| .. |
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abacas
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Rename software/ directory to modules/ to re-organise module structure (#567)
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2021-07-07 10:10:18 +01:00 |
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adapterremoval
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Fix read indexing in AdapterRemoval module (#1051)
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2021-11-10 12:21:12 +00:00 |
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agrvate
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module for agrvate (#693)
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2021-09-16 12:42:23 +02:00 |
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allelecounter
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Add cram support to Allelecounter module (#1013)
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2021-11-02 17:00:25 +01:00 |
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amps
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add Amps (#768)
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2021-09-30 12:54:16 +02:00 |
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arriba
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Added module arriba (#611)
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2021-07-22 15:19:42 +01:00 |
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artic
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Rename software/ directory to modules/ to re-organise module structure (#567)
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2021-07-07 10:10:18 +01:00 |
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assemblyscan
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add new assembly scan module (#971)
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2021-10-29 10:01:23 +02:00 |
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ataqv/ataqv
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Add new module 'ataqv/ataqv' (#998)
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2021-11-15 12:51:40 +00:00 |
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bamaligncleaner
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Add module: bamaligncleaner (#676)
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2021-09-15 10:31:49 +02:00 |
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bamtools/split
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Update module: bamtools/split (#885)
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2021-10-23 19:39:27 +01:00 |
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bamutil/trimbam
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Add bamutil/trimbam (#1060)
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2021-11-15 16:44:12 +00:00 |
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bandage/image
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Fix version commands (#749)
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2021-09-27 22:10:37 +01:00 |
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bbmap
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Add log to output from bbmap/align (#1050)
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2021-11-10 10:27:52 +00:00 |
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bcftools
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Add bcftools/index (#812)
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2021-10-13 10:40:04 +02:00 |
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bedtools
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Bedtools sort add extension choice input (#984)
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2021-10-29 13:22:17 +01:00 |
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bismark
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Fix version commands (#749)
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2021-09-27 22:10:37 +01:00 |
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blast
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nf-core modules bump-versions for all modules (#630)
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2021-07-28 09:10:44 +01:00 |
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bowtie
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Fix version commands (#749)
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2021-09-27 22:10:37 +01:00 |
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bowtie2
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Fix version commands (#749)
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2021-09-27 22:10:37 +01:00 |
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bwa
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Bwa index (#1040)
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2021-11-15 11:26:01 +00:00 |
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bwamem2
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Fix version commands (#749)
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2021-09-27 22:10:37 +01:00 |
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bwameth
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Fix more version commands (#750)
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2021-09-28 06:56:27 +01:00 |
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cat
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Fix flash and cat/fastq modules (#759)
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2021-09-28 21:14:11 +01:00 |
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cellranger/mkref
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new module cellranger mkref (#896)
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2021-10-28 13:33:57 +02:00 |
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checkm/lineagewf
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New module: checkm/lineagewf (#899)
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2021-10-26 21:54:10 +01:00 |
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chromap
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Chromap Module (#659)
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2021-09-15 17:20:55 +01:00 |
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clonalframeml
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add clonalframeml module (#974)
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2021-11-15 19:43:53 +00:00 |
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cmseq/polymut
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Add new module: cmseq/polymut (#918)
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2021-11-09 16:12:51 +01:00 |
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cnvkit
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Rename software/ directory to modules/ to re-organise module structure (#567)
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2021-07-07 10:10:18 +01:00 |
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cooler
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Cooler cload (#634)
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2021-11-15 21:43:55 +00:00 |
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csvtk
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Added new module csvtk/split (#1014)
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2021-11-15 18:29:55 +00:00 |
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custom
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Add module get_chrom_sizes (#1063)
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2021-11-15 19:22:12 +00:00 |
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cutadapt
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Rename software/ directory to modules/ to re-organise module structure (#567)
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2021-07-07 10:10:18 +01:00 |
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damageprofiler
