| .. |
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abacas
|
Update all modules to new NF DSL2 syntax (#1099)
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2021-11-26 07:58:40 +00:00 |
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abricate
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add module for abricate (#1280)
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2022-02-18 18:00:21 -07:00 |
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adapterremoval
|
Refactor adapterremoval (#1491)
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2022-04-04 21:40:35 +02:00 |
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adapterremovalfixprefix
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Set process label to process_single for modules with no task.cpus usage (#2076)
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2022-09-19 11:54:47 +02:00 |
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agrvate
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Update all modules to new NF DSL2 syntax (#1099)
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2021-11-26 07:58:40 +00:00 |
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allelecounter
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Update all modules to new NF DSL2 syntax (#1099)
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2021-11-26 07:58:40 +00:00 |
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ampir
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Add file name collision check + TSV output
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2022-06-10 12:54:39 +02:00 |
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amplify/predict
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add module AMPlify (#1498)
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2022-04-20 11:53:26 +02:00 |
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amps
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Untar unzip meta (#1408)
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2022-03-21 14:49:28 +01:00 |
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amrfinderplus
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Amrfinderplus: add db-version to versions.yml (#1899)
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2022-07-19 09:52:36 +02:00 |
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angsd/docounts
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Add: ANGSD_DOCOUNTS (#2044)
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2022-09-27 13:21:44 +02:00 |
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antismash
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Apply suggestions from code review
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2022-05-12 15:28:19 +02:00 |
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ariba
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add module for ariba (#1731)
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2022-06-15 10:18:31 -06:00 |
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arriba
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Update Arriba to 2.3.0 (#1827)
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2022-06-29 14:39:13 +02:00 |
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artic
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Bump tool versions for modules required in viralrecon (#1859)
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2022-07-07 14:48:04 +01:00 |
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ascat
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Added output files to ASCAT (#1820)
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2022-06-28 14:45:57 +02:00 |
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assemblyscan
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Update all modules to new NF DSL2 syntax (#1099)
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2021-11-26 07:58:40 +00:00 |
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ataqv
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Ataqv mkarv (#1857)
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2022-07-07 22:40:31 +02:00 |
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atlas
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New Module: atlas/recal (#1915)
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2022-07-22 15:36:53 +02:00 |
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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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Update all modules to new NF DSL2 syntax (#1099)
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2021-11-26 07:58:40 +00:00 |
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bamcmp
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bamcmp (#1244)
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2022-02-02 16:38:41 +00:00 |
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bamtools
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Adding module bamtools stats (#2104)
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2022-09-27 06:24:43 +01:00 |
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bamutil/trimbam
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Update all modules to new NF DSL2 syntax (#1099)
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2021-11-26 07:58:40 +00:00 |
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bandage/image
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Update all modules to new NF DSL2 syntax (#1099)
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2021-11-26 07:58:40 +00:00 |
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bases2fastq
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Add bases2fastq (#2054)
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2022-09-15 13:50:33 +00:00 |
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bbmap
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New module - BBMap clumpify (#1978)
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2022-09-05 08:23:08 +02:00 |
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bcftools
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Fix bcftools/stats module (#1953)
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2022-09-21 16:10:38 +02:00 |
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bcl2fastq
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Module/bcl2fastq (#1883)
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2022-07-14 13:18:21 +02:00 |
