nf-core_modules/tests/modules
2022-06-10 11:23:15 +02:00
..
abacas
abricate add module for abricate () 2022-02-18 18:00:21 -07:00
adapterremoval Refactor adapterremoval () 2022-04-04 21:40:35 +02:00
adapterremovalfixprefix Add AdapterRemovalFixPrefix () 2022-03-21 11:26:12 +01:00
agrvate
allelecounter
amplify/predict add module AMPlify () 2022-04-20 11:53:26 +02:00
amps Untar unzip meta () 2022-03-21 14:49:28 +01:00
amrfinderplus add amrfinderplus module () 2022-02-19 23:02:23 +00:00
antismash Apply suggestions from code review 2022-05-12 15:28:19 +02:00
arriba update md5sum 2022-05-09 15:19:16 +02:00
artic Untar unzip meta () 2022-03-21 14:49:28 +01:00
ascat round the < to ( to make markdown work for meta.yml () 2022-03-16 13:29:11 +01:00
assemblyscan
ataqv/ataqv Fix formatting in yaml files, add yamllint config () 2022-02-15 11:15:27 +00:00
bakta update bakta to latest version (v1.4.0) () 2022-03-24 10:49:17 -06:00
bamaligncleaner
bamcmp bamcmp () 2022-02-02 16:38:41 +00:00
bamtools Merge remote-tracking branch 'origin' into motus_profile 2022-05-05 09:41:13 -04:00
bamutil/trimbam
bandage/image
bbmap Samtools version update () 2022-04-11 14:26:28 +02:00
bcftools fix test 2022-06-08 14:48:16 +02:00
bclconvert Module/bclconvert () 2022-04-21 15:39:22 +02:00
bedtools added bedtools split 2022-05-17 14:24:32 +02:00
biobambam fix config 2022-05-17 09:09:19 +02:00
biscuit Add core Biscuit tools () 2022-03-14 09:34:22 -04:00
bismark
blast
bowtie
bowtie2 add PE sorted test 2022-05-13 19:16:50 +02:00
bracken/bracken Add bracken () 2022-03-22 16:40:21 +01:00
busco remove 'auto' test 2022-05-06 13:33:27 +00:00
bwa Samtools version update () 2022-04-11 14:26:28 +02:00
bwamem2
bwameth Fix formatting in yaml files, add yamllint config () 2022-02-15 11:15:27 +00:00
cat Update cat module () 2022-03-31 13:42:44 +02:00
cellranger Trying to fix tests 2022-06-10 11:22:45 +02:00
centrifuge Add centrifuge_kreport module () 2022-04-13 15:33:51 +02:00
checkm/lineagewf Fix formatting in yaml files, add yamllint config () 2022-02-15 11:15:27 +00:00
chromap Samtools version update () 2022-04-11 14:26:28 +02:00
clonalframeml
cmseq/polymut
cnvkit added fasta_fai as input + changed if statements 2022-06-02 12:57:50 +02:00
cnvpytor combine multiple pytor 2022-05-05 23:59:12 +02:00
controlfreec Fix Controlfreec: Add stub runs to test single sample input & make conda work with R scripts () 2022-04-08 11:43:40 +02:00
cooler
csvtk
custom tests: add missing paths to config 2022-05-11 18:17:27 +02:00
cutadapt
damageprofiler
dastool Update DASTool to 1.1.4 () 2022-04-01 11:33:07 +02:00
dedup
deeparg Deeparg singularity container fix 2 () 2022-03-18 16:21:55 +01:00
deeptools changed container + add cram2bam conversion 2022-06-02 10:38:05 +02:00
deepvariant Update version & add intervals usage () 2022-01-17 16:40:31 +01:00
delly/call
diamond Merge remote-tracking branch 'origin' into motus_profile 2022-05-05 09:41:13 -04:00
dragmap Fix formatting in yaml files, add yamllint config () 2022-02-15 11:15:27 +00:00
dragonflye
dshbio Update dsh-bio to version 2.0.7, add support for compressed GFA 1.0 format () 2022-01-17 09:24:40 +00:00
ectyper Fix formatting in yaml files, add yamllint config () 2022-02-15 11:15:27 +00:00
elprep Merge remote-tracking branch 'origin' into motus_profile 2022-05-05 09:41:13 -04:00
emmtyper
ensemblvep Update tests/modules/ensemblvep/main.nf 2022-06-09 11:55:41 +02:00
expansionhunter add stub to modules used in raredisease pipeline () 2022-03-28 17:48:39 +02:00
faqcs Faqcs patch to add tests for --debug output () 2022-03-02 08:53:05 -05:00
fargene
fastani
fastp
fastqc
fastqscan
fasttree
fgbio
filtlong Fix config for tests 2022-05-31 20:07:52 +02:00
flash
freebayes Update intervals () 2022-02-10 10:34:22 +01:00
gamma/gamma fixed test.yml 2022-05-24 19:27:09 -04:00
gatk Add GATK indelrealigner tests 2022-06-08 21:14:08 +02:00
gatk4 Merge branch 'master' into update_spark 2022-06-09 15:49:31 +02:00
