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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 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 Refactor adapterremoval (#1491) 2022-04-04 21:40:35 +02:00
adapterremovalfixprefix Update manual versioning (#1813) 2022-06-27 10:35:41 +02:00
agrvate Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
allelecounter fix incorrect yaml formatting. (#1264) 2022-04-14 13:35:01 +02:00
ampir Apply suggestions from code review 2022-06-10 14:46:58 +02:00
amplify/predict Update manual versioning (#1813) 2022-06-27 10:35:41 +02:00
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
antismash antismashlite: Support GBK input (#1840) 2022-07-01 09:29:53 +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 Add manual version definition for artic modules (#1867) 2022-07-12 11:33:51 +01:00
ascat Added output files to ASCAT (#1820) 2022-06-28 14:45:57 +02:00
assemblyscan Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +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 Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
bamcmp Update manual versioning (#1813) 2022-06-27 10:35:41 +02:00
bamtools Remove a blank line (#1793) 2022-06-17 10:58:24 +01:00
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 Improve descriptions for modules with missing 2022-07-06 12:03:08 +02:00
bcftools Bump tool versions for modules required in viralrecon (#1859) 2022-07-07 14:48:04 +01:00
bclconvert bclconvert: Update Dockerfile (#1819) 2022-06-28 11:11:16 +01:00
bedtools added bedtools split 2022-05-17 14:24:32 +02:00
biobambam replace regex with fixed extensions 2022-05-17 09:54:06 +02:00
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 Improve descriptions for modules with missing 2022-07-06 12:03:08 +02:00
bowtie2 Improve descriptions for modules with missing 2022-07-06 12:03:08 +02:00
bracken/bracken Add bracken (#1423) 2022-03-22 16:40:21 +01:00
busco Update meta.yml 2022-05-06 11:56:43 +00:00
bwa feat: remove read_group which should be set up with task.ext.args (#1521) 2022-04-13 14:30:34 +02:00
bwamem2 feat: remove read_group which should be set up with task.ext.args (#1521) 2022-04-13 14:30:34 +02:00
bwameth Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
cat Replace vanilla Linux Biocontainer with Ubuntu (#1557) 2022-04-22 14:50:07 +01:00
cellranger Bugfix for CellRanger Dockerfile (#1812) 2022-06-27 11:07:33 +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 Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
cmseq/polymut Update manual versioning (#1813) 2022-06-27 10:35:41 +02:00
cnvkit added fasta_fai as input + changed if statements 2022-06-02 12:57:50 +02:00
cnvpytor removed extra ) in the version strings (#1850) 2022-07-05 15:24:08 +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 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 Bump tool versions for modules required in viralrecon (#1859) 2022-07-07 14:48:04 +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 DASTool output channels update (#1489) 2022-04-04 13:31:36 +02:00
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 changed container + add cram2bam conversion 2022-06-02 10:38:05 +02:00
deepvariant Revert recent changes made to some of the modules (#1463) 2022-03-30 20:21:06 +02:00
delly/call Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
diamond Merge remote-tracking branch 'origin' into motus_profile 2022-05-05 09:41:13 -04:00
dragmap feat: remove read_group which should be set up with task.ext.args (#1521) 2022-04-13 14:30:34 +02:00
dragonflye Update dragonflye to latest version (#1442) 2022-03-24 14:56:32 -04:00
dshbio Update dsh-bio to version 2.0.8. (#1483) 2022-04-09 11:13:47 -05:00
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 Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
ensemblvep Same version on conda and in the dockerfile (#1791) 2022-06-16 16:25:54 +02:00
expansionhunter Improve descriptions for modules with missing 2022-07-06 12:03:08 +02:00
faqcs Prettier (#1405) 2022-03-18 14:27:50 +01:00
fargene Update manual versioning (#1813) 2022-06-27 10:35:41 +02:00
fastani Improve descriptions for modules with missing 2022-07-06 12:03:08 +02:00
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 add stub to modules used in raredisease pipeline (#1206) 2022-03-28 17:48:39 +02:00
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
ffq Add ffq module (#1842) 2022-07-01 08:59:13 +02:00
fgbio This updates the fgbio container version (#1863) 2022-07-11 16:17:54 +02:00
filtlong Actually add the changes 2022-05-31 15:49:57 +02:00
flash Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
flye Add new module: Flye (#1164) 2022-06-30 22:45:55 +02:00
freebayes Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
gamma/gamma Update manual versioning (#1813) 2022-06-27 10:35:41 +02:00
gatk Apply suggestions from code review 2022-06-09 08:33:37 +02:00
