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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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Prettier (#1405)
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2022-03-18 14:27:50 +01:00 |
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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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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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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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bamutil/trimbam
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bandage/image
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bbmap
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feat(bbmap): Initialize pileup module (#1441)
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2022-03-24 17:38:24 -06:00 |
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bcftools
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Prettier (#1405)
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2022-03-18 14:27:50 +01:00 |
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bedtools
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biobambam/bammarkduplicates2
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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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bowtie2
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bracken/bracken
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Add bracken (#1423)
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2022-03-22 16:40:21 +01:00 |
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bwa
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Fix indentation in bwa/aln meta (#1392)
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2022-03-15 06:22:44 +01:00 |
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bwamem2
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bwameth
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cat
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CAT: Use meta map and supply output file name via modules.config (#1446)
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2022-03-25 14:01:57 +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 module (#1410)
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2022-03-18 15:39:27 +01:00 |
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checkm/lineagewf
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chromap
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Bump chromap version 0.2.0 (#1374)
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2022-03-10 09:23:45 +01:00 |
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clonalframeml
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cmseq/polymut
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cnvkit/batch
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cnvpytor
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Prettier (#1405)
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2022-03-18 14:27:50 +01:00 |
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controlfreec
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add makegraph script (#1452)
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2022-03-25 20:49:08 +01:00 |
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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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cutadapt
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damageprofiler
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dastool
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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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separate gvcf and vcf in output channels (#1371)
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2022-03-03 11:54:07 +01:00 |
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delly/call
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diamond
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dragmap
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feat: add readgroup info + reorder samtools command line to mimic bwamem (#1447)
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2022-03-25 11:26:47 +01:00 |
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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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ectyper
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emmtyper
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ensemblvep
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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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expansionhunter
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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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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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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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gatk4
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Prettier (#1405)
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2022-03-18 14:27:50 +01:00 |
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genmap
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genrich
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gffread
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glnexus
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graphmap2
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gstama
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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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Prettier (#1405)
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2022-03-18 14:27:50 +01:00 |
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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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Prettier (#1405)
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2022-03-18 14:27:50 +01:00 |
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homer
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Add samtools to homer/maketagdirectory to use bam files (#1437)
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2022-03-25 17:13:30 +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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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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krona
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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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Manta consistancy (#1407)
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2022-03-18 13:30:03 +01:00 |
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mapdamage2
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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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mash
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mashtree
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maxbin2
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Fix for Maxbin2 emitting input files (#1376)
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2022-03-08 15:56:23 +01:00 |
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medaka
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megahit
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Fix formatting in yaml files, add yamllint config (#1279)
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2022-02-15 11:15:27 +00:00 |
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meningotype
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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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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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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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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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Add BAM indexes as input for optitype module. (#1388)
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2022-03-15 17:02:40 +01:00 |
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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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phyloflash
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picard
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Prettier (#1405)
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2022-03-18 14:27:50 +01:00 |
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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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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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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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raven
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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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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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Add when: block (#1261)
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2022-02-04 09:53:32 +01:00 |
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roary
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rsem
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Prettier (#1405)
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2022-03-18 14:27:50 +01:00 |
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rseqc
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salmon
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samblaster
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samtools
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Mpileup also likes intervals (#1445)
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2022-03-25 07:46:51 +01:00 |
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scoary
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seacr/callpeak
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seqkit
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Prettier (#1405)
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2022-03-18 14:27:50 +01:00 |
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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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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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snpdists
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snpeff
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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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ssuissero
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Prettier (#1405)
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2022-03-18 14:27:50 +01:00 |
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staphopiasccmec
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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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star
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update star/align to include an optional sam output (support for --chimOutType SeparateSAMold option) (#1378)
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2022-03-23 13:13:58 +01:00 |
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stranger
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Prettier (#1405)
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2022-03-18 14:27:50 +01:00 |
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strelka
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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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stringtie
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subread/featurecounts
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svdb
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update svdb to version 2.5.2 (#1390)
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2022-03-21 10:39:34 +01:00 |
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tabix
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tbprofiler/profile
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tiddit
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transdecoder
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trimgalore
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ucsc
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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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Untar unzip meta (#1408)
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2022-03-21 14:49:28 +01:00 |
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unzip
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Untar unzip meta (#1408)
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2022-03-21 14:49:28 +01:00 |
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variantbam
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vcfanno
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vcflib/vcfuniq
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vcftools
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yara
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Prettier (#1405)
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2022-03-18 14:27:50 +01:00 |