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fix: reduce number of required input files for damage profiler (#612)
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2021-10-20 10:02:30 +02:00 |
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dastool
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Add new module: Das Tool (#1004)
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2021-11-19 08:33:29 +01:00 |
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dedup
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Add module: dedup (#907)
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2021-10-28 12:10:21 +02:00 |
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deeptools
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nf-core modules bump-versions for all modules (#630)
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2021-07-28 09:10:44 +01:00 |
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delly/call
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few version and test data config fixes (#758)
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2021-09-28 20:42:04 +01:00 |
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diamond
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Diamond (#710)
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2021-09-23 09:13:04 +01:00 |
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dragonflye
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add module for dragonflye (#633)
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2021-08-16 11:51:30 +02:00 |
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dshbio
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Add dsh-bio export-segments module (#631)
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2021-08-17 15:53:41 +02:00 |
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emmtyper
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add emmtyper module (#1028)
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2021-11-08 20:43:15 +01:00 |
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ensemblvep
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Rename software/ directory to modules/ to re-organise module structure (#567)
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2021-07-07 10:10:18 +01:00 |
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expansionhunter
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Expansionhunter (#666)
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2021-08-16 17:47:42 +02:00 |
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fargene
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new module fargene (#1068)
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2021-11-15 16:42:48 +00:00 |
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fastani
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module fastani (#695)
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2021-09-21 20:20:26 +01:00 |
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fastp
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enhance module fastp: add save_merged (#598) (#614)
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2021-07-23 10:44:00 +01:00 |
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fastqc
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Rename software/ directory to modules/ to re-organise module structure (#567)
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2021-07-07 10:10:18 +01:00 |
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fastqscan
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add module for fastq-scan (#935)
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2021-11-15 15:41:36 +01:00 |
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fasttree
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Rename software/ directory to modules/ to re-organise module structure (#567)
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2021-07-07 10:10:18 +01:00 |
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fgbio
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Fgbio group reads by umi (#952)
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2021-10-29 14:00:54 +02:00 |
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filtlong
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add filtlong (#919)
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2021-10-27 17:00:11 +02:00 |
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flash
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Fix flash and cat/fastq modules (#759)
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2021-09-28 21:14:11 +01:00 |
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freebayes
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fix remove md5sum check (#1017)
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2021-11-03 11:41:12 +01:00 |
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gatk4
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Update in GATK4 variantfiltration: Added vcf_index to vcf tuple; output to vcf.gz format. (#1083)
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2021-11-18 21:47:40 +01:00 |
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genmap
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Fix more version commands (#750)
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2021-09-28 06:56:27 +01:00 |
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genrich
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Refactor genrich to avoid params in main (#981)
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2021-10-29 16:37:39 +02:00 |
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gffread
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Fix bug in gffread (#686)
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2021-09-15 19:55:08 +01:00 |
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glnexus
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Add glnexus (#729)
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2021-09-22 13:31:01 +01:00 |
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graphmap2
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Rename software/ directory to modules/ to re-organise module structure (#567)
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2021-07-07 10:10:18 +01:00 |
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gstama
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Update: gstama/collapse (#1057)
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2021-11-11 14:57:55 +00:00 |
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gtdbtk/classifywf
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Add gtdbtk/classifywf module (#765)
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2021-10-05 21:23:01 +01:00 |
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gubbins
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nf-core modules bump-versions for all modules (#630)
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2021-07-28 09:10:44 +01:00 |
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gunc
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New module: gunc run (+ gunc downloaddb) (#880)
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2021-11-03 17:01:23 +01:00 |
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gunzip
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Rename software/ directory to modules/ to re-organise module structure (#567)
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2021-07-07 10:10:18 +01:00 |
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hicap
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[fix] hicap module allow optional outputs (#937)
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2021-11-16 09:23:07 +00:00 |
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hifiasm
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few version and test data config fixes (#758)
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2021-09-28 20:42:04 +01:00 |
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hisat2
