) 2022-03-18 14:27:50 +01:00
ichorcna Prettier (#1405) 2022-03-18 14:27:50 +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: Leehom meta output channel descriptions (#1356) 2022-02-27 14:35:47 +01:00
legsta Prettier (#1405) 2022-03-18 14:27:50 +01:00
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 Prettier (#1405) 2022-03-18 14:27:50 +01:00
mafft Prettier (#1405) 2022-03-18 14:27:50 +01:00
malt Add missing $prefix definition for MALT_RUN (#1373) 2022-03-03 17:58:04 +01:00
maltextract Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
manta Manta consistancy (#1407) 2022-03-18 13:30:03 +01:00
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 for Maxbin2 emitting input files (#1376) 2022-03-08 15:56:23 +01:00
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 Prettier (#1405) 2022-03-18 14:27:50 +01:00
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 Prettier (#1405) 2022-03-18 14:27:50 +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
ngscheckmate/ncm Prettier (#1405) 2022-03-18 14:27:50 +01:00
nucmer Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
optitype Add BAM indexes as input for optitype module. (#1388) 2022-03-15 17:02:40 +01:00
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
panaroo/run add module for panaroo, fix pirate tests (#1444) 2022-03-24 20:11:04 -06:00
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 Prettier (#1405) 2022-03-18 14:27:50 +01:00
pirate add module for panaroo, fix pirate tests (#1444) 2022-03-24 20:11:04 -06:00
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 Prettier (#1405) 2022-03-18 14:27:50 +01:00
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 Split preseq lcextrap and ccurve (#1440) 2022-03-25 17:11:40 +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 Update samtools version (#1361) 2022-02-28 23:13:11 +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 Prettier (#1405) 2022-03-18 14:27:50 +01:00
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 Prettier (#1405) 2022-03-18 14:27:50 +01:00
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 Mpileup also likes intervals (#1445) 2022-03-25 07:46:51 +01:00
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 Prettier (#1405) 2022-03-18 14:27:50 +01:00
seqsero2 Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
seqtk Prettier (#1405) 2022-03-18 14:27:50 +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 Prettier (#1405) 2022-03-18 14:27:50 +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 Prettier (#1405) 2022-03-18 14:27:50 +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
ssuissero Prettier (#1405) 2022-03-18 14:27:50 +01:00
staphopiasccmec Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
star update star/align to include an optional sam output (support for --chimOutType SeparateSAMold option) (#1378) 2022-03-23 13:13:58 +01:00
stranger Prettier (#1405) 2022-03-18 14:27:50 +01:00
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 to version 2.5.2 (#1390) 2022-03-21 10:39:34 +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 Add outputs for umitools dedup summary stats (#1422) 2022-03-18 20:21:41 +00:00
unicycler Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
untar Untar unzip meta (#1408) 2022-03-21 14:49:28 +01:00
unzip Untar unzip meta (#1408) 2022-03-21 14:49:28 +01:00
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 Prettier (#1405) 2022-03-18 14:27:50 +01:00