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bclconvert
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Bump bcl-convert version (#2077)
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2022-09-16 14:34:52 +02:00 |
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bedtools
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added bedtools split
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2022-05-17 14:24:32 +02:00 |
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biobambam
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bamsormadup: add extra test case, fix single file input (#1905)
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2022-07-19 13:52:37 +02:00 |
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biscuit
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Add core Biscuit tools (#1354)
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2022-03-14 09:34:22 -04:00 |
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bismark
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Update all modules to new NF DSL2 syntax (#1099)
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2021-11-26 07:58:40 +00:00 |
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blast
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Add blast/tblastn module (#2092)
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2022-09-26 17:43:41 +02:00 |
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bowtie
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Update all modules to new NF DSL2 syntax (#1099)
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2021-11-26 07:58:40 +00:00 |
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bowtie2
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add PE sorted test
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2022-05-13 19:16:50 +02:00 |
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bracken
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Add bracken/combinebrackenoutputs (#2022)
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2022-09-07 09:18:21 +02:00 |
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busco
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Update busco to v5.4.3 and tar small files (#1970)
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2022-08-30 10:25:01 +02:00 |
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bwa
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Samtools version update (#1507)
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2022-04-11 14:26:28 +02:00 |
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bwamem2
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Added support for meta in bwamem2/index (#1921)
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2022-07-26 21:48:47 +01:00 |
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bwameth
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Fix formatting in yaml files, add yamllint config (#1279)
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2022-02-15 11:15:27 +00:00 |
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cat
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add stub for cat/fastq (#1943)
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2022-08-09 09:18:37 +02:00 |
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cellranger
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Remove empty file md5sum
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2022-06-10 11:53:28 +02:00 |
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centrifuge
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Update module: Use report insted of results for centrifuge/kreport (#1929)
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2022-07-27 14:24:06 +02:00 |
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checkm/lineagewf
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Fix formatting in yaml files, add yamllint config (#1279)
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2022-02-15 11:15:27 +00:00 |
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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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Update all modules to new NF DSL2 syntax (#1099)
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2021-11-26 07:58:40 +00:00 |
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cmseq/polymut
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Update all modules to new NF DSL2 syntax (#1099)
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2021-11-26 07:58:40 +00:00 |
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cnvkit
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added fasta_fai as input + changed if statements
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2022-06-02 12:57:50 +02:00 |
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cnvpytor
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combine multiple pytor
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2022-05-05 23:59:12 +02:00 |
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controlfreec
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Fix Controlfreec: Add stub runs to test single sample input & make conda work with R scripts (#1504)
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2022-04-08 11:43:40 +02:00 |
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cooler
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Update all modules to new NF DSL2 syntax (#1099)
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2021-11-26 07:58:40 +00:00 |
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csvtk
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Update all modules to new NF DSL2 syntax (#1099)
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2021-11-26 07:58:40 +00:00 |
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custom
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Updated dumpsoftwareversions.py to match the pipeline template (#2045)
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2022-09-26 18:45:07 +01:00 |
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cutadapt
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Update all modules to new NF DSL2 syntax (#1099)
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2021-11-26 07:58:40 +00:00 |
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damageprofiler
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Set process label to process_single for modules with no task.cpus usage (#2076)
