| .. |
|
abacas
|
Fix formatting in yaml files, add yamllint config (#1279)
|
2022-02-15 11:15:27 +00:00 |
|
abricate
|
Set process label to process_single for modules with no task.cpus usage (#2076)
|
2022-09-19 11:54:47 +02:00 |
|
adapterremoval
|
Refactor adapterremoval (#1491)
|
2022-04-04 21:40:35 +02:00 |
|
adapterremovalfixprefix
|
Set process label to process_single for modules with no task.cpus usage (#2076)
|
2022-09-19 11:54:47 +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
|
Set process label to process_single for modules with no task.cpus usage (#2076)
|
2022-09-19 11:54:47 +02:00 |
|
amplify/predict
|
Set process label to process_single for modules with no task.cpus usage (#2076)
|
2022-09-19 11:54:47 +02:00 |
|
amps
|
Fix formatting in yaml files, add yamllint config (#1279)
|
2022-02-15 11:15:27 +00:00 |
|
amrfinderplus
|
Set process label to process_single for modules with no task.cpus usage (#2076)
|
2022-09-19 11:54:47 +02:00 |
|
angsd/docounts
|
Add: ANGSD_DOCOUNTS (#2044)
|
2022-09-27 13:21:44 +02:00 |
|
antismash
|
Set process label to process_single for modules with no task.cpus usage (#2076)
|
2022-09-19 11:54:47 +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
|
Fix bakta: variable in main.nf (#2050)
|
2022-09-13 13:03:21 +02:00 |
|
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
|
Adding module bamtools stats (#2104)
|
2022-09-27 06:24:43 +01:00 |
|
bamutil/trimbam
|
Set process label to process_single for modules with no task.cpus usage (#2076)
|
2022-09-19 11:54:47 +02:00 |
|
bandage/image
|
Fix formatting in yaml files, add yamllint config (#1279)
|
2022-02-15 11:15:27 +00:00 |
|
bases2fastq
|
Add bases2fastq (#2054)
|
2022-09-15 13:50:33 +00:00 |
|
bbmap
|
New module - BBMap clumpify (#1978)
|
2022-09-05 08:23:08 +02:00 |
|
bcftools
|
Fix bcftools/stats module (#1953)
|
2022-09-21 16:10:38 +02:00 |
|
bcl2fastq
|
Module/bcl2fastq (#1883)
|
2022-07-14 13:18:21 +02:00 |
|
bclconvert
|
Bump bcl-convert version (#2077)
|
2022-09-16 14:34:52 +02:00 |
|
bedtools
|
Set process label to process_single for modules with no task.cpus usage (#2076)
|
2022-09-19 11:54:47 +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
|
Add blast/tblastn module (#2092)
|
2022-09-26 17:43:41 +02:00 |
|
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
|
Set process label to process_single for modules with no task.cpus usage (#2076)
|
2022-09-19 11:54:47 +02:00 |
|
bwamem2
|
Set process label to process_single for modules with no task.cpus usage (#2076)
|
2022-09-19 11:54:47 +02:00 |
|
bwameth
|
Fix formatting in yaml files, add yamllint config (#1279)
|
2022-02-15 11:15:27 +00:00 |
|
cat
|
bugfix: when there is a single input file, stageAs("?/*) returns the path directly, not in a list (#2114)
|
2022-09-28 13:28:52 +01:00 |
|
cellranger
|
Fixes incorrectly quoted tags (#2113)
|
2022-09-27 20:37:56 +01:00 |
|
centrifuge
|
Set process label to process_single for modules with no task.cpus usage (#2076)
|
2022-09-19 11:54:47 +02:00 |
|
checkm/lineagewf
|
Update checkM version and add support for pre-defined database (#2125)
|
2022-09-28 14:48:18 +02:00 |
|
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
|
Fix broken Quast module and bump MultiQC version in dumpsoftwareversions (#2108)
|
2022-09-27 09:35:52 +01:00 |
|
cutadapt
|
Fix formatting in yaml files, add yamllint config (#1279)
|
2022-02-15 11:15:27 +00:00 |
|
damageprofiler
|
Set process label to process_single for modules with no task.cpus usage (#2076)
|
2022-09-19 11:54:47 +02:00 |
|
dastool
|
Set process label to process_single for modules with no task.cpus usage (#2076)
|
2022-09-19 11:54:47 +02:00 |
|
dedup
|
Set process label to process_single for modules with no task.cpus usage (#2076)
|
2022-09-19 11:54:47 +02:00 |
|
deeparg
|
Set process label to process_single for modules with no task.cpus usage (#2076)
|
2022-09-19 11:54:47 +02:00 |
|
deepbgc
|
Set process label to process_single for modules with no task.cpus usage (#2076)
|
2022-09-19 11:54:47 +02:00 |
|
deeptools
|
changed container + add cram2bam conversion
|
2022-06-02 10:38:05 +02:00 |
|
deepvariant
|
Deepvariant - Update main.nf (#2110)
|
2022-09-27 15:34:10 +02:00 |
|
delly/call
|
updated the version of delly (#2105)
