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nf-core_modules/tests/modules
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James A. Fellows Yates 393dbd6dda
Update UNTAR to account for file-only or multi-directory tar archives (#2055) 
* Update main.nf

* Update meta.yml

* Re-add logos as not staged in a way that works with MultiQC config files

* Fix when only files or multiple directories

* Add test for only-files tar

* Fix bash check
2022-09-14 10:40:45 +02:00
..
abacas Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
abricate add module for abricate (#1280) 2022-02-18 18:00:21 -07:00
adapterremoval Refactor adapterremoval (#1491) 2022-04-04 21:40:35 +02:00
adapterremovalfixprefix Add AdapterRemovalFixPrefix (#1424) 2022-03-21 11:26:12 +01:00
agrvate Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
allelecounter Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
ampir Add file name collision check + TSV output 2022-06-10 12:54:39 +02:00
amplify/predict add module AMPlify (#1498) 2022-04-20 11:53:26 +02:00
amps Untar unzip meta (#1408) 2022-03-21 14:49:28 +01:00
amrfinderplus Amrfinderplus: add db-version to versions.yml (#1899) 2022-07-19 09:52:36 +02:00
antismash Apply suggestions from code review 2022-05-12 15:28:19 +02:00
ariba add module for ariba (#1731) 2022-06-15 10:18:31 -06:00
arriba Update Arriba to 2.3.0 (#1827) 2022-06-29 14:39:13 +02:00
artic Bump tool versions for modules required in viralrecon (#1859) 2022-07-07 14:48:04 +01:00
ascat Added output files to ASCAT (#1820) 2022-06-28 14:45:57 +02:00
assemblyscan Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
ataqv Ataqv mkarv (#1857) 2022-07-07 22:40:31 +02:00
atlas New Module: atlas/recal (#1915) 2022-07-22 15:36:53 +02:00
bakta update bakta to latest version (v1.4.0) (#1428) 2022-03-24 10:49:17 -06:00
bamaligncleaner Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
bamcmp bamcmp (#1244) 2022-02-02 16:38:41 +00:00
bamtools Update tests/modules/bamtools/split/test.yml 2022-04-22 19:35:34 +02:00
bamutil/trimbam Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
bandage/image Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
bbmap New module - BBMap clumpify (#1978) 2022-09-05 08:23:08 +02:00
bcftools update for bcftools merge (#1908) 2022-07-20 11:22:51 +02:00
bcl2fastq Module/bcl2fastq (#1883) 2022-07-14 13:18:21 +02:00
bclconvert bump bclconvert version (#1806) 2022-06-24 07:14:42 +02:00
bedtools added bedtools split 2022-05-17 14:24:32 +02:00
biobambam bamsormadup: add extra test case, fix single file input (#1905) 2022-07-19 13:52:37 +02:00
biscuit Add core Biscuit tools (#1354) 2022-03-14 09:34:22 -04:00
bismark Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
blast Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
bowtie Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
bowtie2 add PE sorted test 2022-05-13 19:16:50 +02:00
bracken Add bracken/combinebrackenoutputs (#2022) 2022-09-07 09:18:21 +02:00
busco Update busco to v5.4.3 and tar small files (#1970) 2022-08-30 10:25:01 +02:00
bwa Samtools version update (#1507) 2022-04-11 14:26:28 +02:00
bwamem2 Added support for meta in bwamem2/index (#1921) 2022-07-26 21:48:47 +01:00
bwameth Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
cat add stub for cat/fastq (#1943) 2022-08-09 09:18:37 +02:00
cellranger Remove empty file md5sum 2022-06-10 11:53:28 +02:00
centrifuge Update module: Use report insted of results for centrifuge/kreport (#1929) 2022-07-27 14:24:06 +02:00
checkm/lineagewf Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
chromap Samtools version update (#1507) 2022-04-11 14:26:28 +02:00
clonalframeml Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
cmseq/polymut Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
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 (#1504) 2022-04-08 11:43:40 +02:00
cooler Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
csvtk Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
custom Upgraded getchromsizes to support meta and output the gzi index (#2046) 2022-09-12 13:17:13 +01:00
cutadapt Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
