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Felipe Marques de Almeida ec806cebf1
diminish memory demand (#1872) 
* diminish memory demand

Kallisto was being told to ask for the same amount of memory as it was said for nextflow to limit.

So, when kallisto tried to use it, nextflow was killing it. Thus, diminishing it per 1 GB solved the issue.

* fix prettier

* removing TODOs
2022-07-12 15:53:02 +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 add amrfinderplus module (#1284) 2022-02-19 23:02:23 +00:00
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 Add atlas/call (#1809) 2022-07-01 15:06:07 +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 Merge remote-tracking branch 'origin' into motus_profile 2022-05-05 09:41:13 -04:00
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 Samtools version update (#1507) 2022-04-11 14:26:28 +02:00
bcftools Bump tool versions for modules required in viralrecon (#1859) 2022-07-07 14:48:04 +01:00
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 fix config 2022-05-17 09:09:19 +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/bracken Add bracken (#1423) 2022-03-22 16:40:21 +01:00
busco Change busco multi-fasta test md5sum to contains 2022-06-13 08:51:41 +00:00
bwa Samtools version update (#1507) 2022-04-11 14:26:28 +02:00
bwamem2 Add new boolean sort_bam as input to be able to chose between sort and view in bwamem and bwamem2mem (#1125) 2021-12-08 14:31:27 +00:00
bwameth Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
cat Update cat module (#1469) 2022-03-31 13:42:44 +02:00
cellranger Remove empty file md5sum 2022-06-10 11:53:28 +02:00
centrifuge Add centrifuge_kreport module (#1514) 2022-04-13 15:33:51 +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 Bump tool versions for modules required in viralrecon (#1859) 2022-07-07 14:48:04 +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
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 Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
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 (#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
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 Optional output from the VEP-moduel (#1775) 2022-06-15 13:52:12 +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
fastk Add FastK/Merge (#1828) 2022-06-29 18:04:36 +02:00
fastp Proposal: Rename output from fastp module (#1802) 2022-06-24 10:01:14 +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 Added UMI sub-workflow (#1098) 2021-12-09 11:16:40 +01:00
filtlong Fix config for tests 2022-05-31 20:07:52 +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
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
gatk Add GATK indelrealigner tests 2022-06-08 21:14:08 +02:00
gatk4 Add module: gatk4/leftalignandtrimvariants (#1808) 2022-06-28 10:44:08 +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
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
glnexus Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
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
hamronization new module hamronization/rgi (#1844) 2022-07-01 12:03:08 +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 Prettier (#1405) 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 (#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 Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
kallistobustools diminish memory demand (#1872) 2022-07-12 15:53:02 +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/kreport2krona New module: krakentools/kreport2krona (#1746) 2022-06-13 20:14:44 +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
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 Untar unzip meta (#1408) 2022-03-21 14:49:28 +01:00
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 Update minimap2/align module (#1537) 2022-04-26 16:32:20 +02:00
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 Add MOTUS/MERGE (#1734) 2022-07-07 09:47:41 +02:00
msisensor Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
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 formatting 2022-06-08 14:42:58 +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
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
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 Bump tool versions for modules required in viralrecon (#1859) 2022-07-07 14:48:04 +01:00
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 Change syntax from task.ext.suffix to tast.ext.prefix in all modules (#1110) 2021-12-02 12:39:55 +00:00
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 samtools/*stats*: use prefix for outputs (#1788) 2022-06-16 13:42:01 +02:00
scoary Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
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 Merge remote-tracking branch 'origin' into motus_profile 2022-05-05 09:41:13 -04:00
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/run make prettier 2022-05-11 18:00:36 +00:00
snpdists Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
snpeff greatly simplify syntax (#1121) 2021-12-07 11:18:12 +01:00
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: 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 (#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 Fix tests 2022-05-27 12:14:10 +01:00
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 Rename process from STRINGTIE to STRINGTIE_STRINGTIE (#1546) 2022-04-22 15:13:06 +01:00
subread/featurecounts Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
svdb update svdb to version 2.5.2 (#1390) 2022-03-21 10:39:34 +01:00
tabix fix bgziptabix extension (#1784) 2022-06-15 10:33:10 +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 ucsc/wigtobigwig: add meta map (#1199) 2022-01-11 21:31:37 +00:00
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 fix untar output dir 2022-06-02 11:09:55 +02:00
unzip Untar unzip meta (#1408) 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 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
yara Add samtools index to yara_mapper module (#1353) 2022-03-04 10:08:02 -05:00