.. |
abacas
|
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abricate
|
add module for abricate (#1280)
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2022-02-18 18:00:21 -07:00 |
adapterremoval
|
Refactor adapterremoval (#1491)
|
2022-04-04 21:40:35 +02:00 |
adapterremovalfixprefix
|
Add AdapterRemovalFixPrefix (#1424)
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2022-03-21 11:26:12 +01:00 |
agrvate
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allelecounter
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amplify/predict
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add module AMPlify (#1498)
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2022-04-20 11:53:26 +02:00 |
amps
|
Untar unzip meta (#1408)
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2022-03-21 14:49:28 +01:00 |
amrfinderplus
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add amrfinderplus module (#1284)
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2022-02-19 23:02:23 +00:00 |
antismash
|
Apply suggestions from code review
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2022-05-12 15:28:19 +02:00 |
arriba
|
update md5sum
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2022-05-09 15:19:16 +02:00 |
artic
|
Untar unzip meta (#1408)
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2022-03-21 14:49:28 +01:00 |
ascat
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round the < to ( to make markdown work for meta.yml (#1395)
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2022-03-16 13:29:11 +01:00 |
assemblyscan
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ataqv/ataqv
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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 |
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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bamcmp
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bamcmp (#1244)
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2022-02-02 16:38:41 +00:00 |
bamtools
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Merge remote-tracking branch 'origin' into motus_profile
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2022-05-05 09:41:13 -04:00 |
bamutil/trimbam
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bandage/image
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bbmap
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Samtools version update (#1507)
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2022-04-11 14:26:28 +02:00 |
bcftools
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fix test
|
2022-06-08 14:48:16 +02:00 |
bclconvert
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Module/bclconvert (#1485)
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2022-04-21 15:39:22 +02:00 |
bedtools
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added bedtools split
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2022-05-17 14:24:32 +02:00 |
biobambam
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fix config
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2022-05-17 09:09:19 +02:00 |
biscuit
|
Add core Biscuit tools (#1354)
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2022-03-14 09:34:22 -04:00 |
bismark
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blast
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bowtie
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bowtie2
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add PE sorted test
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2022-05-13 19:16:50 +02:00 |
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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remove 'auto' test
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2022-05-06 13:33:27 +00:00 |
bwa
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Samtools version update (#1507)
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2022-04-11 14:26:28 +02:00 |
bwamem2
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bwameth
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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 |
cat
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Update cat module (#1469)
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2022-03-31 13:42:44 +02:00 |
cellranger
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Trying to fix tests
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2022-06-10 11:22:45 +02:00 |
centrifuge
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Add centrifuge_kreport module (#1514)
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2022-04-13 15:33:51 +02:00 |
checkm/lineagewf
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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 |
chromap
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Samtools version update (#1507)
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2022-04-11 14:26:28 +02:00 |
clonalframeml
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cmseq/polymut
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cnvkit
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added fasta_fai as input + changed if statements
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2022-06-02 12:57:50 +02:00 |
cnvpytor
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combine multiple pytor
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2022-05-05 23:59:12 +02:00 |
controlfreec
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Fix Controlfreec: Add stub runs to test single sample input & make conda work with R scripts (#1504)
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2022-04-08 11:43:40 +02:00 |
cooler
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csvtk
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custom
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tests: add missing paths to config