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2022-09-19 11:54:47 +02:00 |
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dastool
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Update DASTool to 1.1.4 (#1471)
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2022-04-01 11:33:07 +02:00 |
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dedup
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Update all modules to new NF DSL2 syntax (#1099)
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2021-11-26 07:58:40 +00:00 |
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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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deepbgc
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new module: deepbgc/pipeline (#2014)
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2022-09-07 14:59:01 +02:00 |
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deeptools
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changed container + add cram2bam conversion
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2022-06-02 10:38:05 +02:00 |
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deepvariant
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Update version & add intervals usage (#1214)
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2022-01-17 16:40:31 +01:00 |
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delly/call
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updated the version of delly (#2105)
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2022-09-27 08:57:36 +02:00 |
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diamond
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Update DIAMOND module to output log file (#1879)
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2022-07-14 16:18:28 +02:00 |
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dragmap
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Fix formatting in yaml files, add yamllint config (#1279)
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2022-02-15 11:15:27 +00:00 |
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dragonflye
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Update all modules to new NF DSL2 syntax (#1099)
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2021-11-26 07:58:40 +00:00 |
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dshbio
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Update dsh-bio to version 2.0.7, add support for compressed GFA 1.0 format (#1207)
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2022-01-17 09:24:40 +00:00 |
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ectyper
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Fix formatting in yaml files, add yamllint config (#1279)
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2022-02-15 11:15:27 +00:00 |
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eido
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Update eido/validate module (#2071)
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2022-09-16 09:00:03 -04:00 |
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elprep
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Merge remote-tracking branch 'origin' into motus_profile
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2022-05-05 09:41:13 -04:00 |
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emmtyper
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Update all modules to new NF DSL2 syntax (#1099)
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2021-11-26 07:58:40 +00:00 |
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endorspy
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New Module: endorspy (#1916)
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2022-09-28 11:28:11 +02:00 |
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ensemblvep
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update ensemblvep to 106.1 and cache to 106 (#1876)
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2022-07-13 13:43:03 +02:00 |
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entrezdirect
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Set process label to process_single for modules with no task.cpus usage (#2076)
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2022-09-19 11:54:47 +02:00 |
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epang
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epang: Output gzipped jplace (#2037)
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2022-09-09 09:54:03 +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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Faqcs patch to add tests for --debug output (#1368)
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2022-03-02 08:53:05 -05:00 |
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fargene
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Add HAMRONIZATION/FARGENE and updates all HARMONIZATION tools to 1.1.1 (#2107)
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2022-09-27 15:32:18 +02:00 |
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fastani
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Update all modules to new NF DSL2 syntax (#1099)
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2021-11-26 07:58:40 +00:00 |
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fastawindows
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New module: fasta_windows (#1956)
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2022-09-09 08:41:38 +01:00 |
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fastk
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Add FastK/Merge (#1828)
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2022-06-29 18:04:36 +02:00 |
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fastp
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Fix duplicated input in single-end fastp command (#2034)
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2022-09-09 11:08:52 +02:00 |
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fastqc
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Update all modules to new NF DSL2 syntax (#1099)
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2021-11-26 07:58:40 +00:00 |
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fastqscan
|
Update all modules to new NF DSL2 syntax (#1099)
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2021-11-26 07:58:40 +00:00 |
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fasttree
