.. |
abacas
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Fix formatting in yaml files, add yamllint config (#1279)
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2022-02-15 11:15:27 +00:00 |
abricate
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Prettier (#1405)
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2022-03-18 14:27:50 +01:00 |
adapterremoval
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Refactor adapterremoval (#1491)
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2022-04-04 21:40:35 +02:00 |
adapterremovalfixprefix
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Update manual versioning (#1813)
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2022-06-27 10:35:41 +02:00 |
agrvate
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Fix formatting in yaml files, add yamllint config (#1279)
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2022-02-15 11:15:27 +00:00 |
allelecounter
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fix incorrect yaml formatting. (#1264)
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2022-04-14 13:35:01 +02:00 |
ampir
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Apply suggestions from code review
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2022-06-10 14:46:58 +02:00 |
amplify/predict
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Update manual versioning (#1813)
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2022-06-27 10:35:41 +02:00 |
amps
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Fix formatting in yaml files, add yamllint config (#1279)
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2022-02-15 11:15:27 +00:00 |
amrfinderplus
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Prettier (#1405)
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2022-03-18 14:27:50 +01:00 |
antismash
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Apply suggestions from code review
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2022-05-12 15:28:19 +02:00 |
ariba
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add module for ariba (#1731)
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2022-06-15 10:18:31 -06:00 |
arriba
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Update Arriba to 2.3.0 (#1827)
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2022-06-29 14:39:13 +02:00 |
artic
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Patch fix artic/minion and ivar/variants modules (#1326)
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2022-02-18 17:36:09 +00:00 |
ascat
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Added output files to ASCAT (#1820)
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2022-06-28 14:45:57 +02:00 |
assemblyscan
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Fix formatting in yaml files, add yamllint config (#1279)
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2022-02-15 11:15:27 +00:00 |
ataqv/ataqv
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atlas
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Add Atlas/PMD (#1810)
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2022-06-24 16:53:51 +02:00 |
bakta
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update bakta to latest version (v1.4.0) (#1428)
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2022-03-24 10:49:17 -06:00 |
bamaligncleaner
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Fix formatting in yaml files, add yamllint config (#1279)
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2022-02-15 11:15:27 +00:00 |
bamcmp
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Update manual versioning (#1813)
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2022-06-27 10:35:41 +02:00 |
bamtools
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Remove a blank line (#1793)
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2022-06-17 10:58:24 +01:00 |
bamutil/trimbam
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bandage/image
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bbmap
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bcftools
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added an optional vcf index to bcftools/norm (#1821)
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2022-06-28 16:18:12 +02:00 |
bclconvert
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bclconvert: Update Dockerfile (#1819)
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2022-06-28 11:11:16 +01:00 |
bedtools
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biobambam
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replace regex with fixed extensions
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2022-05-17 09:54:06 +02:00 |
biscuit
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bismark
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blast
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bowtie
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bowtie2
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bracken/bracken
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Add bracken (#1423)
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2022-03-22 16:40:21 +01:00 |
busco
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Update meta.yml
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2022-05-06 11:56:43 +00:00 |
bwa
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bwamem2
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bwameth
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cat
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cellranger
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Bugfix for CellRanger Dockerfile (#1812)
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2022-06-27 11:07:33 +02:00 |
centrifuge
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checkm/lineagewf
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chromap
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clonalframeml
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Fix formatting in yaml files, add yamllint config (#1279)
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2022-02-15 11:15:27 +00:00 |
cmseq/polymut
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Update manual versioning (#1813)
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2022-06-27 10:35:41 +02:00 |
cnvkit
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cnvpytor
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controlfreec
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cooler
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csvtk
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custom
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cutadapt
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damageprofiler
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Fix formatting in yaml files, add yamllint config (#1279)
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2022-02-15 11:15:27 +00:00 |
dastool
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dedup
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Fix formatting in yaml files, add yamllint config (#1279)
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2022-02-15 11:15:27 +00:00 |
deeparg
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deeptools
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deepvariant
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Revert recent changes made to some of the modules (#1463)
