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nf-core_modules/modules
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Daniel Lundin 74b569b66a
Add epang/place (#2023) 
* Created epang module from template

* Module seems to be working

* Namechange to epang_place

* Move model to meta map

* Fix linting problems

* Prettier

* Forgot --threads!

* Moved module to epang

* Move reference file params

* Directory output

* Make all args optional

* Added inputs for three other types of file arguments

* Update modules/epang/main.nf

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>

* Add directory to output doc, reorder the other

* Make model specification less hardcoded

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
2022-09-08 10:05:57 +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 Amrfinderplus add tool and db version as output (#1912) 2022-07-20 11:55:44 +02:00
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 New Module: atlas/recal (#1915) 2022-07-22 15:36:53 +02:00
bakta [update] bump Bakta to 1.5.0 (#2000) 2022-09-02 15:15:12 -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 New module - BBMap clumpify (#1978) 2022-09-05 08:23:08 +02:00
bcftools Reduce resource requests (#2021) 2022-09-07 10:33:05 +02:00
bcl2fastq Module/bcl2fastq (#1883) 2022-07-14 13:18:21 +02:00
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 bamsormadup: add extra test case, fix single file input (#1905) 2022-07-19 13:52:37 +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 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 feat: remove read_group which should be set up with task.ext.args (#1521) 2022-04-13 14:30:34 +02:00
bwamem2 typo in bwamem2 index meta.yml (#1963) 2022-08-24 10:31:05 +02:00
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 Bugfix for CellRanger Dockerfile (#1812) 2022-06-27 11:07:33 +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 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 Reduce resource requests (#2021) 2022-09-07 10:33:05 +02:00
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
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 Revert recent changes made to some of the modules (#1463) 2022-03-30 20:21:06 +02:00
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 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 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 Add epang/place (#2023) 2022-09-08 10:05:57 +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 module FASTP: Support for interleaved FASTQ (#1891) 2022-07-19 16:27:15 +01:00
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 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 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
fq/lint Added fq/lint module (#1968) 2022-08-24 10:20:39 +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 MD finally supports cram output (#2019) 2022-09-07 11:04:58 +02:00
gecco/run Update module: Gecco fix to no file generated if no hits found (#1930) 2022-07-27 15:19:43 +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
genmod update options (#1959) 2022-08-22 16:26:05 +02:00
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
glimpse/chunk Creation of Glimpse Chunk (#1985) 2022-09-01 10:01:49 +02:00
glnexus add stub to modules used in raredisease pipeline (#1206) 2022-03-28 17:48:39 +02:00
goat/taxonsearch Add module: goat/taxonsearch (#1866) 2022-08-18 08:34:58 -06:00
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
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: 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 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 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 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 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 Improves kraken2 output glob (#1987) 2022-08-31 15:42:44 +02:00
krakentools Add krakentools/combinekreports (#2018) 2022-09-06 11:32:30 -06:00
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 Reduce resource requests (#2021) 2022-09-07 10:33:05 +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
merqury Add Merqury (#1647) 2022-07-14 10:38:50 +02:00
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 Move MetaPhlAn3 to a subcommand and add mergemetaphlantables (#2026) 2022-09-07 21:58:03 +02:00
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 Update MOTUS/PROFILE module to output log file (#1871) 2022-07-13 11:26:27 +02:00
msisensor Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
msisensor2 1976 msisensor2 (#1977) 2022-09-05 13:00:18 +02:00
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 Modify MULTIQC: separate logo from config file (#2027) 2022-09-08 09:12:53 +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 Use a newer container version because the previous one is broken (#1933) 2022-08-22 11:18:09 +01:00
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
pasty add module for pasty (#2003) 2022-09-07 09:29:28 -06:00
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
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 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 new module: Picard/fastqtosam (#1911) 2022-08-30 14:27:00 +02:00
pints/caller fix(pints): Remove update check (#1989) 2022-09-08 05:03:48 +02:00
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 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 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 add stub for qualimap/rnaseq (#1946) 2022-08-09 15:24:35 +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 RGI/main export versions as explicit emission strings (#1909) 2022-07-20 10:33:53 +02:00
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 Reduce resource requests (#2021) 2022-09-07 10:33:05 +02:00
scoary Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
scramble New module: scramble (#2015) 2022-09-07 13:19:18 +02:00
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 add snippy/core module (#1855) 2022-09-08 06:58:10 +02:00
snpdists Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
snpeff DRAFT: Extend output from snpeff (#1895) 2022-07-16 20:08:52 +02:00
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 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 Reduce resource requests (#2021) 2022-09-07 10:33:05 +02:00
stringtie add stub for stringtie (#1949) 2022-08-09 10:11:37 +02:00
subread/featurecounts Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
svdb SVDB MERGE samtools version (#1913) 2022-07-20 12:42:40 +02:00
tabix Reduce resource requests (#2021) 2022-09-07 10:33:05 +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 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 Newer container version because the previous one is misconfigured (#1961) 2022-08-22 21:01:13 +01:00
ultra Adjust requested ressources for gstama/merge, isoseq3/refine, lima, ultra/align (#1858) 2022-07-07 11:10:18 +01:00
umitools Set PYTHONHASHSEED for umitools dedup (#1932) 2022-08-31 14:05:12 +01:00
unicycler Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
untar Reduce resource requests (#2021) 2022-09-07 10:33:05 +02:00
unzip Reduce resource requests (#2021) 2022-09-07 10:33:05 +02:00
vardictjava Added java options to vardict java (#1695) 2022-08-10 14:13:03 +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 Reduce resource requests (#2021) 2022-09-07 10:33:05 +02:00
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
whamg New module: Whamg (#1994) 2022-09-02 13:33:48 +02:00
yara Samtools version update (#1507) 2022-04-11 14:26:28 +02:00