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nf-core modules bump-versions for all modules (#630)
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2021-07-28 09:10:44 +01:00 |
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hmmcopy
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readcounter module for hmmcopy (#1001)
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2021-11-02 11:01:13 +00:00 |
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hmmer/hmmalign
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Rename software/ directory to modules/ to re-organise module structure (#567)
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2021-07-07 10:10:18 +01:00 |
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homer
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Homer Modules (#75)
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2021-09-08 15:40:34 +00:00 |
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idr
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Add IDR module (#908)
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2021-10-30 10:52:13 +02:00 |
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imputeme/vcftoprs
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Imputeme (#882)
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2021-11-05 10:25:54 +01:00 |
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iqtree
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Module new version reporting fixes (#753)
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2021-09-28 10:51:19 +01:00 |
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ismapper
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add ismapper module (#773)
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2021-10-05 21:55:41 +01:00 |
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isoseq3
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Update isoseq3/cluster (#856)
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2021-10-14 11:07:53 +01:00 |
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ivar
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Fix more version commands (#750)
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2021-09-28 06:56:27 +01:00 |
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jupyternotebook
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Notebook modules (#617)
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2021-10-24 20:51:56 +02:00 |
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kallisto/index
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Fix yml ver (#756)
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2021-09-28 18:33:07 +02:00 |
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kallistobustools
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Fix yml ver (#756)
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2021-09-28 18:33:07 +02:00 |
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khmer/normalizebymedian
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Khmer normalizebymedian (#985)
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2021-10-29 13:23:34 +02:00 |
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kleborate
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Add module kleborate (#711)
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2021-09-21 20:45:42 +01:00 |
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kraken2/kraken2
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Rename software/ directory to modules/ to re-organise module structure (#567)
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2021-07-07 10:10:18 +01:00 |
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kronatools
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add Kronatools KTImportTaxonomy (#928)
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2021-11-15 17:40:46 +00:00 |
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last
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nf-core modules bump-versions for all modules (#630)
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2021-07-28 09:10:44 +01:00 |
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leehom
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Add leehom module (#1052)
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2021-11-15 15:26:06 +01:00 |
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lima
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New module: LIMA (#719)
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2021-09-27 16:14:35 +01:00 |
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lissero
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add lissero module (#1026)
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2021-11-08 20:52:07 +01:00 |
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lofreq
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fix: lofreq/callparallel missing arg (#562) (#586)
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2021-07-19 09:19:27 +01:00 |
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macs2/callpeak
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Macs2 calllpeak (#1038)
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2021-11-15 18:17:40 +01:00 |
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malt
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update: MALT build version bump (#699)
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2021-09-15 16:46:29 +01:00 |
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maltextract
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add: MALTEXTRACT (#725)
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2021-09-21 19:57:27 +01:00 |
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manta
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adding new manta/germline + manta/tumoronly modules (#906)
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2021-10-27 18:24:48 +02:00 |
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mapdamage2
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Add new module Mapdamage2 (#975)
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2021-11-09 14:05:23 +01:00 |
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mash/sketch
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Rename software/ directory to modules/ to re-organise module structure (#567)
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2021-07-07 10:10:18 +01:00 |
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mashtree
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add mashtree module (#767)
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2021-10-05 21:27:30 +01:00 |
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maxbin2
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New module: maxbin2 (#895)
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2021-10-26 22:07:33 +01:00 |
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medaka
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Add Medaka module (#992)
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2021-11-15 17:26:37 +00:00 |
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megahit
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Add MEGAHIT (#810)
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2021-10-12 16:06:06 +01:00 |
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meningotype
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add meningotype module (#1022)
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2021-11-06 16:44:26 +01:00 |
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metabat2
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New module: metabat2 (#875)
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2021-11-08 21:08:26 +01:00 |
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metaphlan3
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Rename software/ directory to modules/ to re-organise module structure (#567)
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2021-07-07 10:10:18 +01:00 |