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2022-03-30 20:21:06 +02:00 |
delly/call
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diamond
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dragmap
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feat: remove read_group which should be set up with task.ext.args (#1521)
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2022-04-13 14:30:34 +02:00 |
dragonflye
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Update dragonflye to latest version (#1442)
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2022-03-24 14:56:32 -04:00 |
dshbio
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ectyper
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elprep
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emmtyper
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ensemblvep
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Same version on conda and in the dockerfile (#1791)
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2022-06-16 16:25:54 +02:00 |
expansionhunter
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faqcs
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fargene
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Update manual versioning (#1813)
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2022-06-27 10:35:41 +02:00 |
fastani
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Fix formatting in yaml files, add yamllint config (#1279)
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2022-02-15 11:15:27 +00:00 |
fastk
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Add FastK/Merge (#1828)
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2022-06-29 18:04:36 +02:00 |
fastp
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Proposal: Rename output from fastp module (#1802)
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2022-06-24 10:01:14 +02:00 |
fastqc
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add stub to modules used in raredisease pipeline (#1206)
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2022-03-28 17:48:39 +02:00 |
fastqscan
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Fix formatting in yaml files, add yamllint config (#1279)
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2022-02-15 11:15:27 +00:00 |
fasttree
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Fix formatting in yaml files, add yamllint config (#1279)
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2022-02-15 11:15:27 +00:00 |
fgbio
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filtlong
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flash
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Fix formatting in yaml files, add yamllint config (#1279)
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2022-02-15 11:15:27 +00:00 |
freebayes
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gamma/gamma
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Update manual versioning (#1813)
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2022-06-27 10:35:41 +02:00 |
gatk
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gatk4
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Add module: gatk4/leftalignandtrimvariants (#1808)
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2022-06-28 10:44:08 +02:00 |
gecco/run
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Add gecco/run module (#1790)
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2022-06-22 13:43:45 +02:00 |
genescopefk
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Update manual versioning (#1813)
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2022-06-27 10:35:41 +02:00 |
genmap
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genomescope2
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genrich
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gffread
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Fix formatting in yaml files, add yamllint config (#1279)
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2022-02-15 11:15:27 +00:00 |
glnexus
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graphmap2
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gstama
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gtdbtk/classifywf
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Update manual versioning (#1813)
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2022-06-27 10:35:41 +02:00 |
gubbins
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Fix formatting in yaml files, add yamllint config (#1279)
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2022-02-15 11:15:27 +00:00 |
gunc
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gunzip
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Replace vanilla Linux Biocontainer with Ubuntu (#1557)
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2022-04-22 14:50:07 +01:00 |
hamronization
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haplocheck
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fix: stub output name
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2022-06-08 10:10:24 -03:00 |
happy
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Update manual versioning (#1813)
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2022-06-27 10:35:41 +02:00 |
hicap
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hifiasm
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Add when: block (#1261)
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2022-02-04 09:53:32 +01:00 |
hisat2
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Update manual versioning (#1813)
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2022-06-27 10:35:41 +02:00 |
hmmcopy
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Update manual versioning (#1813)
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2022-06-27 10:35:41 +02:00 |
hmmer
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hmtnote
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Update main.nf
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2022-05-16 15:20:15 +00:00 |
homer
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Update manual versioning (#1813)
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2022-06-27 10:35:41 +02:00 |
hpsuissero
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Update manual versioning (#1813)
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2022-06-27 10:35:41 +02:00 |
ichorcna
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Update manual versioning (#1813)
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2022-06-27 10:35:41 +02:00 |
idr
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Fix formatting in yaml files, add yamllint config (#1279)
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2022-02-15 11:15:27 +00:00 |
imputeme/vcftoprs
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iqtree
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ismapper
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Fix formatting in yaml files, add yamllint config (#1279)
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2022-02-15 11:15:27 +00:00 |
isoseq3
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ivar
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jupyternotebook
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Add when: block (#1261)
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2022-02-04 09:53:32 +01:00 |