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2022-05-11 18:17:27 +02:00 |
cutadapt
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damageprofiler
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dastool
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Update DASTool to 1.1.4 (#1471)
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2022-04-01 11:33:07 +02:00 |
dedup
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deeparg
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Deeparg singularity container fix 2 (#1406)
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2022-03-18 16:21:55 +01:00 |
deeptools
|
changed container + add cram2bam conversion
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2022-06-02 10:38:05 +02:00 |
deepvariant
|
Update version & add intervals usage (#1214)
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2022-01-17 16:40:31 +01:00 |
delly/call
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diamond
|
Merge remote-tracking branch 'origin' into motus_profile
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2022-05-05 09:41:13 -04:00 |
dragmap
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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 |
dragonflye
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dshbio
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Update dsh-bio to version 2.0.7, add support for compressed GFA 1.0 format (#1207)
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2022-01-17 09:24:40 +00:00 |
ectyper
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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 |
elprep
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Merge remote-tracking branch 'origin' into motus_profile
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2022-05-05 09:41:13 -04:00 |
emmtyper
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ensemblvep
|
Update tests/modules/ensemblvep/main.nf
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2022-06-09 11:55:41 +02:00 |
expansionhunter
|
add stub to modules used in raredisease pipeline (#1206)
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2022-03-28 17:48:39 +02:00 |
faqcs
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Faqcs patch to add tests for --debug output (#1368)
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2022-03-02 08:53:05 -05:00 |
fargene
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fastani
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fastp
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fastqc
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fastqscan
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fasttree
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fgbio
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filtlong
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Fix config for tests
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2022-05-31 20:07:52 +02:00 |
flash
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freebayes
|
Update intervals (#1278)
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2022-02-10 10:34:22 +01:00 |
gamma/gamma
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fixed test.yml
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2022-05-24 19:27:09 -04:00 |
gatk
|
Add GATK indelrealigner tests
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2022-06-08 21:14:08 +02:00 |
gatk4
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Merge branch 'master' into update_spark
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2022-06-09 15:49:31 +02:00 |
genmap
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genomescope2
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Update tests/modules/genomescope2/test.yml
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2022-05-13 11:27:42 +02:00 |
genrich
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gffread
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glnexus
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graphmap2
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gstama
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New Module: gstama/polyacleanup (#1468)
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2022-03-31 09:11:51 -04:00 |
gtdbtk/classifywf
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gubbins
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gunc
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gunzip
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hamronization
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Add hamronization/summarize (#1366)
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2022-03-03 08:02:04 +01:00 |
happy
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Merge remote-tracking branch 'origin' into motus_profile
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2022-05-05 09:41:13 -04:00 |
hicap
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hifiasm
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hisat2
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hmmcopy
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hmmer
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Prettier (#1405)
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2022-03-18 14:27:50 +01:00 |
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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Fix homer/maketagdirectory output collision (#1456)
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2022-03-27 03:17:42 +00:00 |
hpsuissero
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add module for hpsuisero (#1331)
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2022-02-27 17:58:35 -07:00 |
ichorcna
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Prettier (#1405)
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2022-03-18 14:27:50 +01:00 |