damageprofiler Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
dastool Update DASTool to 1.1.4 (#1471) 2022-04-01 11:33:07 +02:00
dedup Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
deeparg Deeparg singularity container fix 2 (#1406) 2022-03-18 16:21:55 +01:00
deepbgc new module: deepbgc/pipeline (#2014) 2022-09-07 14:59:01 +02:00
deeptools changed container + add cram2bam conversion 2022-06-02 10:38:05 +02:00
deepvariant Update version & add intervals usage (#1214) 2022-01-17 16:40:31 +01:00
delly/call Another update to delly/call (#2011) 2022-09-05 16:06:56 +02:00
diamond Update DIAMOND module to output log file (#1879) 2022-07-14 16:18:28 +02:00
dragmap Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
dragonflye Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
dshbio Update dsh-bio to version 2.0.7, add support for compressed GFA 1.0 format (#1207) 2022-01-17 09:24:40 +00:00
ectyper Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
eido Add eido/convert module (#2051) 2022-09-13 12:17:29 -04:00
elprep Merge remote-tracking branch 'origin' into motus_profile 2022-05-05 09:41:13 -04:00
emmtyper Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
ensemblvep update ensemblvep to 106.1 and cache to 106 (#1876) 2022-07-13 13:43:03 +02:00
entrezdirect new (fixed) module: entrezdirect/esearch (#1927) 2022-07-26 09:07:38 -06:00
epang epang: Output gzipped jplace (#2037) 2022-09-09 09:54:03 +02:00
expansionhunter add stub to modules used in raredisease pipeline (#1206) 2022-03-28 17:48:39 +02:00
faqcs Faqcs patch to add tests for --debug output (#1368) 2022-03-02 08:53:05 -05:00
fargene takes gunzip out of fargene main.nf (#1090) 2021-11-29 14:32:23 +01:00
fastani Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
fastawindows New module: fasta_windows (#1956) 2022-09-09 08:41:38 +01:00
fastk Add FastK/Merge (#1828) 2022-06-29 18:04:36 +02:00
fastp Fix duplicated input in single-end fastp command (#2034) 2022-09-09 11:08:52 +02:00
fastqc Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
fastqscan Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
fasttree Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
ffq Add ffq module (#1842) 2022-07-01 08:59:13 +02:00
fgbio Fgbio/fastqtobam (#1980) 2022-09-05 11:57:55 +02:00
filtlong Update filtlong module to output log file (#1873) 2022-07-12 17:05:31 +02:00
flash Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
flye Add new module: Flye (#1164) 2022-06-30 22:45:55 +02:00
fq/lint Added fq/lint module (#1968) 2022-08-24 10:20:39 +02:00
freebayes Update intervals (#1278) 2022-02-10 10:34:22 +01:00
gamma/gamma fixed test.yml 2022-05-24 19:27:09 -04:00
gappa/examinegraft Add gappa/examinegraft (#2035) 2022-09-09 09:26:41 +02:00
gatk Add GATK indelrealigner tests 2022-06-08 21:14:08 +02:00
gatk4 new module gatk4/collectsvevidence (#2039) 2022-09-09 10:58:47 +02:00
gecco/run Add gecco/run module (#1790) 2022-06-22 13:43:45 +02:00
genescopefk Add GeneScopeFK (#1781) 2022-06-14 20:49:06 +02:00
genmap Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
genmod update options (#1959) 2022-08-22 16:26:05 +02:00
genomescope2 Update tests/modules/genomescope2/test.yml 2022-05-13 11:27:42 +02:00
genrich Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
gffread Replace remaining task.ext.suffix with task.ext.prefix (#1117) 2021-12-07 15:00:43 +01:00
glimpse/chunk Creation of Glimpse Chunk (#1985) 2022-09-01 10:01:49 +02:00
glnexus Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
goat/taxonsearch Add module: goat/taxonsearch (#1866) 2022-08-18 08:34:58 -06:00
graphmap2 Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
gstama New Module: gstama/polyacleanup (#1468) 2022-03-31 09:11:51 -04:00
gtdbtk/classifywf Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
gubbins Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
gunc Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
gunzip Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
gvcftools/extractvariants added gvcftools/extractvariants (#1924) 2022-07-25 13:30:35 +02:00
hamronization Add module hamronization/abricate (#1925) 2022-07-26 12:55:53 +02:00