kaiju
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Add KAIJU2KRONA module (#1800)
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2022-06-23 16:38:50 +00:00 |
kallisto/index
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Fix formatting in yaml files, add yamllint config (#1279)
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2022-02-15 11:15:27 +00:00 |
kallistobustools
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update kb-python version (#1823)
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2022-06-29 11:19:34 +02:00 |
kat/hist
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Add module kat hist
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2022-05-06 07:54:10 +00:00 |
khmer
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Add khmer unique-kmers.py module (#1838)
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2022-06-30 16:23:30 +01:00 |
kleborate
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Fix formatting in yaml files, add yamllint config (#1279)
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2022-02-15 11:15:27 +00:00 |
kraken2/kraken2
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krakentools/kreport2krona
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Update manual versioning (#1813)
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2022-06-27 10:35:41 +02:00 |
krona
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Update manual versioning (#1813)
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2022-06-27 10:35:41 +02:00 |
last
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leehom
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Update manual versioning (#1813)
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2022-06-27 10:35:41 +02:00 |
legsta
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Prettier (#1405)
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2022-03-18 14:27:50 +01:00 |
lima
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Fix formatting in yaml files, add yamllint config (#1279)
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2022-02-15 11:15:27 +00:00 |
lissero
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Fix formatting in yaml files, add yamllint config (#1279)
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2022-02-15 11:15:27 +00:00 |
lofreq
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macrel/contigs
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macs2/callpeak
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Prettier (#1405)
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2022-03-18 14:27:50 +01:00 |
mafft
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Prettier (#1405)
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2022-03-18 14:27:50 +01:00 |
malt
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Update MALT to older version due to major bug in most recent version (#1796)
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2022-06-20 08:20:22 +02:00 |
maltextract
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manta
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Update modules/manta/convertinversion/main.nf
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2022-06-13 09:26:29 +02:00 |
mapdamage2
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mash
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mashtree
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Fix formatting in yaml files, add yamllint config (#1279)
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2022-02-15 11:15:27 +00:00 |
maxbin2
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Fix for Maxbin2 emitting input files (#1376)
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2022-03-08 15:56:23 +01:00 |
maxquant/lfq
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mcroni
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Update manual versioning (#1813)
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2022-06-27 10:35:41 +02:00 |
md5sum
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medaka
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Fix formatting in yaml files, add yamllint config (#1279)
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2022-02-15 11:15:27 +00:00 |
megahit
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Fix formatting in yaml files, add yamllint config (#1279)
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2022-02-15 11:15:27 +00:00 |
megan/rma2info
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meningotype
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Fix formatting in yaml files, add yamllint config (#1279)
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2022-02-15 11:15:27 +00:00 |
merquryfk
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Update manual versioning (#1813)
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2022-06-27 10:35:41 +02:00 |
meryl
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metabat2
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metaphlan3
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Add additional handling of fq.gz file name suffix
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2022-05-02 14:16:12 +02:00 |
methyldackel
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minia
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Fix formatting in yaml files, add yamllint config (#1279)
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2022-02-15 11:15:27 +00:00 |
miniasm
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Fix formatting in yaml files, add yamllint config (#1279)
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2022-02-15 11:15:27 +00:00 |
minimap2
|
Fix typo (#1586)
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2022-04-29 09:37:23 +02:00 |
mlst
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Fix formatting in yaml files, add yamllint config (#1279)
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2022-02-15 11:15:27 +00:00 |
mobsuite/recon
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Prettier (#1405)
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2022-03-18 14:27:50 +01:00 |
mosdepth
|
Update main.nf
|
2022-05-25 19:42:15 +01:00 |
motus
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fix the typo in motus_profile.
|
2022-05-12 09:20:32 -04:00 |
msisensor
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msisensorpro
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mtnucratio
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Fix formatting in yaml files, add yamllint config (#1279)
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2022-02-15 11:15:27 +00:00 |
multiqc
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Bump MultiQC to v1.13a (dev) (#1814)
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2022-06-29 08:40:42 +02:00 |
mummer
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Update manual versioning (#1813)
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2022-06-27 10:35:41 +02:00 |
muscle
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Fix formatting in yaml files, add yamllint config (#1279)
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2022-02-15 11:15:27 +00:00 |
nanolyse
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Fix formatting in yaml files, add yamllint config (#1279)
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2022-02-15 11:15:27 +00:00 |
nanoplot