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Update all modules to new NF DSL2 syntax (#1099)
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2021-11-26 07:58:40 +00:00 |
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ffq
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Add ffq module (#1842)
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2022-07-01 08:59:13 +02:00 |
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fgbio
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Fgbio/fastqtobam (#1980)
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2022-09-05 11:57:55 +02:00 |
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filtlong
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Update filtlong module to output log file (#1873)
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2022-07-12 17:05:31 +02:00 |
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flash
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Update all modules to new NF DSL2 syntax (#1099)
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2021-11-26 07:58:40 +00:00 |
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flye
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Add new module: Flye (#1164)
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2022-06-30 22:45:55 +02:00 |
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fq/lint
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Added fq/lint module (#1968)
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2022-08-24 10:20:39 +02:00 |
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freebayes
|
Update intervals (#1278)
|
2022-02-10 10:34:22 +01:00 |
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gamma/gamma
|
fixed test.yml
|
2022-05-24 19:27:09 -04:00 |
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gappa
|
Adding gappa/examineheattree (#2084)
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2022-09-22 15:51:25 +02:00 |
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gatk
|
Add GATK indelrealigner tests
|
2022-06-08 21:14:08 +02:00 |
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gatk4
|
Adding stubs to PicardLiftovervcf, GATK4_mergevcfs and filterMutectCalls (#1621)
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2022-09-28 09:50:11 +02:00 |
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gecco/run
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Add gecco/run module (#1790)
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2022-06-22 13:43:45 +02:00 |
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genescopefk
|
Add GeneScopeFK (#1781)
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2022-06-14 20:49:06 +02:00 |
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genmap
|
Update all modules to new NF DSL2 syntax (#1099)
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2021-11-26 07:58:40 +00:00 |
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genmod
|
update options (#1959)
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2022-08-22 16:26:05 +02:00 |
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genomescope2
|
Update tests/modules/genomescope2/test.yml
|
2022-05-13 11:27:42 +02:00 |
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genotyphi/parse
|
add module for mykrobe predict and genotyphi parse (#1818)
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2022-09-26 15:18:04 +01:00 |
|
genrich
|
Update all modules to new NF DSL2 syntax (#1099)
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2021-11-26 07:58:40 +00:00 |
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gfaffix
|
Adding new module gfaffix (#1149)
|
2022-09-28 10:23:18 +02:00 |
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gffread
|
Replace remaining task.ext.suffix with task.ext.prefix (#1117)
|
2021-12-07 15:00:43 +01:00 |
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glimpse/chunk
|
Creation of Glimpse Chunk (#1985)
|
2022-09-01 10:01:49 +02:00 |
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glnexus
|
Update all modules to new NF DSL2 syntax (#1099)
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2021-11-26 07:58:40 +00:00 |
|
goat/taxonsearch
|
2012 bug related to species input in goattaxonsearch module (#2099)
|
2022-09-23 10:58:40 -06:00 |
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graphmap2
|
Update all modules to new NF DSL2 syntax (#1099)
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2021-11-26 07:58:40 +00:00 |
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gstama
|
New Module: gstama/polyacleanup (#1468)
|
2022-03-31 09:11:51 -04:00 |
|
gtdbtk/classifywf
|
Update all modules to new NF DSL2 syntax (#1099)
|
2021-11-26 07:58:40 +00:00 |
|
gubbins
|
Update all modules to new NF DSL2 syntax (#1099)
|
2021-11-26 07:58:40 +00:00 |
|
gunc
|
Update all modules to new NF DSL2 syntax (#1099)
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2021-11-26 07:58:40 +00:00 |
|
gunzip
|
Update all modules to new NF DSL2 syntax (#1099)
|
2021-11-26 07:58:40 +00:00 |
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gvcftools/extractvariants
|
added gvcftools/extractvariants (#1924)
|
2022-07-25 13:30:35 +02:00 |
|
hamronization
|
Add HAMRONIZATION/FARGENE and updates all HARMONIZATION tools to 1.1.1 (#2107)
|
2022-09-27 15:32:18 +02:00 |
|
haplocheck
|
fix: string interpolation and test input access
|
2022-06-08 09:08:59 -03:00 |
|
haplogrep2/classify
|
Add haplogrep2 (#2030)
|
2022-09-14 14:58:02 +02:00 |
|
happy
|
Merge remote-tracking branch 'origin' into motus_profile
|
2022-05-05 09:41:13 -04:00 |
|
hicap
|
Update all modules to new NF DSL2 syntax (#1099)
|
2021-11-26 07:58:40 +00:00 |
|
hifiasm
|
Update all modules to new NF DSL2 syntax (#1099)
|
2021-11-26 07:58:40 +00:00 |
|
hisat2
|
Update all modules to new NF DSL2 syntax (#1099)
|
2021-11-26 07:58:40 +00:00 |
|
hmmcopy
|
hmmcopy/mapCounter (#1175)
|
2021-12-17 15:39:50 +00:00 |
|
hmmer
|
eslreformat: descriptive suffix (#2081)
|
2022-09-19 09:49:00 +02:00 |
|
hmtnote
|
Update main.nf
|
2022-05-16 15:20:15 +00:00 |
|
homer
|
Fix homer/maketagdirectory output collision (#1456)
|
2022-03-27 03:17:42 +00:00 |
|
hpsuissero
|
add module for hpsuisero (#1331)
|
2022-02-27 17:58:35 -07:00 |
|
ichorcna
|
Prettier (#1405)
|
2022-03-18 14:27:50 +01:00 |
|
idr
|
Update all modules to new NF DSL2 syntax (#1099)
|
2021-11-26 07:58:40 +00:00 |
|
imputeme/vcftoprs
|
Fix formatting in yaml files, add yamllint config (#1279)
|
2022-02-15 11:15:27 +00:00 |
|
instrain/profile
|
Instrain profile (#1822)
|
2022-06-30 18:44:41 +02:00 |
|