haplocheck fix: string interpolation and test input access 2022-06-08 09:08:59 -03:00
happy Merge remote-tracking branch 'origin' into motus_profile 2022-05-05 09:41:13 -04:00
hicap Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
hifiasm Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
hisat2 Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
hmmcopy hmmcopy/mapCounter (#1175) 2021-12-17 15:39:50 +00:00
hmmer Add hmmer/eslreformat (#2009) 2022-09-05 15:21:09 +02:00
hmtnote Update main.nf 2022-05-16 15:20:15 +00:00
homer Fix homer/maketagdirectory output collision (#1456) 2022-03-27 03:17:42 +00:00
hpsuissero add module for hpsuisero (#1331) 2022-02-27 17:58:35 -07:00
ichorcna Prettier (#1405) 2022-03-18 14:27:50 +01:00
idr Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
imputeme/vcftoprs Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
instrain/profile Instrain profile (#1822) 2022-06-30 18:44:41 +02:00
iqtree Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
ismapper Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +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 Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
kaiju Add KAIJU2KRONA module (#1800) 2022-06-23 16:38:50 +00:00
kallisto/index add stub for kallisto/index (#1944) 2022-08-09 09:23:55 +02:00
kallistobustools Improved kbtools/count (#1884) 2022-07-14 14:27:56 +02:00
kat/hist Update tests/modules/kat/hist/test.yml 2022-05-23 08:51:49 +02:00
khmer Add khmer unique-kmers.py module (#1838) 2022-06-30 16:23:30 +01:00
kleborate Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
kraken2/kraken2 update to kraken2: breaking change - output channels renamed (#1525) 2022-04-21 14:33:59 +02:00
krakentools Update KRAKENTOOLS/COMBINEKREPORTS (#2043) 2022-09-13 14:31:27 +02:00
krona Fix Krona ktimporttaxonomy to allow multiple input files and simplifies database input (#1841) 2022-07-01 15:18:29 +02:00
last Untar unzip meta (#1408) 2022-03-21 14:49:28 +01:00
leehom Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +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 Add new module macrel/contigs (#1109) 2021-12-09 13:17:50 +01:00
macs2/callpeak Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
mafft Add MAFFT module (#1351) 2022-02-28 00:40:24 -07:00
malt Update MALT to older version due to major bug in most recent version (#1796) 2022-06-20 08:20:22 +02:00
maltextract Untar unzip meta (#1408) 2022-03-21 14:49:28 +01:00
manta Update tests/modules/manta/convertinversion/main.nf 2022-06-13 09:26:35 +02:00
mapdamage2 Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
mash Patch mash screen 2022-05-25 12:29:14 +00:00
mashtree Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
maxbin2 Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
maxquant/lfq corrected typos 2022-02-07 13:07:16 +01:00
mcroni add module for mcroni (#1750) 2022-06-13 15:04:01 +02:00
md5sum new module: md5sum 2022-05-06 09:20:40 +02:00
medaka Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
megahit Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
megan Add MEGAN/DAA2INFO (#1848) 2022-07-05 09:36:22 +02:00
meningotype Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
merqury Add Merqury (#1647) 2022-07-14 10:38:50 +02:00
merquryfk Add MerquryFK KatGC (#1798) 2022-06-23 20:57:15 +02:00
meryl Merge branch 'master' into meryl_unionsum 2022-05-09 16:16:08 +02:00
metabat2 Update metabat2 output channels and compression (#1111) 2021-12-09 15:00:32 +01:00
metaphlan3 Update METAPHLAN3/MERGEMETAPHLANTABLES (#2041) 2022-09-13 14:37:46 +02:00
methyldackel Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
minia Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
miniasm Change syntax from task.ext.suffix to tast.ext.prefix in all modules (#1110) 2021-12-02 12:39:55 +00:00
minimap2 Added the meta map to minimap2/index (#1934) 2022-09-08 09:27:14 +01:00
mlst Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
mobsuite/recon add mobsuite_recon module (#1270) 2022-02-18 17:52:38 -07:00
mosdepth Update main.nf 2022-05-25 19:38:12 +01:00
motus Update MOTUS/PROFILE module to output log file (#1871) 2022-07-13 11:26:27 +02:00