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methyldackel
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Fix version commands (#749)
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2021-09-27 22:10:37 +01:00 |
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minia
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Fix version commands (#749)
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2021-09-27 22:10:37 +01:00 |
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miniasm
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Add Miniasm module (#962)
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2021-11-15 17:50:56 +00:00 |
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minimap2
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Add Racon module to nf-core/modules (#949)
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2021-10-29 13:33:38 +01:00 |
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mlst
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added classic mlst module (#742)
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2021-10-05 20:49:46 +01:00 |
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mosdepth
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Rename software/ directory to modules/ to re-organise module structure (#567)
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2021-07-07 10:10:18 +01:00 |
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msisensor
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Rename software/ directory to modules/ to re-organise module structure (#567)
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2021-07-07 10:10:18 +01:00 |
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mtnucratio
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Mtnucratio (#986)
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2021-10-29 15:02:02 +02:00 |
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multiqc
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Rename software/ directory to modules/ to re-organise module structure (#567)
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2021-07-07 10:10:18 +01:00 |
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mummer
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Initial commit mummer module (#940)
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2021-11-15 16:53:41 +01:00 |
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muscle
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Rename software/ directory to modules/ to re-organise module structure (#567)
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2021-07-07 10:10:18 +01:00 |
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nanolyse
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Rename software/ directory to modules/ to re-organise module structure (#567)
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2021-07-07 10:10:18 +01:00 |
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nanoplot
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Rename software/ directory to modules/ to re-organise module structure (#567)
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2021-07-07 10:10:18 +01:00 |
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ncbigenomedownload
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add ncbi-genome-download module (#980)
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2021-11-15 18:32:53 +00:00 |
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nextclade
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Update Nextclade to output all files by default (#638)
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2021-07-28 19:49:50 +01:00 |
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ngmaster
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add ngmaster module (#1024)
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2021-11-10 11:25:50 -07:00 |
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nucmer
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add new nucmer module (#945)
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2021-11-15 22:05:34 +00:00 |
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optitype
|
Updating test file for optitype (#782)
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2021-10-28 14:24:52 +02:00 |
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pairix
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Rename software/ directory to modules/ to re-organise module structure (#567)
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2021-07-07 10:10:18 +01:00 |
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pairtools
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Rename software/ directory to modules/ to re-organise module structure (#567)
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2021-07-07 10:10:18 +01:00 |
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pangolin
|
Update pangolin to 3.1.11 (#721)
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2021-09-20 19:59:05 +01:00 |
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paraclu
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add paraclu (#909)
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2021-10-27 15:48:49 +02:00 |
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pbbam/pbmerge
|
New module: pbbam/pbmerge (#752)
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2021-10-05 23:16:45 +01:00 |
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pbccs
|
Update module: pbccs (#1018)
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2021-11-11 14:19:26 +00:00 |
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picard
|
Fix picard markduplicates (#1084)
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2021-11-18 21:54:14 +01:00 |
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pirate
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add pirate module (#777)
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2021-10-05 22:28:25 +01:00 |
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plasmidid
|
Fix yml ver (#756)
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2021-09-28 18:33:07 +02:00 |
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plink
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Implement plink/extract module (#901)
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2021-11-09 14:03:13 +00:00 |
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plink2/vcf
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New module: plink2/vcf (#1006)
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2021-11-15 13:55:18 +00:00 |
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pmdtools/filter
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add new module pmdtools/filter #847 (#963)
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2021-11-13 15:09:14 +00:00 |
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porechop
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add porechop module (#914)
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2021-10-28 13:21:36 +02:00 |
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preseq/lcextrap
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Rename software/ directory to modules/ to re-organise module structure (#567)
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2021-07-07 10:10:18 +01:00 |
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prodigal
|
Rename software/ directory to modules/ to re-organise module structure (#567)
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2021-07-07 10:10:18 +01:00 |
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prokka
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Rename software/ directory to modules/ to re-organise module structure (#567)
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2021-07-07 10:10:18 +01:00 |
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pycoqc
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Rename software/ directory to modules/ to re-organise module structure (#567)