genmap
genomescope2 Update tests/modules/genomescope2/test.yml 2022-05-13 11:27:42 +02:00
genrich
gffread
glnexus
graphmap2
gstama New Module: gstama/polyacleanup () 2022-03-31 09:11:51 -04:00
gtdbtk/classifywf
gubbins
gunc
gunzip
hamronization Add hamronization/summarize () 2022-03-03 08:02:04 +01:00
happy Merge remote-tracking branch 'origin' into motus_profile 2022-05-05 09:41:13 -04:00
hicap
hifiasm
hisat2
hmmcopy
hmmer Prettier () 2022-03-18 14:27:50 +01:00
hmtnote Update main.nf 2022-05-16 15:20:15 +00:00
homer Fix homer/maketagdirectory output collision () 2022-03-27 03:17:42 +00:00
hpsuissero add module for hpsuisero () 2022-02-27 17:58:35 -07:00
ichorcna Prettier () 2022-03-18 14:27:50 +01:00
idr
imputeme/vcftoprs Fix formatting in yaml files, add yamllint config () 2022-02-15 11:15:27 +00:00
iqtree Fix formatting in yaml files, add yamllint config () 2022-02-15 11:15:27 +00:00
ismapper
isoseq3 Fix formatting in yaml files, add yamllint config () 2022-02-15 11:15:27 +00:00
ivar Patch fix artic/minion and ivar/variants modules () 2022-02-18 17:36:09 +00:00
jupyternotebook
kaiju Kaiju2table module () 2022-04-22 11:26:30 +02:00
kallisto/index
kallistobustools
kat/hist Update tests/modules/kat/hist/test.yml 2022-05-23 08:51:49 +02:00
khmer/normalizebymedian Fix formatting in yaml files, add yamllint config () 2022-02-15 11:15:27 +00:00
kleborate Fix formatting in yaml files, add yamllint config () 2022-02-15 11:15:27 +00:00
kraken2/kraken2 update to kraken2: breaking change - output channels renamed () 2022-04-21 14:33:59 +02:00
krona Merge remote-tracking branch 'origin' into motus_profile 2022-05-05 09:41:13 -04:00
last Untar unzip meta () 2022-03-21 14:49:28 +01:00
leehom
legsta add module for legsta () 2022-02-18 17:42:18 -07:00
lima Fix formatting in yaml files, add yamllint config () 2022-02-15 11:15:27 +00:00
lissero Fix formatting in yaml files, add yamllint config () 2022-02-15 11:15:27 +00:00
lofreq Fix formatting in yaml files, add yamllint config () 2022-02-15 11:15:27 +00:00
macrel/contigs
macs2/callpeak
mafft Add MAFFT module () 2022-02-28 00:40:24 -07:00
malt Untar unzip meta () 2022-03-21 14:49:28 +01:00
maltextract Untar unzip meta () 2022-03-21 14:49:28 +01:00
manta Revert manta changes () 2022-04-12 10:40:06 +02:00
mapdamage2
mash Patch mash screen 2022-05-25 12:29:14 +00:00
mashtree
maxbin2
maxquant/lfq corrected typos 2022-02-07 13:07:16 +01:00
md5sum new module: md5sum 2022-05-06 09:20:40 +02:00
medaka Fix formatting in yaml files, add yamllint config () 2022-02-15 11:15:27 +00:00
megahit
megan/rma2info Add MEGAN/RMA2INFO () 2022-04-12 08:35:36 +02:00
meningotype
meryl Merge branch 'master' into meryl_unionsum 2022-05-09 16:16:08 +02:00
metabat2
metaphlan3 Untar unzip meta () 2022-03-21 14:49:28 +01:00
methyldackel
minia
miniasm
minimap2 Update minimap2/align module () 2022-04-26 16:32:20 +02:00
mlst
mobsuite/recon add mobsuite_recon module () 2022-02-18 17:52:38 -07:00
mosdepth Update main.nf 2022-05-25 19:38:12 +01:00
motus Update tests/modules/motus/profile/test.yml 2022-05-12 20:55:54 +01:00
msisensor
msisensorpro Add msisensorpro () 2022-02-09 21:05:49 +01:00
mtnucratio
multiqc formatting 2022-06-08 14:42:58 +02:00
mummer
muscle
nanolyse
nanoplot Fix formatting in yaml files, add yamllint config () 2022-02-15 11:15:27 +00:00
ncbigenomedownload
nextclade Bump Nextclade version to 1.10.1 () 2022-01-27 12:53:14 +00:00
ngmaster
ngscheckmate/ncm New module: NGSCheckMate () 2022-03-11 09:02:10 +00:00
nucmer Fix formatting in yaml files, add yamllint config () 2022-02-15 11:15:27 +00:00
optitype Add BAM indexes as input for optitype module. () 2022-03-15 17:02:40 +01:00
pairix
pairtools
panaroo/run add module for panaroo, fix pirate tests () 2022-03-24 20:11:04 -06:00
pangolin Bump Pangolin version to 3.1.20 () 2022-02-15 10:46:20 +00:00
paraclu
pbbam/pbmerge
pbccs Fix formatting in yaml files, add yamllint config () 2022-02-15 11:15:27 +00:00
peddy
