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abacas
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abricate
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adapterremoval
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Refactor adapterremoval (#1491)
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2022-04-04 21:40:35 +02:00 |
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adapterremovalfixprefix
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agrvate
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allelecounter
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ampir
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Add file name collision check + TSV output
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2022-06-10 12:54:39 +02:00 |
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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 |
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amps
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amrfinderplus
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antismash
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Apply suggestions from code review
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2022-05-12 15:28:19 +02:00 |
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ariba
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add module for ariba (#1731)
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2022-06-15 10:18:31 -06:00 |
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arriba
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Update Arriba to 2.3.0 (#1827)
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2022-06-29 14:39:13 +02:00 |
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artic
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ascat
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Added output files to ASCAT (#1820)
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2022-06-28 14:45:57 +02:00 |
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assemblyscan
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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 |
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bakta
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bamaligncleaner
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bamcmp
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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 |
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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 |
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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 |
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bclconvert
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bump bclconvert version (#1806)
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2022-06-24 07:14:42 +02:00 |
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bedtools
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added bedtools split
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2022-05-17 14:24:32 +02:00 |
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biobambam
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fix config
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2022-05-17 09:09:19 +02:00 |
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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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add PE sorted test
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2022-05-13 19:16:50 +02:00 |
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bracken/bracken
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busco
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Change busco multi-fasta test md5sum to contains
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2022-06-13 08:51:41 +00:00 |
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bwa
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Samtools version update (#1507)
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2022-04-11 14:26:28 +02:00 |
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bwamem2
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bwameth
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cat
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Update cat module (#1469)
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2022-03-31 13:42:44 +02:00 |
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cellranger
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Remove empty file md5sum
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2022-06-10 11:53:28 +02:00 |
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centrifuge
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Add centrifuge_kreport module (#1514)
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2022-04-13 15:33:51 +02:00 |
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checkm/lineagewf
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chromap
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Samtools version update (#1507)
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2022-04-11 14:26:28 +02:00 |
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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 |
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cnvpytor
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combine multiple pytor
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2022-05-05 23:59:12 +02:00 |
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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 |
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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 |
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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 |
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dedup
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deeparg
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deeptools
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changed container + add cram2bam conversion
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2022-06-02 10:38:05 +02:00 |
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deepvariant
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delly/call
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diamond
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Merge remote-tracking branch 'origin' into motus_profile
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2022-05-05 09:41:13 -04:00 |
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dragmap
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dragonflye
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dshbio
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ectyper
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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 |
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emmtyper
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ensemblvep
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Optional output from the VEP-moduel (#1775)
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2022-06-15 13:52:12 +02:00 |
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expansionhunter
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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 |
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faqcs
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fargene
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fastani
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fastk
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Add FastK/Merge (#1828)
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2022-06-29 18:04:36 +02:00 |
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fastp
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Proposal: Rename output from fastp module (#1802)
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2022-06-24 10:01:14 +02:00 |
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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 |
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flash
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freebayes
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gamma/gamma
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fixed test.yml
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2022-05-24 19:27:09 -04:00 |
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gatk
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Add GATK indelrealigner tests
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2022-06-08 21:14:08 +02:00 |
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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 |
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gecco/run
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Add gecco/run module (#1790)
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2022-06-22 13:43:45 +02:00 |
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genescopefk
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Add GeneScopeFK (#1781)
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2022-06-14 20:49:06 +02:00 |
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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 |
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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 |
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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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haplocheck
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fix: string interpolation and test input access
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2022-06-08 09:08:59 -03:00 |
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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 |
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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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hmtnote
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Update main.nf
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2022-05-16 15:20:15 +00:00 |
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homer
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hpsuissero
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add module for hpsuisero (#1331)
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2022-02-27 17:58:35 -07:00 |
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ichorcna
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idr
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imputeme/vcftoprs
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iqtree
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ismapper
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isoseq3
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ivar
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jupyternotebook
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kaiju
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Add KAIJU2KRONA module (#1800)
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2022-06-23 16:38:50 +00:00 |
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kallisto/index
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kallistobustools
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kat/hist
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Update tests/modules/kat/hist/test.yml
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2022-05-23 08:51:49 +02:00 |
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khmer
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Add khmer unique-kmers.py module (#1838)
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2022-06-30 16:23:30 +01:00 |
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kleborate
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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 |
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krakentools/kreport2krona
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New module: krakentools/kreport2krona (#1746)
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2022-06-13 20:14:44 +02:00 |
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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 |
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last
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leehom
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legsta
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lima
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lissero
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lofreq
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macrel/contigs
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macs2/callpeak
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mafft
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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 |
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maltextract
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manta
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Update tests/modules/manta/convertinversion/main.nf
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2022-06-13 09:26:35 +02:00 |
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mapdamage2
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mash
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Patch mash screen
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2022-05-25 12:29:14 +00:00 |
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mashtree
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maxbin2
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maxquant/lfq
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mcroni
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add module for mcroni (#1750)
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2022-06-13 15:04:01 +02:00 |
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md5sum
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new module: md5sum
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2022-05-06 09:20:40 +02:00 |