|
2022-09-27 08:57:36 +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 2.1 (#2100)
|
2022-09-26 10:41:33 +01:00 |
|
ectyper
|
Fix formatting in yaml files, add yamllint config (#1279)
|
2022-02-15 11:15:27 +00:00 |
|
eido
|
Fixes incorrectly quoted tags (#2113)
|
2022-09-27 20:37:56 +01:00 |
|
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 |
|
endorspy
|
New Module: endorspy (#1916)
|
2022-09-28 11:28:11 +02:00 |
|
ensemblvep
|
add stub and the option to compress output for vep (#2111)
|
2022-09-28 14:34:41 +02:00 |
|
entrezdirect
|
Set process label to process_single for modules with no task.cpus usage (#2076)
|
2022-09-19 11:54:47 +02:00 |
|
epang
|
Make epang output meta with the jplace channel (#2073)
|
2022-09-16 10:22:50 +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
|
Add HAMRONIZATION/FARGENE and updates all HARMONIZATION tools to 1.1.1 (#2107)
|
2022-09-27 15:32:18 +02:00 |
|
fastani
|
Improve descriptions for modules with missing
|
2022-07-06 12:03:08 +02:00 |
|
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
|
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 |
|
gappa
|
Adding gappa/examineheattree (#2084)
|
2022-09-22 15:51:25 +02:00 |
|
gatk
|
Set process label to process_single for modules with no task.cpus usage (#2076)
|
2022-09-19 11:54:47 +02:00 |
|
gatk4
|
Adding stubs to PicardLiftovervcf, GATK4_mergevcfs and filterMutectCalls (#1621)
|
2022-09-28 09:50:11 +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
|
Fixes incorrectly quoted tags (#2113)
|
2022-09-27 20:37:56 +01:00 |
|
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 |
|
genotyphi/parse
|
add module for mykrobe predict and genotyphi parse (#1818)
|
2022-09-26 15:18:04 +01:00 |
|
genrich
|
Fix formatting in yaml files, add yamllint config (#1279)
|
2022-02-15 11:15:27 +00:00 |
|
gfaffix
|
Adding new module gfaffix (#1149)
|
2022-09-28 10:23:18 +02:00 |
|
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
|
2012 bug related to species input in goattaxonsearch module (#2099)
|
2022-09-23 10:58:40 -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
|
Fixes incorrectly quoted tags (#2113)
|
2022-09-27 20:37:56 +01:00 |
|
gunzip
|
Set process label to process_single for modules with no task.cpus usage (#2076)
|
2022-09-19 11:54:47 +02:00 |
|
gvcftools/extractvariants
|
added gvcftools/extractvariants (#1924)
|
2022-07-25 13:30:35 +02:00 |
|
hamronization
|
Add HAMRONIZATION/FARGENE and updates all HARMONIZATION tools to 1.1.1 (#2107)
|
2022-09-27 15:32:18 +02:00 |
|
haplocheck
|
fix: stub output name
|
2022-06-08 10:10:24 -03:00 |
|
haplogrep2/classify
|
Add haplogrep2 (#2030)
|
2022-09-14 14:58:02 +02:00 |
|
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
|
Fixes incorrectly quoted tags (#2113)
|
2022-09-27 20:37:56 +01:00 |
|
hmmer
|
Fixes incorrectly quoted tags (#2113)
|
2022-09-27 20:37:56 +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
|
Set process label to process_single for modules with no task.cpus usage (#2076)
|
2022-09-19 11:54:47 +02:00 |
|
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
|
Set process label to process_single for modules with no task.cpus usage (#2076)
|
2022-09-19 11:54:47 +02:00 |
|
krona
|
Set process label to process_single for modules with no task.cpus usage (#2076)
|
2022-09-19 11:54:47 +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
|
Set process label to process_single for modules with no task.cpus usage (#2076)
|
2022-09-19 11:54:47 +02:00 |
|
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
|
Set process label to process_single for modules with no task.cpus usage (#2076)
|
2022-09-19 11:54:47 +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
|
Set process label to process_single for modules with no task.cpus usage (#2076)
|
2022-09-19 11:54:47 +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 Merqury version and sha (#2132)
|
2022-09-29 15:23:58 +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
|
Update METAPHLAN3_METAPHLAN3 to correct module name (#2056)
|
2022-09-15 09:09:55 +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
|
Added the meta map to minimap2/index (#1934)
|
2022-09-08 09:27:14 +01:00 |
|
mlst
|
Add args to mlst (#1962)
|