iqtree
|
Fix formatting in yaml files, add yamllint config (#1279)
|
2022-02-15 11:15:27 +00:00 |
|
ismapper
|
Update all modules to new NF DSL2 syntax (#1099)
|
2021-11-26 07:58:40 +00:00 |
|
isoseq3
|
Fix formatting in yaml files, add yamllint config (#1279)
|
2022-02-15 11:15:27 +00:00 |
|
ivar
|
Patch fix artic/minion and ivar/variants modules (#1326)
|
2022-02-18 17:36:09 +00:00 |
|
jupyternotebook
|
Update all modules to new NF DSL2 syntax (#1099)
|
2021-11-26 07:58:40 +00:00 |
|
kaiju
|
Add KAIJU2KRONA module (#1800)
|
2022-06-23 16:38:50 +00:00 |
|
kallisto/index
|
add stub for kallisto/index (#1944)
|
2022-08-09 09:23:55 +02:00 |
|
kallistobustools
|
Improved kbtools/count (#1884)
|
2022-07-14 14:27:56 +02:00 |
|
kat/hist
|
Update tests/modules/kat/hist/test.yml
|
2022-05-23 08:51:49 +02:00 |
|
khmer
|
Add khmer unique-kmers.py module (#1838)
|
2022-06-30 16:23:30 +01:00 |
|
kleborate
|
Fix formatting in yaml files, add yamllint config (#1279)
|
2022-02-15 11:15:27 +00:00 |
|
kraken2/kraken2
|
update to kraken2: breaking change - output channels renamed (#1525)
|
2022-04-21 14:33:59 +02:00 |
|
krakentools
|
Update KRAKENTOOLS/COMBINEKREPORTS (#2043)
|
2022-09-13 14:31:27 +02:00 |
|
krona
|
Fix Krona ktimporttaxonomy to allow multiple input files and simplifies database input (#1841)
|
2022-07-01 15:18:29 +02:00 |
|
last
|
Untar unzip meta (#1408)
|
2022-03-21 14:49:28 +01:00 |
|
leehom
|
Update all modules to new NF DSL2 syntax (#1099)
|
2021-11-26 07:58:40 +00:00 |
|
legsta
|
add module for legsta (#1319)
|
2022-02-18 17:42:18 -07:00 |
|
lima
|
Fix formatting in yaml files, add yamllint config (#1279)
|
2022-02-15 11:15:27 +00:00 |
|
lissero
|
Fix formatting in yaml files, add yamllint config (#1279)
|
2022-02-15 11:15:27 +00:00 |
|
lofreq
|
Fix formatting in yaml files, add yamllint config (#1279)
|
2022-02-15 11:15:27 +00:00 |
|
macrel/contigs
|
Add new module macrel/contigs (#1109)
|
2021-12-09 13:17:50 +01:00 |
|
macs2/callpeak
|
Update all modules to new NF DSL2 syntax (#1099)
|
2021-11-26 07:58:40 +00:00 |
|
mafft
|
Add MAFFT module (#1351)
|
2022-02-28 00:40:24 -07:00 |
|
malt
|
Update MALT to older version due to major bug in most recent version (#1796)
|
2022-06-20 08:20:22 +02:00 |
|
maltextract
|
Untar unzip meta (#1408)
|
2022-03-21 14:49:28 +01:00 |
|
manta
|
Update tests/modules/manta/convertinversion/main.nf
|
2022-06-13 09:26:35 +02:00 |
|
mapdamage2
|
Update all modules to new NF DSL2 syntax (#1099)
|
2021-11-26 07:58:40 +00:00 |
|
mash
|
Patch mash screen
|
2022-05-25 12:29:14 +00:00 |
|
mashtree
|
Update all modules to new NF DSL2 syntax (#1099)
|
2021-11-26 07:58:40 +00:00 |
|
maxbin2
|
Update all modules to new NF DSL2 syntax (#1099)
|
2021-11-26 07:58:40 +00:00 |
|
maxquant/lfq
|
corrected typos
|
2022-02-07 13:07:16 +01:00 |
|
mcroni
|
add module for mcroni (#1750)
|
2022-06-13 15:04:01 +02:00 |
|
md5sum
|
new module: md5sum
|
2022-05-06 09:20:40 +02:00 |
|
medaka
|
Fix formatting in yaml files, add yamllint config (#1279)
|
2022-02-15 11:15:27 +00:00 |
|
megahit
|
Update all modules to new NF DSL2 syntax (#1099)
|
2021-11-26 07:58:40 +00:00 |
|
megan
|
Add MEGAN/DAA2INFO (#1848)
|
2022-07-05 09:36:22 +02:00 |
|
meningotype
|
Update all modules to new NF DSL2 syntax (#1099)
|
2021-11-26 07:58:40 +00:00 |
|
merqury
|
Add Merqury (#1647)
|
2022-07-14 10:38:50 +02:00 |
|
merquryfk
|
Add MerquryFK KatGC (#1798)
|
2022-06-23 20:57:15 +02:00 |
|
meryl
|
Merge branch 'master' into meryl_unionsum
|
2022-05-09 16:16:08 +02:00 |
|
metabat2
|
Update metabat2 output channels and compression (#1111)
|
2021-12-09 15:00:32 +01:00 |
|
metaphlan3
|
Update METAPHLAN3_METAPHLAN3 to correct module name (#2056)
|
2022-09-15 09:09:55 +02:00 |
|
methyldackel
|
Update all modules to new NF DSL2 syntax (#1099)
|
2021-11-26 07:58:40 +00:00 |
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minia
|
Update all modules to new NF DSL2 syntax (#1099)
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2021-11-26 07:58:40 +00:00 |
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miniasm
|
Change syntax from task.ext.suffix to tast.ext.prefix in all modules (#1110)
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2021-12-02 12:39:55 +00:00 |
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minimap2
|
Added the meta map to minimap2/index (#1934)
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2022-09-08 09:27:14 +01:00 |
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mlst
|
Update all modules to new NF DSL2 syntax (#1099)
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2021-11-26 07:58:40 +00:00 |
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mobsuite/recon
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add mobsuite_recon module (#1270)
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2022-02-18 17:52:38 -07:00 |
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mosdepth
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Update main.nf
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2022-05-25 19:38:12 +01:00 |
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motus
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Update mOTUs to remove now unused channel (#2075)
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2022-09-16 10:23:21 +02:00 |
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msisensor
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Update all modules to new NF DSL2 syntax (#1099)
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2021-11-26 07:58:40 +00:00 |
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msisensor2
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1976 msisensor2 (#1977)
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2022-09-05 13:00:18 +02:00 |
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msisensorpro
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Add msisensorpro (#1267)
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2022-02-09 21:05:49 +01:00 |
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mtnucratio
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Update all modules to new NF DSL2 syntax (#1099)
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2021-11-26 07:58:40 +00:00 |
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multiqc
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Update MULTIQC for an additional custom config (#2063)
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2022-09-15 13:53:15 +02:00 |
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multivcfanalyzer
