| .. |
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abacas
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abricate
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Prettier (#1405)
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2022-03-18 14:27:50 +01:00 |
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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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Add AdapterRemovalFixPrefix (#1424)
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2022-03-21 11:26:12 +01:00 |
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agrvate
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allelecounter
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fix incorrect yaml formatting. (#1264)
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2022-04-14 13:35:01 +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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Prettier (#1405)
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2022-03-18 14:27:50 +01:00 |
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antismash/antismashlitedownloaddatabases
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Fix commented-out command
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2022-05-02 16:56:39 +02:00 |
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arriba
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artic
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ascat
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Prettier (#1405)
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2022-03-18 14:27:50 +01:00 |
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assemblyscan
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ataqv/ataqv
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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 |
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bamaligncleaner
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bamcmp
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bamtools
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Update modules/bamtools/split/main.nf
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2022-04-22 19:36:08 +02:00 |
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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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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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bclconvert
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Module/bclconvert (#1485)
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2022-04-21 15:39:22 +02:00 |
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bedtools
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biobambam
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New tool: biobambam/bamsormadup (#1478)
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2022-04-06 08:18:23 +02:00 |
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biscuit
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Prettier (#1405)
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2022-03-18 14:27:50 +01:00 |
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bismark
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blast
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bowtie
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Samtools version update (#1507)
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2022-04-11 14:26:28 +02:00 |
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bowtie2
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Merge branch 'master' into expected_error_fix
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2022-05-03 11:49:35 +01:00 |
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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 |
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busco
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Update meta.yml
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2022-05-06 11:56:43 +00:00 |
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bwa
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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 |
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bwamem2
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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 |
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bwameth
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cat
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Replace vanilla Linux Biocontainer with Ubuntu (#1557)
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2022-04-22 14:50:07 +01:00 |
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cellranger
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Prettier (#1405)
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2022-03-18 14:27:50 +01:00 |
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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/batch
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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 |
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cnvpytor
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remove prefix def in callcnvs
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2022-05-06 10:56:58 +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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Prettier (#1405)
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2022-03-18 14:27:50 +01:00 |
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custom
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Bump SAMtools version for custom/getchromsizes (#1572)
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2022-04-27 19:15:11 +02:00 |
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cutadapt
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damageprofiler
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dastool
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DASTool output channels update (#1489)
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2022-04-04 13:31:36 +02:00 |
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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 |
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deeptools
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style(deeptools): Indent script (#1439)
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2022-03-24 19:44:31 +00:00 |
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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 |
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delly/call
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diamond
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Add warn of default being used
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2022-05-02 12:41:24 +02:00 |
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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 |
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dragonflye
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Update dragonflye to latest version (#1442)
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2022-03-24 14:56:32 -04:00 |
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dshbio
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Update dsh-bio to version 2.0.8. (#1483)
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2022-04-09 11:13:47 -05:00 |
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ectyper
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elprep
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Update modules/elprep/merge/main.nf
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2022-04-29 15:07:09 +02:00 |
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emmtyper
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ensemblvep
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update ensemblvep and snpeff modules
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2022-05-05 12:57:14 +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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Prettier (#1405)
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2022-03-18 14:27:50 +01:00 |
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fargene
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fastani
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fastp
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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 |
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fastqscan
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fasttree
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fgbio
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filtlong
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flash
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freebayes
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gamma
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new module: GAMMA (#1532)
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2022-04-23 10:12:06 -04:00 |
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gatk4
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revert markduplciatespark container
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2022-05-12 17:40:42 +02:00 |
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genmap
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genrich
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gffread
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glnexus
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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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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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Replace vanilla Linux Biocontainer with Ubuntu (#1557)
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2022-04-22 14:50:07 +01:00 |
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hamronization
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Prettier (#1405)
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2022-03-18 14:27:50 +01:00 |
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happy
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Split the module into two parts
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2022-05-04 15:29:48 +02:00 |
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hicap
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hifiasm
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hisat2
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Samtools version update (#1507)
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2022-04-11 14:26:28 +02:00 |
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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 |
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homer
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Fix homer/maketagdirectory output collision (#1456)
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2022-03-27 03:17:42 +00:00 |
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hpsuissero
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Prettier (#1405)
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2022-03-18 14:27:50 +01:00 |
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ichorcna
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Prettier (#1405)
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2022-03-18 14:27:50 +01:00 |
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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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Kaiju2table module (#1545)
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2022-04-22 11:26:30 +02:00 |
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kallisto/index
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kallistobustools
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khmer/normalizebymedian
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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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krona
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integrating suggestions from PR comments, including recovery of tests for kronadb and more detailed explanation of input database in yml file
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2022-05-05 13:51:41 +02:00 |
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last
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leehom
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legsta