idr
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imputeme/vcftoprs
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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 |
iqtree
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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 |
ismapper
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isoseq3
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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 |
ivar
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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 |
jupyternotebook
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kaiju
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Kaiju2table module (#1545)
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2022-04-22 11:26:30 +02:00 |
kallisto/index
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kallistobustools
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kat/hist
|
Update tests/modules/kat/hist/test.yml
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2022-05-23 08:51:49 +02:00 |
khmer/normalizebymedian
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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 |
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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update to kraken2: breaking change - output channels renamed (#1525)
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2022-04-21 14:33:59 +02:00 |
krona
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Merge remote-tracking branch 'origin' into motus_profile
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2022-05-05 09:41:13 -04:00 |
last
|
Untar unzip meta (#1408)
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2022-03-21 14:49:28 +01:00 |
leehom
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legsta
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add module for legsta (#1319)
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2022-02-18 17:42:18 -07:00 |
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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Fix formatting in yaml files, add yamllint config (#1279)
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2022-02-15 11:15:27 +00:00 |
macrel/contigs
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macs2/callpeak
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mafft
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Add MAFFT module (#1351)
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2022-02-28 00:40:24 -07:00 |
malt
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Untar unzip meta (#1408)
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2022-03-21 14:49:28 +01:00 |
maltextract
|
Untar unzip meta (#1408)
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2022-03-21 14:49:28 +01:00 |
manta
|
Revert manta changes (#1518)
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2022-04-12 10:40:06 +02:00 |
mapdamage2
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mash
|
Patch mash screen
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2022-05-25 12:29:14 +00:00 |
mashtree
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maxbin2
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maxquant/lfq
|
corrected typos
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2022-02-07 13:07:16 +01:00 |
md5sum
|
new module: md5sum
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2022-05-06 09:20:40 +02:00 |
medaka
|
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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megan/rma2info
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Add MEGAN/RMA2INFO (#1513)
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2022-04-12 08:35:36 +02:00 |
meningotype
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meryl
|
Merge branch 'master' into meryl_unionsum
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2022-05-09 16:16:08 +02:00 |
metabat2
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metaphlan3
|
Untar unzip meta (#1408)
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2022-03-21 14:49:28 +01:00 |
methyldackel
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minia
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miniasm
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minimap2
|
Update minimap2/align module (#1537)
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2022-04-26 16:32:20 +02:00 |
mlst
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mobsuite/recon
|
add mobsuite_recon module (#1270)
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2022-02-18 17:52:38 -07:00 |
mosdepth
|
Update main.nf
|
2022-05-25 19:38:12 +01:00 |
motus
|
Update tests/modules/motus/profile/test.yml
|
2022-05-12 20:55:54 +01:00 |
msisensor
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msisensorpro
|
Add msisensorpro (#1267)
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2022-02-09 21:05:49 +01:00 |
mtnucratio
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multiqc
|
formatting
|
2022-06-08 14:42:58 +02:00 |
mummer
|
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muscle
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nanolyse
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nanoplot
|
Fix formatting in yaml files, add yamllint config (#1279)
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2022-02-15 11:15:27 +00:00 |
ncbigenomedownload
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nextclade
|
Bump Nextclade version to 1.10.1 (#1236)
|
2022-01-27 12:53:14 +00:00 |
ngmaster
|
|
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ngscheckmate/ncm
|
New module: NGSCheckMate (#1290)
|
2022-03-11 09:02:10 +00:00 |
nucmer
|
Fix formatting in yaml files, add yamllint config (#1279)
|
2022-02-15 11:15:27 +00:00 |
optitype
|
Add BAM indexes as input for optitype module. (#1388)