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Add MultiVCFAnalyzer (#1845)
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2022-07-05 09:47:10 +02:00 |
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mummer
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Update all modules to new NF DSL2 syntax (#1099)
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2021-11-26 07:58:40 +00:00 |
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muscle
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Update all modules to new NF DSL2 syntax (#1099)
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2021-11-26 07:58:40 +00:00 |
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mykrobe/predict
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add module for mykrobe predict and genotyphi parse (#1818)
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2022-09-26 15:18:04 +01:00 |
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nanolyse
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Change syntax from task.ext.suffix to tast.ext.prefix in all modules (#1110)
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2021-12-02 12:39:55 +00:00 |
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nanoplot
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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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ncbigenomedownload
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Update all modules to new NF DSL2 syntax (#1099)
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2021-11-26 07:58:40 +00:00 |
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nextclade
|
Bump tool versions for modules required in viralrecon (#1859)
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2022-07-07 14:48:04 +01:00 |
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nextgenmap
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New Module: NextGenMap (#1938)
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2022-09-27 20:44:47 +01:00 |
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ngmaster
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Update all modules to new NF DSL2 syntax (#1099)
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2021-11-26 07:58:40 +00:00 |
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ngscheckmate/ncm
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New module: NGSCheckMate (#1290)
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2022-03-11 09:02:10 +00:00 |
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nucmer
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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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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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Update all modules to new NF DSL2 syntax (#1099)
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2021-11-26 07:58:40 +00:00 |
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pairtools
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Change syntax from task.ext.suffix to tast.ext.prefix in all modules (#1110)
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2021-12-02 12:39:55 +00:00 |
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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
|
Bump tool versions for modules required in viralrecon (#1859)
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2022-07-07 14:48:04 +01:00 |
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paraclu
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Update all modules to new NF DSL2 syntax (#1099)
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2021-11-26 07:58:40 +00:00 |
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pasty
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add module for pasty (#2003)
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2022-09-07 09:29:28 -06:00 |
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pbbam/pbmerge
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Change syntax from task.ext.suffix to tast.ext.prefix in all modules (#1110)
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2021-12-02 12:39:55 +00:00 |
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pbccs
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Fix formatting in yaml files, add yamllint config (#1279)
|
2022-02-15 11:15:27 +00:00 |
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pbptyper
|
add module for pbptyper (#2005)
|
2022-09-07 15:29:03 -06:00 |
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pear
|
Add new module: Pear (#1779)
|
2022-07-15 10:28:31 +02:00 |
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peddy
|
Update all modules to new NF DSL2 syntax (#1099)
|
2021-11-26 07:58:40 +00:00 |
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phantompeakqualtools
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Add task.ext.args to phantompeakqualtools and finish the module (#1474)
|
2022-03-31 22:59:21 +01:00 |
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phyloflash
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Update all modules to new NF DSL2 syntax (#1099)
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2021-11-26 07:58:40 +00:00 |
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picard
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Adding stubs to PicardLiftovervcf, GATK4_mergevcfs and filterMutectCalls (#1621)
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2022-09-28 09:50:11 +02:00 |
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pints/caller
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feat(pints): Add initial caller module (#1983)
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2022-08-31 14:04:48 +00:00 |
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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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plasmidfinder
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add module for plasmidfinder (#1773)
|
2022-06-15 10:25:51 -06:00 |
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plasmidid
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Update all modules to new NF DSL2 syntax (#1099)
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2021-11-26 07:58:40 +00:00 |
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plink
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Change syntax from task.ext.suffix to tast.ext.prefix in all modules (#1110)