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Prettier (#1405)
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2022-03-18 14:27:50 +01:00 |
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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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Prettier (#1405)
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2022-03-18 14:27:50 +01:00 |
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mafft
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Prettier (#1405)
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2022-03-18 14:27:50 +01:00 |
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malt
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maltextract
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manta
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Revert manta changes (#1518)
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2022-04-12 10:40:06 +02:00 |
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mapdamage2
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mash
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mashtree
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maxbin2
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md5sum
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fix software definitions
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2022-05-06 11:07:05 +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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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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Add additional handling of fq.gz file name suffix
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2022-05-02 14:16:12 +02:00 |
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methyldackel
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minia
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miniasm
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minimap2
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Fix typo (#1586)
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2022-04-29 09:37:23 +02:00 |
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mlst
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mobsuite/recon
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Prettier (#1405)
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2022-03-18 14:27:50 +01:00 |
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mosdepth
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motus/downloaddb
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Apply suggestions from code review
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2022-05-05 08:23:51 +02:00 |
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msisensor
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msisensorpro
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Prettier (#1405)
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2022-03-18 14:27:50 +01:00 |
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mtnucratio
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multiqc
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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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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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Prettier (#1405)
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2022-03-18 14:27:50 +01:00 |
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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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add module for panaroo, fix pirate tests (#1444)
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2022-03-24 20:11:04 -06:00 |
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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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Allow to pass arguments to the phantompeakqualtools script itself (#1562)
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2022-04-25 19:07:43 +02:00 |
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phyloflash
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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 |
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picard
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fix reference arg
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2022-04-29 11:12:24 +02:00 |
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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 |
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plasmidid
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plink
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plink2
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Prettier (#1405)
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2022-03-18 14:27:50 +01:00 |
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pmdtools/filter
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porechop
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preseq
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Split preseq lcextrap and ccurve (#1440)
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2022-03-25 17:11:40 +00:00 |
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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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Update PyDamage module (#1467)
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2022-03-31 09:18:18 -04:00 |
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qcat
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qualimap
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Samtools version update (#1507)
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2022-04-11 14:26:28 +02:00 |
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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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Prettier (#1405)
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2022-03-18 14:27:50 +01:00 |
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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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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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rename aligned to alignment
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2022-05-09 16:07:49 +02:00 |
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scoary
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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 |
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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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Prettier (#1405)
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2022-03-18 14:27:50 +01:00 |
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sequenzautils
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seqwish/induce
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shasum
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fix software definitions
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2022-05-06 11:07:05 +02:00 |
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shigatyper
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Update modules/shigatyper/main.nf
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2022-04-22 08:49:44 -06:00 |
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shovill
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sistr
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Prettier (#1405)
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2022-03-18 14:27:50 +01:00 |
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slimfastq
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feat: add module for slimfastq
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2022-05-02 23:16:59 +02:00 |
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snapaligner
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merge snapaligner modes into one
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2022-05-06 14:10:44 +02:00 |
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snpdists
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snpeff
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update ensemblvep and snpeff modules
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2022-05-05 12:57:14 +02:00 |
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snpsift/split
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snpsites
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sortmerna
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sourmash/sketch
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Prettier (#1405)
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2022-03-18 14:27:50 +01:00 |
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spades
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spatyper
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sratools
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fix: remove retry label
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2022-05-06 17:28:56 +02:00 |
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srst2/srst2
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added tests
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2022-05-02 11:30:19 -04:00 |
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ssuissero
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Prettier (#1405)
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2022-03-18 14:27:50 +01:00 |
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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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Samtools version update (#1507)
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2022-04-11 14:26:28 +02:00 |
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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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update svdb version
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2022-05-06 00:18:16 +02:00 |
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tabix
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csi output in TABIX (#1579)
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2022-04-28 14:41:01 +02:00 |
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tbprofiler/profile
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tiddit
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Fix tiddit/sv (#1580)
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2022-04-28 14:06:38 +02:00 |
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transdecoder
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trimgalore
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Add Trimgalore output for unpaired reads (#1568)
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2022-04-26 19:15:24 +01:00 |
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ucsc
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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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ultra/pipeline
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umitools
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Add outputs for umitools dedup summary stats (#1422)
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2022-03-18 20:21:41 +00:00 |
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unicycler
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untar
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Replace vanilla Linux Biocontainer with Ubuntu (#1557)
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2022-04-22 14:50:07 +01:00 |
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unzip
|
Untar unzip meta (#1408)
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2022-03-21 14:49:28 +01:00 |
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vardictjava
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Moved the BED file to the main tuple
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2022-05-03 15:31:05 +02:00 |
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variantbam
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vcfanno
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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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vcflib/vcfuniq
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vcftools
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yara
|
Samtools version update (#1507)
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2022-04-11 14:26:28 +02:00 |