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medaka
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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 |
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meningotype
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merquryfk
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Add MerquryFK KatGC (#1798)
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2022-06-23 20:57:15 +02:00 |
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meryl
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Merge branch 'master' into meryl_unionsum
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2022-05-09 16:16:08 +02:00 |
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metabat2
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metaphlan3
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methyldackel
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minia
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miniasm
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minimap2
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Update minimap2/align module (#1537)
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2022-04-26 16:32:20 +02:00 |
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mlst
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mobsuite/recon
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mosdepth
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Update main.nf
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2022-05-25 19:38:12 +01:00 |
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motus
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Update tests/modules/motus/profile/test.yml
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2022-05-12 20:55:54 +01:00 |
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msisensor
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msisensorpro
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mtnucratio
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multiqc
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formatting
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2022-06-08 14:42:58 +02:00 |
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mummer
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muscle
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nanolyse
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nanoplot
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ncbigenomedownload
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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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pairix
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pairtools
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panaroo/run
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pangolin
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paraclu
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pbbam/pbmerge
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pbccs
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peddy
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phantompeakqualtools
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Add task.ext.args to phantompeakqualtools and finish the module (#1474)
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2022-03-31 22:59:21 +01:00 |
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phyloflash
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picard
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fix tests (again)
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2022-05-22 06:54:09 +02:00 |
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pirate
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plasmidfinder
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add module for plasmidfinder (#1773)
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2022-06-15 10:25:51 -06:00 |
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plasmidid
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plink
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plink2
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pmdtools/filter
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porechop
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preseq
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prinseqplusplus
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Add PRINSEQPLUSPLUS (#1481)
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2022-04-03 16:06:22 +02:00 |
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prodigal
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prokka
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pycoqc
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pydamage
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qcat
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qualimap
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quast
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racon
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rapidnj
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rasusa
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raven
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raxmlng
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rgi/main
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Update RGI: add database version reporting to module (#1824)
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2022-06-29 16:30:51 -06:00 |
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rhocall/annotate
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update test
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2022-06-08 16:36:02 +02:00 |
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rmarkdownnotebook
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roary
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rsem
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Bump STAR version to 2.7.10a for RSEM modules (#1573)
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2022-04-27 19:21:26 +01:00 |
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rseqc
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rtgtools
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new module rtgtools/pedfilter (#1777)
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2022-06-14 16:02:18 +02:00 |
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salmon
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samblaster
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Samtools version update (#1507)
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2022-04-11 14:26:28 +02:00 |
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samtools
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samtools/*stats*: use prefix for outputs (#1788)
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2022-06-16 13:42:01 +02:00 |
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scoary
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seacr/callpeak
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seqkit
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feat: add module for seqkit stats (#1466)
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2022-03-30 23:01:17 +02:00 |
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seqsero2
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seqtk
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sequenzautils
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seqwish/induce
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sexdeterrmine
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Corrected test-datasets input
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2022-05-23 17:08:40 +02:00 |
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shasum
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added sha256sum
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2022-05-06 10:28:14 +02:00 |
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shigatyper
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Merge remote-tracking branch 'origin' into motus_profile
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2022-05-05 09:41:13 -04:00 |
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shovill
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sistr
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slimfastq
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Merge remote-tracking branch 'origin' into motus_profile
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2022-05-05 09:41:13 -04:00 |
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snapaligner
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snapaligner: improve index detection (#1836)
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2022-06-30 12:19:46 +02:00 |
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snippy/run
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make prettier
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2022-05-11 18:00:36 +00:00 |
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snpdists
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snpeff
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snpsift/split
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snpsites
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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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refactor: move files to custom section
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2022-05-11 17:33:45 +02:00 |
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srst2/srst2
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Merge remote-tracking branch 'origin' into motus_profile
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2022-05-05 09:41:13 -04:00 |
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ssuissero
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stadeniolib/scramble
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new tool: staden_io_lib (#1499)
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2022-04-08 09:54:15 -04:00 |
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staphopiasccmec
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star
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Fix tests
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2022-05-27 12:14:10 +01:00 |
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stranger
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add stubs for stranger (#1543)
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2022-04-22 10:10:43 +02:00 |
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strelka
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stringtie
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Rename process from STRINGTIE to STRINGTIE_STRINGTIE (#1546)
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2022-04-22 15:13:06 +01:00 |
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subread/featurecounts
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svdb
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tabix
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fix bgziptabix extension (#1784)
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2022-06-15 10:33:10 +02:00 |
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tbprofiler/profile
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tiddit
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TIDDIT - add --skip_assembly when no bwa specified (#1769)
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2022-06-13 17:02:59 +02:00 |
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transdecoder
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trimgalore
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Update all modules to new NF DSL2 syntax (#1099)
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2021-11-26 07:58:40 +00:00 |
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trimmomatic
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Trimmomatic (#1757)
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2022-06-17 13:18:15 +00:00 |
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ucsc
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ultra/pipeline
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umitools
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Fix Conda tests
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2022-05-23 22:39:12 +01:00 |
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unicycler
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untar
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fix untar output dir
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2022-06-02 11:09:55 +02:00 |
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unzip
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vardictjava
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Merge remote-tracking branch 'origin' into motus_profile
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2022-05-05 09:41:13 -04:00 |
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variantbam
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vcf2db
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new module vcf2db (#1795)
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2022-06-17 15:54:02 +02:00 |
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vcf2maf
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vcf2maf module with built in VEP (#1768)
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2022-06-20 18:27:12 +02:00 |
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vcfanno
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small changes to vcfanno (#1804)
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2022-06-24 08:58:26 +02:00 |
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vcflib/vcfuniq
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vcftools
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vsearch/usearchglobal
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prettier
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2022-05-30 13:35:12 +02:00 |
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yara
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