msisensor Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
msisensor2 1976 msisensor2 (#1977) 2022-09-05 13:00:18 +02:00
msisensorpro Add msisensorpro (#1267) 2022-02-09 21:05:49 +01:00
mtnucratio Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
multiqc Update MultiQC to re-add staging logos as a separate input channel (#2032) 2022-09-08 12:36:15 +02:00
multivcfanalyzer Add MultiVCFAnalyzer (#1845) 2022-07-05 09:47:10 +02:00
mummer Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
muscle Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
nanolyse Change syntax from task.ext.suffix to tast.ext.prefix in all modules (#1110) 2021-12-02 12:39:55 +00:00
nanoplot Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
ncbigenomedownload Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
nextclade Bump tool versions for modules required in viralrecon (#1859) 2022-07-07 14:48:04 +01:00
ngmaster Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
ngscheckmate/ncm New module: NGSCheckMate (#1290) 2022-03-11 09:02:10 +00:00
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 Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
pairtools Change syntax from task.ext.suffix to tast.ext.prefix in all modules (#1110) 2021-12-02 12:39:55 +00:00
panaroo/run add module for panaroo, fix pirate tests (#1444) 2022-03-24 20:11:04 -06:00
pangolin Bump tool versions for modules required in viralrecon (#1859) 2022-07-07 14:48:04 +01:00
paraclu Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
pasty add module for pasty (#2003) 2022-09-07 09:29:28 -06:00
pbbam/pbmerge Change syntax from task.ext.suffix to tast.ext.prefix in all modules (#1110) 2021-12-02 12:39:55 +00:00
pbccs Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
pbptyper add module for pbptyper (#2005) 2022-09-07 15:29:03 -06:00
pear Add new module: Pear (#1779) 2022-07-15 10:28:31 +02:00
peddy Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
phantompeakqualtools Add task.ext.args to phantompeakqualtools and finish the module (#1474) 2022-03-31 22:59:21 +01:00
phyloflash Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
picard new module: Picard/fastqtosam (#1911) 2022-08-30 14:27:00 +02:00
pints/caller feat(pints): Add initial caller module (#1983) 2022-08-31 14:04:48 +00:00
pirate add module for panaroo, fix pirate tests (#1444) 2022-03-24 20:11:04 -06:00
plasmidfinder add module for plasmidfinder (#1773) 2022-06-15 10:25:51 -06:00
plasmidid Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
plink Change syntax from task.ext.suffix to tast.ext.prefix in all modules (#1110) 2021-12-02 12:39:55 +00:00
plink2 implement plink2/score module (#1259) 2022-03-07 13:02:40 -05:00
pmdtools/filter Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
porechop Update PORECHOP module to output log file (#1870) 2022-07-12 16:07:31 +02:00
preseq Split preseq lcextrap and ccurve (#1440) 2022-03-25 17:11:40 +00:00
prinseqplusplus Add PRINSEQPLUSPLUS (#1481) 2022-04-03 16:06:22 +02:00
prodigal Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
prokka Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
pycoqc Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
pydamage Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +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 Bump tool versions for modules required in viralrecon (#1859) 2022-07-07 14:48:04 +01:00
racon Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
rapidnj Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
rasusa Change syntax from task.ext.suffix to tast.ext.prefix in all modules (#1110) 2021-12-02 12:39:55 +00:00
raven Raven assembler (#1087) 2022-02-01 11:47:01 +01:00
raxmlng Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
rgi/main Update RGI: add database version reporting to module (#1824) 2022-06-29 16:30:51 -06:00
rhocall/annotate update test 2022-06-08 16:36:02 +02:00
rmarkdownnotebook Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
roary Update test.yml (#1419) 2022-03-19 15:06:21 +00:00
rsem Bump STAR version to 2.7.10a for RSEM modules (#1573) 2022-04-27 19:21:26 +01:00