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2021-07-07 10:10:18 +01:00 |
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pydamage
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Pydamage analyzer update (#863)
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2021-10-18 15:24:49 +02:00 |
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qcat
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Rename software/ directory to modules/ to re-organise module structure (#567)
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2021-07-07 10:10:18 +01:00 |
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qualimap/bamqc
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Fix more version commands (#750)
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2021-09-28 06:56:27 +01:00 |
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quast
|
Rename software/ directory to modules/ to re-organise module structure (#567)
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2021-07-07 10:10:18 +01:00 |
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racon
|
Add Racon module to nf-core/modules (#949)
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2021-10-29 13:33:38 +01:00 |
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rapidnj
|
Rename software/ directory to modules/ to re-organise module structure (#567)
|
2021-07-07 10:10:18 +01:00 |
|
rasusa
|
Rename software/ directory to modules/ to re-organise module structure (#567)
|
2021-07-07 10:10:18 +01:00 |
|
raxmlng
|
Rename software/ directory to modules/ to re-organise module structure (#567)
|
2021-07-07 10:10:18 +01:00 |
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rmarkdownnotebook
|
Notebook modules (#617)
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2021-10-24 20:51:56 +02:00 |
|
roary
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add roary module (#776)
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2021-10-05 22:08:47 +01:00 |
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rsem
|
Update checksum modules using human GTF (#900)
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2021-10-26 23:09:04 +01:00 |
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rseqc
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Rename software/ directory to modules/ to re-organise module structure (#567)
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2021-07-07 10:10:18 +01:00 |
|
salmon
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Fix version commands (#749)
|
2021-09-27 22:10:37 +01:00 |
|
samblaster
|
New module: Samblaster (#954)
|
2021-11-04 18:18:56 +01:00 |
|
samtools
|
Add thread option to samtools modules (#1069)
|
2021-11-18 22:24:47 +01:00 |
|
scoary
|
add scoary module (#1034)
|
2021-11-06 16:34:39 +01:00 |
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seacr/callpeak
|
I accidently deleted a branch before the PR merged for PR 800 (#881)
|
2021-10-21 12:28:59 +01:00 |
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seqkit/split2
|
Fix version commands: round 3 (#754)
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2021-09-28 14:37:47 +01:00 |
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seqsero2
|
add seqsero2 module (#1016)
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2021-11-04 07:49:30 +00:00 |
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seqtk
|
New module seqtk/mergepe (#951)
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2021-10-28 16:53:33 +02:00 |
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sequenzautils
|
Fix version commands: round 3 (#754)
|
2021-09-28 14:37:47 +01:00 |
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seqwish/induce
|
Rename software/ directory to modules/ to re-organise module structure (#567)
|
2021-07-07 10:10:18 +01:00 |
|
shovill
|
Rename software/ directory to modules/ to re-organise module structure (#567)
|
2021-07-07 10:10:18 +01:00 |
|
snpdists
|
module: snp-dists (#697)
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2021-09-15 16:36:49 +01:00 |
|
snpeff
|
Rename software/ directory to modules/ to re-organise module structure (#567)
|
2021-07-07 10:10:18 +01:00 |
|
snpsites
|
Rename software/ directory to modules/ to re-organise module structure (#567)
|
2021-07-07 10:10:18 +01:00 |
|
spades
|
Change Spades input (#1039)
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2021-11-15 11:53:07 +00:00 |
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spatyper
|
add spatyper module (#784)
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2021-10-05 22:21:35 +01:00 |
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sratools
|
Fix subworkflows seperate from modules (#933)
|
2021-11-15 18:18:46 +00:00 |
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staphopiasccmec
|
add staphopia-sccmec module (#702)
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2021-09-15 17:24:11 +01:00 |
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star
|
Update checksum modules using human GTF (#900)
|
2021-10-26 23:09:04 +01:00 |
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strelka
|
Update strelka, by enabling BP if Manta candidates are present (#923)
|
2021-10-27 17:49:54 +02:00 |
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stringtie
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Update checksum modules using human GTF (#900)
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2021-10-26 23:09:04 +01:00 |
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subread/featurecounts
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fix more ver yml (#757)
|
2021-09-28 20:25:10 +01:00 |
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tabix
|
nf-core modules bump-versions for all modules (#630)
|
2021-07-28 09:10:44 +01:00 |
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tbprofiler/profile
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add module for tbprofiler (#947)
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2021-11-15 15:35:55 +01:00 |
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tiddit
|
Add TIDDIT cov (#822)
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2021-10-13 12:59:35 +02:00 |
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trimgalore
|
Rename software/ directory to modules/ to re-organise module structure (#567)
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2021-07-07 10:10:18 +01:00 |
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ucsc
|
New module: ucsc/liftover (#868)
|
2021-10-21 18:04:15 +02:00 |
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ultra/pipeline
|
New module: Ultra (#871)
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2021-11-15 15:57:58 +00:00 |
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unicycler
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Unicycler with long read input (#1041)
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2021-11-15 11:48:56 +00:00 |
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untar
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Rename software/ directory to modules/ to re-organise module structure (#567)
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2021-07-07 10:10:18 +01:00 |
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unzip
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Unzip update (#730)
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2021-09-22 11:02:32 +01:00 |
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variantbam
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Add variantbam (#618)
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2021-07-26 19:07:29 +01:00 |
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vcftools
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Rename software/ directory to modules/ to re-organise module structure (#567)
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2021-07-07 10:10:18 +01:00 |
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yara
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fix more ver yml (#757)
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2021-09-28 20:25:10 +01:00 |
72c94dbed9