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Fix formatting in yaml files, add yamllint config (#1279)
|
2022-02-15 11:15:27 +00:00 |
ncbigenomedownload
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Fix formatting in yaml files, add yamllint config (#1279)
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2022-02-15 11:15:27 +00:00 |
nextclade
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ngmaster
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ngscheckmate/ncm
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nucmer
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optitype
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Add BAM indexes as input for optitype module. (#1388)
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2022-03-15 17:02:40 +01:00 |
pairix
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Fix formatting in yaml files, add yamllint config (#1279)
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2022-02-15 11:15:27 +00:00 |
pairtools
|
|
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panaroo/run
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add module for panaroo, fix pirate tests (#1444)
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2022-03-24 20:11:04 -06:00 |
pangolin
|
Fix formatting in yaml files, add yamllint config (#1279)
|
2022-02-15 11:15:27 +00:00 |
paraclu
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Update manual versioning (#1813)
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2022-06-27 10:35:41 +02:00 |
pbbam/pbmerge
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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)
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2022-02-15 11:15:27 +00:00 |
peddy
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Fix formatting in yaml files, add yamllint config (#1279)
|
2022-02-15 11:15:27 +00:00 |
phantompeakqualtools
|
Update manual versioning (#1813)
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2022-06-27 10:35:41 +02:00 |
phyloflash
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Fix formatting in yaml files, add yamllint config (#1279)
|
2022-02-15 11:15:27 +00:00 |
picard
|
|
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pirate
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add module for panaroo, fix pirate tests (#1444)
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2022-03-24 20:11:04 -06:00 |
plasmidfinder
|
Update manual versioning (#1813)
|
2022-06-27 10:35:41 +02:00 |
plasmidid
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Fix formatting in yaml files, add yamllint config (#1279)
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2022-02-15 11:15:27 +00:00 |
plink
|
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plink2
|
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pmdtools/filter
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porechop
|
Add when: block (#1261)
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2022-02-04 09:53:32 +01:00 |
preseq
|
|
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prinseqplusplus
|
Add PRINSEQPLUSPLUS (#1481)
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2022-04-03 16:06:22 +02:00 |
prodigal
|
fix yml formatting (#1263)
|
2022-02-07 18:16:43 +01:00 |
prokka
|
Fix formatting in yaml files, add yamllint config (#1279)
|
2022-02-15 11:15:27 +00:00 |
pycoqc
|
Fix formatting in yaml files, add yamllint config (#1279)
|
2022-02-15 11:15:27 +00:00 |
pydamage
|
|
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qcat
|
Fix formatting in yaml files, add yamllint config (#1279)
|
2022-02-15 11:15:27 +00:00 |
qualimap
|
|
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quast
|
Fix formatting in yaml files, add yamllint config (#1279)
|
2022-02-15 11:15:27 +00:00 |
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
|
|
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rmarkdownnotebook
|
Add when: block (#1261)
|
2022-02-04 09:53:32 +01:00 |
roary
|
|
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rsem
|
|
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rseqc
|
|
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rtgtools
|
new module rtgtools/pedfilter (#1777)
|
2022-06-14 16:02:18 +02:00 |
salmon
|
|
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samblaster
|
|
|
samtools
|
samtools/*stats*: use prefix for outputs (#1788)
|
2022-06-16 13:42:01 +02:00 |
scoary
|
|
|
seacr/callpeak
|
Update manual versioning (#1813)
|
2022-06-27 10:35:41 +02:00 |
seqkit
|
|
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seqsero2
|
|
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seqtk
|
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sequenzautils
|
|
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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
|
|
|
shigatyper
|
Update modules/shigatyper/main.nf
|
2022-04-22 08:49:44 -06:00 |
shovill
|
|
|
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
|
update ensemblvep and snpeff modules
|
2022-05-05 12:57:14 +02:00 |
snpsift/split
|
|
|
snpsites
|
Fix formatting in yaml files, add yamllint config (#1279)
|
2022-02-15 11:15:27 +00:00 |
sortmerna
|
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sourmash/sketch
|
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spades
|
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spatyper
|
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sratools
|
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srst2/srst2
|
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ssuissero
|
Update manual versioning (#1813)
|
2022-06-27 10:35:41 +02:00 |
stadeniolib/scramble
|
|
|
staphopiasccmec
|
|
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star
|
|
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stranger
|
add stubs for stranger (#1543)
|
2022-04-22 10:10:43 +02:00 |
strelka
|
|
|
stringtie
|
Rename process from STRINGTIE to STRINGTIE_STRINGTIE (#1546)
|
2022-04-22 15:13:06 +01:00 |
subread/featurecounts
|
|
|
svdb
|
|
|
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
|
|
|
trimgalore
|
|
|
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/pipeline
|
|
|
umitools
|
Set randomseed for UMI tools if not otherwise set (#1837)
|
2022-06-30 16:30:38 +01:00 |
unicycler
|
|
|
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)
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2022-06-27 10:35:41 +02:00 |
vcf2db
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Update manual versioning (#1813)
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2022-06-27 10:35:41 +02:00 |
vcf2maf
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Update manual versioning (#1813)
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2022-06-27 10:35:41 +02:00 |
vcfanno
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small changes to vcfanno (#1804)
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2022-06-24 08:58:26 +02:00 |
vcflib/vcfuniq
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Update manual versioning (#1813)
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2022-06-27 10:35:41 +02:00 |
vcftools
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Fix formatting in yaml files, add yamllint config (#1279)
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2022-02-15 11:15:27 +00:00 |
vsearch/usearchglobal
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yara
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