gatk4 Improve descriptions for modules with missing 2022-07-06 12:03:08 +02:00
gecco/run Add gecco/run module (#1790) 2022-06-22 13:43:45 +02:00
genescopefk Update manual versioning (#1813) 2022-06-27 10:35:41 +02:00
genmap Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
genomescope2 Update outputs and test data set 2022-05-11 10:42:17 +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 add stub to modules used in raredisease pipeline (#1206) 2022-03-28 17:48:39 +02:00
graphmap2 Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
gstama Adjust requested ressources for gstama/merge, isoseq3/refine, lima, ultra/align (#1858) 2022-07-07 11:10:18 +01:00
gtdbtk/classifywf Update manual versioning (#1813) 2022-06-27 10:35:41 +02:00
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 Add stub run to gunzip module (#1849) 2022-07-04 17:33:55 +02:00
hamronization new module hamronization/rgi (#1844) 2022-07-01 12:03:08 +02:00
haplocheck fix: stub output name 2022-06-08 10:10:24 -03:00
happy Update manual versioning (#1813) 2022-06-27 10:35:41 +02:00
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 Update manual versioning (#1813) 2022-06-27 10:35:41 +02:00
hmmcopy Update manual versioning (#1813) 2022-06-27 10:35:41 +02:00
hmmer Prettier (#1405) 2022-03-18 14:27:50 +01:00
hmtnote Update main.nf 2022-05-16 15:20:15 +00:00
homer Update manual versioning (#1813) 2022-06-27 10:35:41 +02:00
hpsuissero Update manual versioning (#1813) 2022-06-27 10:35:41 +02:00
ichorcna Update manual versioning (#1813) 2022-06-27 10:35:41 +02:00
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
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 Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
isoseq3 Adjust requested ressources for gstama/merge, isoseq3/refine, lima, ultra/align (#1858) 2022-07-07 11:10:18 +01:00
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
kaiju Add KAIJU2KRONA module (#1800) 2022-06-23 16:38:50 +00:00
kallisto/index Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
kallistobustools diminish memory demand (#1872) 2022-07-12 15:53:02 +02:00
kat/hist Add module kat hist 2022-05-06 07:54:10 +00:00
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 Update manual versioning (#1813) 2022-06-27 10:35:41 +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 Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
leehom Update manual versioning (#1813) 2022-06-27 10:35:41 +02:00
legsta Prettier (#1405) 2022-03-18 14:27:50 +01:00
lima Adjust requested ressources for gstama/merge, isoseq3/refine, lima, ultra/align (#1858) 2022-07-07 11:10:18 +01:00
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 Update MALT to older version due to major bug in most recent version (#1796) 2022-06-20 08:20:22 +02:00
maltextract Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
manta Update modules/manta/convertinversion/main.nf 2022-06-13 09:26:29 +02:00
mapdamage2 Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
mash Patch mash screen 2022-05-25 12:29:14 +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
maxquant/lfq ran prettier 2022-05-16 14:30:40 +02:00
mcroni Update manual versioning (#1813) 2022-06-27 10:35:41 +02:00
md5sum fix software definitions 2022-05-06 11:07:05 +02:00
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
megan Add MEGAN/DAA2INFO (#1848) 2022-07-05 09:36:22 +02:00
meningotype Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
merquryfk Update manual versioning (#1813) 2022-06-27 10:35:41 +02:00
meryl Merge branch 'master' into meryl_unionsum 2022-05-09 16:16:08 +02:00
metabat2 Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
metaphlan3 Merge remote-tracking branch 'origin' into motus_profile 2022-05-05 09:41:13 -04:00
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 Merge remote-tracking branch 'origin' into motus_profile 2022-05-05 09:41:13 -04:00
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 Update main.nf 2022-05-25 19:42:15 +01:00
motus Add MOTUS/MERGE (#1734) 2022-07-07 09:47:41 +02:00
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 MultiQC conda (#1856) 2022-07-06 10:16:34 +02:00
multivcfanalyzer Add MultiVCFAnalyzer (#1845) 2022-07-05 09:47:10 +02:00
mummer Update manual versioning (#1813) 2022-06-27 10:35:41 +02:00
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 Bump tool versions for modules required in viralrecon (#1859) 2022-07-07 14:48:04 +01:00
ncbigenomedownload Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
nextclade Bump tool versions for modules required in viralrecon (#1859) 2022-07-07 14:48:04 +01:00
ngmaster Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
ngscheckmate/ncm NGSCheckMate doesn't generate a pdf for only one sample, made optional output (#1839) 2022-06-30 17:43:34 +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 Bump tool versions for modules required in viralrecon (#1859) 2022-07-07 14:48:04 +01:00