2022-09-26 15:48:35 +01:00 |
|
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
|
Set process label to process_single for modules with no task.cpus usage (#2076)
|
2022-09-19 11:54:47 +02:00 |
|
msisensor
|
Fix formatting in yaml files, add yamllint config (#1279)
|
2022-02-15 11:15:27 +00:00 |
|
msisensor2
|
Fixes incorrectly quoted tags (#2113)
|
2022-09-27 20:37:56 +01:00 |
|
msisensorpro
|
Prettier (#1405)
|
2022-03-18 14:27:50 +01:00 |
|
mtnucratio
|
Set process label to process_single for modules with no task.cpus usage (#2076)
|
2022-09-19 11:54:47 +02:00 |
|
multiqc
|
Set process label to process_single for modules with no task.cpus usage (#2076)
|
2022-09-19 11:54:47 +02:00 |
|
multivcfanalyzer
|
Fixes incorrectly quoted tags (#2113)
|
2022-09-27 20:37:56 +01:00 |
|
mummer
|
Update manual versioning (#1813)
|
2022-06-27 10:35:41 +02:00 |
|
muscle
|
Set process label to process_single for modules with no task.cpus usage (#2076)
|
2022-09-19 11:54:47 +02:00 |
|
mykrobe/predict
|
add module for mykrobe predict and genotyphi parse (#1818)
|
2022-09-26 15:18:04 +01:00 |
|
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 |
|
nextgenmap
|
New Module: NextGenMap (#1938)
|
2022-09-27 20:44:47 +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
|
Adding stubs to PicardLiftovervcf, GATK4_mergevcfs and filterMutectCalls (#1621)
|
2022-09-28 09:50:11 +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
|
Set process label to process_single for modules with no task.cpus usage (#2076)
|
2022-09-19 11:54:47 +02:00 |
|
prinseqplusplus
|
Add PRINSEQPLUSPLUS (#1481)
|
2022-04-03 16:06:22 +02:00 |
|
prodigal
|
Set process label to process_single for modules with no task.cpus usage (#2076)
|
2022-09-19 11:54:47 +02:00 |
|
prokka
|
[bug] pin bioperl version in Prokka module (#1307)
|
2022-09-28 01:34:23 +01:00 |
|
pycoqc
|
Fix formatting in yaml files, add yamllint config (#1279)
|
2022-02-15 11:15:27 +00:00 |
|
pydamage
|
Set process label to process_single for modules with no task.cpus usage (#2076)
|
2022-09-19 11:54:47 +02:00 |
|
qcat
|
Fix formatting in yaml files, add yamllint config (#1279)
|
2022-02-15 11:15:27 +00:00 |
|
qualimap
|
Fix broken Quast module and bump MultiQC version in dumpsoftwareversions (#2108)
|
2022-09-27 09:35:52 +01:00 |
|
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
|
samtools fasta module (#2128)
|
2022-09-29 08:10:44 +01:00 |
|
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
|
Fixes incorrectly quoted tags (#2113)
|
2022-09-27 20:37:56 +01:00 |
|
sequenzautils
|
Fix formatting in yaml files, add yamllint config (#1279)
|
2022-02-15 11:15:27 +00:00 |
|
seqwish/induce
|
Bump seqwish/induce to v0.7.6 (#2083)
|
2022-09-26 17:01:21 +01:00 |
|
seroba/run
|
add module for seroba (#1816)
|
2022-09-26 16:06:08 +01:00 |
|
sexdeterrmine
|
Set process label to process_single for modules with no task.cpus usage (#2076)
|
2022-09-19 11:54:47 +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 |
|
somalier
|
Somalier relate (#2001)
|
2022-09-19 13:22:24 +02:00 |
|
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
|
Make stringtie/merge arguments configurable (#2049)
|
2022-09-26 14:26:53 +01:00 |
|
subread/featurecounts
|
Fix formatting in yaml files, add yamllint config (#1279)
|
2022-02-15 11:15:27 +00:00 |
|
svdb
|
update stub for svdb/merge (#2066)
|
2022-09-15 14:20:09 +02:00 |
|
svtk/standardize
|
new module: svtk/standardize (#2031)
|
2022-09-08 15:03:08 +02:00 |
|
tabix
|
Added an output channel for the gzi index (#2036)
|
2022-09-26 21:47:41 +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
|
Update cores specification in TrimGalore module (#2127)
|
2022-09-28 15:47:27 +02:00 |
|
trimmomatic
|
Trimmomatic (#1757)
|
2022-06-17 13:18:15 +00:00 |
|
ucsc
|
Set process label to process_single for modules with no task.cpus usage (#2076)
|
2022-09-19 11:54:47 +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 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
|
Fix for nested directories in tar archive (#2062)
|
2022-09-15 11:32:36 +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
|
New module: Vsearch sintax (#2094)
|
2022-09-26 14:45:01 +01:00 |
|
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 |