phantompeakqualtools Add task.ext.args to phantompeakqualtools and finish the module () 2022-03-31 22:59:21 +01:00
phyloflash
picard fix tests (again) 2022-05-22 06:54:09 +02:00
pirate add module for panaroo, fix pirate tests () 2022-03-24 20:11:04 -06:00
plasmidid
plink
plink2 implement plink2/score module () 2022-03-07 13:02:40 -05:00
pmdtools/filter
porechop
preseq Split preseq lcextrap and ccurve () 2022-03-25 17:11:40 +00:00
prinseqplusplus Add PRINSEQPLUSPLUS () 2022-04-03 16:06:22 +02:00
prodigal
prokka
pycoqc
pydamage
qcat Fix formatting in yaml files, add yamllint config () 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 () 2022-02-18 09:43:53 +01:00
quast
racon
rapidnj
rasusa
raven Raven assembler () 2022-02-01 11:47:01 +01:00
raxmlng Fix formatting in yaml files, add yamllint config () 2022-02-15 11:15:27 +00:00
rgi/main add module for rgi () 2022-02-18 17:23:44 -07:00
rhocall/annotate update test 2022-06-08 16:36:02 +02:00
rmarkdownnotebook
roary Update test.yml () 2022-03-19 15:06:21 +00:00
rsem Bump STAR version to 2.7.10a for RSEM modules () 2022-04-27 19:21:26 +01:00
rseqc
rtgtools/vcfeval Small update on the output channels 2022-05-10 12:34:52 +02:00
salmon
samblaster Samtools version update () 2022-04-11 14:26:28 +02:00
samtools Generalize Bam2Cram do either conversion 2022-05-09 15:22:54 +02:00
scoary
seacr/callpeak Fix formatting in yaml files, add yamllint config () 2022-02-15 11:15:27 +00:00
seqkit feat: add module for seqkit stats () 2022-03-30 23:01:17 +02:00
seqsero2 Fix formatting in yaml files, add yamllint config () 2022-02-15 11:15:27 +00:00
seqtk Decrease indent in seqtk/seq versions.yml output () 2022-03-09 11:56:35 -05:00
sequenzautils
seqwish/induce
sexdeterrmine Corrected test-datasets input 2022-05-23 17:08:40 +02:00
shasum added sha256sum 2022-05-06 10:28:14 +02:00
shigatyper Merge remote-tracking branch 'origin' into motus_profile 2022-05-05 09:41:13 -04:00
shovill
sistr add module for sistr () 2022-02-18 17:33:48 -07:00
slimfastq Merge remote-tracking branch 'origin' into motus_profile 2022-05-05 09:41:13 -04:00
snapaligner fix tags 2022-05-06 18:57:17 +02:00
snippy/run make prettier 2022-05-11 18:00:36 +00:00
snpdists
snpeff
snpsift/split
snpsites Fix formatting in yaml files, add yamllint config () 2022-02-15 11:15:27 +00:00
sourmash/sketch feat: add sourmash sketch () 2022-02-15 12:30:28 +01:00
spades
spatyper
sratools refactor: move files to custom section 2022-05-11 17:33:45 +02:00
srst2/srst2 Merge remote-tracking branch 'origin' into motus_profile 2022-05-05 09:41:13 -04:00
ssuissero add module for ssuisero () 2022-02-27 20:04:03 -07:00
stadeniolib/scramble new tool: staden_io_lib () 2022-04-08 09:54:15 -04:00
staphopiasccmec
star Fix tests 2022-05-27 12:14:10 +01:00
stranger add stubs for stranger () 2022-04-22 10:10:43 +02:00
strelka Update intervals () 2022-02-10 10:34:22 +01:00
stringtie Rename process from STRINGTIE to STRINGTIE_STRINGTIE () 2022-04-22 15:13:06 +01:00
subread/featurecounts
svdb update svdb to version 2.5.2 () 2022-03-21 10:39:34 +01:00
tabix Merge remote-tracking branch 'origin' into motus_profile 2022-05-05 09:41:13 -04:00
tbprofiler/profile Fix formatting in yaml files, add yamllint config () 2022-02-15 11:15:27 +00:00
tiddit add test + fix issues 2022-06-03 15:51:02 +02:00
transdecoder Transdecoder predict () 2022-02-02 09:46:07 +01:00
trimgalore
ucsc
ultra/pipeline
umitools Fix Conda tests 2022-05-23 22:39:12 +01:00
unicycler
untar fix untar output dir 2022-06-02 11:09:55 +02:00
unzip Untar unzip meta () 2022-03-21 14:49:28 +01:00
vardictjava Merge remote-tracking branch 'origin' into motus_profile 2022-05-05 09:41:13 -04:00
variantbam
vcfanno Untar unzip meta () 2022-03-21 14:49:28 +01:00
vcflib/vcfuniq Add new vcflib/vcfuniq module () 2022-01-14 18:18:11 +00:00
vcftools
vsearch/usearchglobal prettier 2022-05-30 13:35:12 +02:00
yara Add samtools index to yara_mapper module () 2022-03-04 10:08:02 -05:00