paraclu Update manual versioning (#1813) 2022-06-27 10:35:41 +02:00
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 Update manual versioning (#1813) 2022-06-27 10:35:41 +02:00
phyloflash Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +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 Update manual versioning (#1813) 2022-06-27 10:35:41 +02:00
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
prinseqplusplus Add PRINSEQPLUSPLUS (#1481) 2022-04-03 16:06:22 +02:00
prodigal fix yml formatting (#1263) 2022-02-07 18:16:43 +01:00
prokka Prokka: Fix typo in variable name (#1846) 2022-07-04 15:04:59 +02:00
pycoqc Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
pydamage Update PyDamage module (#1467) 2022-03-31 09:18:18 -04:00
qcat Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
qualimap Samtools version update (#1507) 2022-04-11 14:26:28 +02:00
quast Bump tool versions for modules required in viralrecon (#1859) 2022-07-07 14:48:04 +01:00
racon Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
rapidnj Update manual versioning (#1813) 2022-06-27 10:35:41 +02:00
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 Update RGI: add database version reporting to module (#1824) 2022-06-29 16:30:51 -06:00
rhocall/annotate fix versions.yaml 2022-06-07 14:43:35 +02:00
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 Bump STAR version to 2.7.10a for RSEM modules (#1573) 2022-04-27 19:21:26 +01:00
rseqc Change label for rseqc/tin to process_high (#1327) 2022-02-21 13:26:51 +00:00
rtgtools new module rtgtools/pedfilter (#1777) 2022-06-14 16:02:18 +02:00
salmon Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
samblaster Samtools version update (#1507) 2022-04-11 14:26:28 +02:00
samtools Improve descriptions for modules with missing 2022-07-06 12:03:08 +02:00
scoary Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
seacr/callpeak Update manual versioning (#1813) 2022-06-27 10:35:41 +02:00
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 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 Update manual versioning (#1813) 2022-06-27 10:35:41 +02:00
sexdeterrmine Apply suggestions from code review 2022-06-10 11:03:01 +02:00
shasum fix software definitions 2022-05-06 11:07:05 +02:00
shigatyper Merge remote-tracking branch 'origin' into motus_profile 2022-05-05 09:41:13 -04:00
shovill Add when: block (#1261) 2022-02-04 09:53:32 +01:00
sistr Prettier (#1405) 2022-03-18 14:27:50 +01:00
slimfastq Update manual versioning (#1813) 2022-06-27 10:35:41 +02:00
snapaligner snapaligner: improve index detection (#1836) 2022-06-30 12:19:46 +02:00
snippy/run Update main.nf 2022-06-03 13:05:43 -06:00
snpdists Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
snpeff Merge remote-tracking branch 'origin' into motus_profile 2022-05-05 09:41:13 -04:00
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 Bump tool versions for modules required in viralrecon (#1859) 2022-07-07 14:48:04 +01:00
spatyper Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +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 Update manual versioning (#1813) 2022-06-27 10:35:41 +02:00
stadeniolib/scramble new tool: staden_io_lib (#1499) 2022-04-08 09:54:15 -04:00
staphopiasccmec Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
star Bump container version for STAR to 2.7.10a 2022-05-27 11:35:04 +01:00
stranger add stubs for stranger (#1543) 2022-04-22 10:10:43 +02:00
strelka Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
stringtie Rename process from STRINGTIE to STRINGTIE_STRINGTIE (#1546) 2022-04-22 15:13:06 +01:00
subread/featurecounts Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
svdb update svdb version 2022-05-06 00:18:16 +02:00
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 Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
trimgalore Add Trimgalore output for unpaired reads (#1568) 2022-04-26 19:15:24 +01:00
trimmomatic Trimmomatic (#1757) 2022-06-17 13:18:15 +00:00
ucsc Update manual versioning (#1813) 2022-06-27 10:35:41 +02:00
ultra Adjust requested ressources for gstama/merge, isoseq3/refine, lima, ultra/align (#1858) 2022-07-07 11:10:18 +01:00
umitools Set randomseed for UMI tools if not otherwise set (#1837) 2022-06-30 16:30:38 +01:00
unicycler Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +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 Update manual versioning (#1813) 2022-06-27 10:35:41 +02:00
variantbam Update manual versioning (#1813) 2022-06-27 10:35:41 +02:00
vcf2db Update manual versioning (#1813) 2022-06-27 10:35:41 +02:00
vcf2maf Update manual versioning (#1813) 2022-06-27 10:35:41 +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 Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
vsearch/usearchglobal Merge branch 'vsearch_usearch_global' of https://github.com/jtangrot/nf-core_modules into vsearch_usearch_global 2022-05-30 13:05:00 +02:00
yara Samtools version update (#1507) 2022-04-11 14:26:28 +02:00