rseqc Provide BAI when running rseqc/tin (#1177) 2021-12-17 10:00:09 +00:00
rtgtools new module rtgtools/pedfilter (#1777) 2022-06-14 16:02:18 +02:00
salmon Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
samblaster Samtools version update (#1507) 2022-04-11 14:26:28 +02:00
samtools Added the optional .gzi output of "samtools faidx" (#1935) 2022-09-08 13:35:23 +01:00
scoary Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
scramble New module: scramble (#2015) 2022-09-07 13:19:18 +02:00
seacr/callpeak Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
seqkit feat: add module for seqkit stats (#1466) 2022-03-30 23:01:17 +02:00
seqsero2 Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
seqtk Decrease indent in seqtk/seq versions.yml output (#1384) 2022-03-09 11:56:35 -05:00
sequenzautils Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
seqwish/induce Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
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 make prettier 2022-04-21 12:55:56 -06:00
shovill Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
sistr add module for sistr (#1323) 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 snapaligner: improve index detection (#1836) 2022-06-30 12:19:46 +02:00
snippy add snippy/core module (#1855) 2022-09-08 06:58:10 +02:00
snpdists Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
snpeff DRAFT: Extend output from snpeff (#1895) 2022-07-16 20:08:52 +02:00
snpsift/split Added new module snpsift/split (#1031) 2021-12-17 09:08:14 +01:00
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 Bump tool versions for modules required in viralrecon (#1859) 2022-07-07 14:48:04 +01:00
spatyper Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
sratools refactor: require NCBI user settings always 2022-05-11 13:02:52 +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 (#1329) 2022-02-27 20:04:03 -07:00
stadeniolib/scramble new tool: staden_io_lib (#1499) 2022-04-08 09:54:15 -04:00
staphopiasccmec Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
star Add stub star align genomegenerate (#1948) 2022-08-09 09:42:19 +02:00
stranger add stubs for stranger (#1543) 2022-04-22 10:10:43 +02:00
strelka Update intervals (#1278) 2022-02-10 10:34:22 +01:00
stringtie add stub for stringtie (#1949) 2022-08-09 10:11:37 +02:00
subread/featurecounts Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
svdb SVDB_MERGE bgzip (#1910) 2022-07-20 10:54:06 +02:00
svtk/standardize new module: svtk/standardize (#2031) 2022-09-08 15:03:08 +02:00
tabix fix bgziptabix extension (#1784) 2022-06-15 10:33:10 +02:00
tailfindr Tailfindr (#1904) 2022-07-22 16:20:53 +02:00
tbprofiler/profile Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
tiddit TIDDIT - add --skip_assembly when no bwa specified (#1769) 2022-06-13 17:02:59 +02:00
transdecoder Transdecoder predict (#1251) 2022-02-02 09:46:07 +01:00
trimgalore Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
trimmomatic Trimmomatic (#1757) 2022-06-17 13:18:15 +00:00
ucsc bedToBigBed AutoSql option (#1981) 2022-09-09 09:27:47 +01:00
ultra New modules: ultra/index and ultra/align (#1830) 2022-07-04 07:46:49 +01:00
umitools Fix Conda tests 2022-05-23 22:39:12 +01:00
unicycler Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
untar Update UNTAR to account for file-only or multi-directory tar archives (#2055) 2022-09-14 10:40:45 +02:00
unzip Untar unzip meta (#1408) 2022-03-21 14:49:28 +01:00
vardictjava Added java options to vardict java (#1695) 2022-08-10 14:13:03 +02:00
variantbam Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
vcf2db new module vcf2db (#1795) 2022-06-17 15:54:02 +02:00
vcf2maf vcf2maf module with built in VEP (#1768) 2022-06-20 18:27:12 +02:00
vcfanno small changes to vcfanno (#1804) 2022-06-24 08:58:26 +02:00
vcflib/vcfuniq Bump tool versions for modules required in viralrecon (#1859) 2022-07-07 14:48:04 +01:00
vcftools Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
vsearch/usearchglobal prettier 2022-05-30 13:35:12 +02:00
whamg New module: Whamg (#1994) 2022-09-02 13:33:48 +02:00
yara Add samtools index to yara_mapper module (#1353) 2022-03-04 10:08:02 -05:00