|
2022-03-15 17:02:40 +01:00 |
pairix
|
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pairtools
|
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panaroo/run
|
add module for panaroo, fix pirate tests (#1444)
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2022-03-24 20:11:04 -06:00 |
pangolin
|
Bump Pangolin version to 3.1.20 (#1296)
|
2022-02-15 10:46:20 +00:00 |
paraclu
|
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pbbam/pbmerge
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pbccs
|
Fix formatting in yaml files, add yamllint config (#1279)
|
2022-02-15 11:15:27 +00:00 |
peddy
|
|
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phantompeakqualtools
|
Add task.ext.args to phantompeakqualtools and finish the module (#1474)
|
2022-03-31 22:59:21 +01:00 |
phyloflash
|
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picard
|
fix tests (again)
|
2022-05-22 06:54:09 +02:00 |
pirate
|
add module for panaroo, fix pirate tests (#1444)
|
2022-03-24 20:11:04 -06:00 |
plasmidid
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plink
|
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plink2
|
implement plink2/score module (#1259)
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2022-03-07 13:02:40 -05:00 |
pmdtools/filter
|
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porechop
|
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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
|
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prokka
|
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pycoqc
|
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pydamage
|
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qcat
|
Fix formatting in yaml files, add yamllint config (#1279)
|
2022-02-15 11:15:27 +00:00 |
qualimap
|
add qualimap with cram files + remove val from qualimap/bam, instead use empty list as everywhere else (#1320)
|
2022-02-18 09:43:53 +01:00 |
quast
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racon
|
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rapidnj
|
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rasusa
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raven
|
Raven assembler (#1087)
|
2022-02-01 11:47:01 +01:00 |
raxmlng
|
Fix formatting in yaml files, add yamllint config (#1279)
|
2022-02-15 11:15:27 +00:00 |
rgi/main
|
add module for rgi (#1321)
|
2022-02-18 17:23:44 -07:00 |
rhocall/annotate
|
update test
|
2022-06-08 16:36:02 +02:00 |
rmarkdownnotebook
|
|
|
roary
|
Update test.yml (#1419)
|
2022-03-19 15:06:21 +00:00 |
rsem
|
Bump STAR version to 2.7.10a for RSEM modules (#1573)
|
2022-04-27 19:21:26 +01:00 |
rseqc
|
|
|
rtgtools/vcfeval
|
Small update on the output channels
|
2022-05-10 12:34:52 +02:00 |
salmon
|
|
|
samblaster
|
Samtools version update (#1507)
|
2022-04-11 14:26:28 +02:00 |
samtools
|
Generalize Bam2Cram do either conversion
|
2022-05-09 15:22:54 +02:00 |
scoary
|
|
|
seacr/callpeak
|
Fix formatting in yaml files, add yamllint config (#1279)
|
2022-02-15 11:15:27 +00:00 |
seqkit
|
feat: add module for seqkit stats (#1466)
|
2022-03-30 23:01:17 +02:00 |
seqsero2
|
Fix formatting in yaml files, add yamllint config (#1279)
|
2022-02-15 11:15:27 +00:00 |
seqtk
|
Decrease indent in seqtk/seq versions.yml output (#1384)
|
2022-03-09 11:56:35 -05:00 |
sequenzautils
|
|
|
seqwish/induce
|
|
|
sexdeterrmine
|
Corrected test-datasets input
|
2022-05-23 17:08:40 +02:00 |
shasum
|
added sha256sum
|
2022-05-06 10:28:14 +02:00 |
shigatyper
|
Merge remote-tracking branch 'origin' into motus_profile
|
2022-05-05 09:41:13 -04:00 |
shovill
|
|
|
sistr
|
add module for sistr (#1323)
|
2022-02-18 17:33:48 -07:00 |
slimfastq
|
Merge remote-tracking branch 'origin' into motus_profile
|
2022-05-05 09:41:13 -04:00 |
snapaligner
|
fix tags
|
2022-05-06 18:57:17 +02:00 |
snippy/run
|
make prettier
|
2022-05-11 18:00:36 +00:00 |
snpdists
|
|
|
snpeff
|
|
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snpsift/split
|
|
|
snpsites
|
Fix formatting in yaml files, add yamllint config (#1279)
|
2022-02-15 11:15:27 +00:00 |
sourmash/sketch
|
feat: add sourmash sketch (#1287)
|
2022-02-15 12:30:28 +01:00 |
spades
|
|
|
spatyper
|
|
|
sratools
|
refactor: move files to custom section
|
2022-05-11 17:33:45 +02:00 |
srst2/srst2
|
Merge remote-tracking branch 'origin' into motus_profile
|
2022-05-05 09:41:13 -04:00 |
ssuissero
|
add module for ssuisero (#1329)
|
2022-02-27 20:04:03 -07:00 |
stadeniolib/scramble
|
new tool: staden_io_lib (#1499)
|
2022-04-08 09:54:15 -04:00 |
staphopiasccmec
|
|
|
star
|
Fix tests
|
2022-05-27 12:14:10 +01:00 |
stranger
|
add stubs for stranger (#1543)
|
2022-04-22 10:10:43 +02:00 |
strelka
|
Update intervals (#1278)
|
2022-02-10 10:34:22 +01:00 |
stringtie
|
Rename process from STRINGTIE to STRINGTIE_STRINGTIE (#1546)
|
2022-04-22 15:13:06 +01:00 |
subread/featurecounts
|
|
|
svdb
|
update svdb to version 2.5.2 (#1390)
|
2022-03-21 10:39:34 +01:00 |
tabix
|
Merge remote-tracking branch 'origin' into motus_profile
|
2022-05-05 09:41:13 -04:00 |
tbprofiler/profile
|
Fix formatting in yaml files, add yamllint config (#1279)
|
2022-02-15 11:15:27 +00:00 |
tiddit
|
add test + fix issues
|
2022-06-03 15:51:02 +02:00 |
transdecoder
|
Transdecoder predict (#1251)
|
2022-02-02 09:46:07 +01:00 |
trimgalore
|
|
|
ucsc
|
|
|
ultra/pipeline
|
|
|
umitools
|
Fix Conda tests
|
2022-05-23 22:39:12 +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
|
Merge remote-tracking branch 'origin' into motus_profile
|
2022-05-05 09:41:13 -04:00 |
variantbam
|
|
|
vcfanno
|
Untar unzip meta (#1408)
|
2022-03-21 14:49:28 +01:00 |
vcflib/vcfuniq
|
Add new vcflib/vcfuniq module (#1208)
|
2022-01-14 18:18:11 +00:00 |
vcftools
|
|
|
vsearch/usearchglobal
|
prettier
|
2022-05-30 13:35:12 +02:00 |
yara
|
Add samtools index to yara_mapper module (#1353)
|
2022-03-04 10:08:02 -05:00 |