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2021-12-02 12:39:55 +00:00 |
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plink2
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implement plink2/score module (#1259)
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2022-03-07 13:02:40 -05:00 |
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pmdtools/filter
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Update all modules to new NF DSL2 syntax (#1099)
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2021-11-26 07:58:40 +00:00 |
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porechop
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Update PORECHOP module to output log file (#1870)
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2022-07-12 16:07:31 +02:00 |
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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)
|
2022-04-03 16:06:22 +02:00 |
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prodigal
|
Update all modules to new NF DSL2 syntax (#1099)
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2021-11-26 07:58:40 +00:00 |
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prokka
|
Update all modules to new NF DSL2 syntax (#1099)
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2021-11-26 07:58:40 +00:00 |
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pycoqc
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Update all modules to new NF DSL2 syntax (#1099)
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2021-11-26 07:58:40 +00:00 |
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pydamage
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Update all modules to new NF DSL2 syntax (#1099)
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2021-11-26 07:58:40 +00:00 |
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qcat
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Fix formatting in yaml files, add yamllint config (#1279)
|
2022-02-15 11:15:27 +00:00 |
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qualimap
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add qualimap with cram files + remove val from qualimap/bam, instead use empty list as everywhere else (#1320)
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2022-02-18 09:43:53 +01:00 |
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quast
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Bump tool versions for modules required in viralrecon (#1859)
|
2022-07-07 14:48:04 +01:00 |
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racon
|
Update all modules to new NF DSL2 syntax (#1099)
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2021-11-26 07:58:40 +00:00 |
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rapidnj
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Update all modules to new NF DSL2 syntax (#1099)
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2021-11-26 07:58:40 +00:00 |
|
rasusa
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Change syntax from task.ext.suffix to tast.ext.prefix in all modules (#1110)
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2021-12-02 12:39:55 +00:00 |
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raven
|
Raven assembler (#1087)
|
2022-02-01 11:47:01 +01:00 |
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raxmlng
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Fix formatting in yaml files, add yamllint config (#1279)
|
2022-02-15 11:15:27 +00:00 |
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rgi/main
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Update RGI: add database version reporting to module (#1824)
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2022-06-29 16:30:51 -06:00 |
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rhocall/annotate
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update test
|
2022-06-08 16:36:02 +02:00 |
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rmarkdownnotebook
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Update all modules to new NF DSL2 syntax (#1099)
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2021-11-26 07:58:40 +00:00 |
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roary
|
Update test.yml (#1419)
|
2022-03-19 15:06:21 +00:00 |
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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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Provide BAI when running rseqc/tin (#1177)
|
2021-12-17 10:00:09 +00:00 |
|
rtgtools
|
new module rtgtools/pedfilter (#1777)
|
2022-06-14 16:02:18 +02:00 |
|
salmon
|
Update all modules to new NF DSL2 syntax (#1099)
|
2021-11-26 07:58:40 +00:00 |
|
samblaster
|
Samtools version update (#1507)
|
2022-04-11 14:26:28 +02:00 |
|
samtools
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new module: samtools/getrg (#2123)
|
2022-09-28 14:00:10 +02:00 |
|
scoary
|
Update all modules to new NF DSL2 syntax (#1099)
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2021-11-26 07:58:40 +00:00 |
|
scramble
|
New module: scramble (#2015)
|
2022-09-07 13:19:18 +02:00 |
|
seacr/callpeak
|
Fix formatting in yaml files, add yamllint config (#1279)
|
2022-02-15 11:15:27 +00:00 |
|
seqkit
|
feat: add module for seqkit stats (#1466)
|
2022-03-30 23:01:17 +02:00 |
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seqsero2
|
Fix formatting in yaml files, add yamllint config (#1279)
|
2022-02-15 11:15:27 +00:00 |
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seqtk
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Set process label to process_single for modules with no task.cpus usage (#2076)
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2022-09-19 11:54:47 +02:00 |
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sequenzautils
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Update all modules to new NF DSL2 syntax (#1099)
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2021-11-26 07:58:40 +00:00 |
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seqwish/induce
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Bump seqwish/induce to v0.7.6 (#2083)
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2022-09-26 17:01:21 +01:00 |
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seroba/run
|
add module for seroba (#1816)
|
2022-09-26 16:06:08 +01:00 |
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sexdeterrmine
|
Corrected test-datasets input
|
2022-05-23 17:08:40 +02:00 |
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shasum
|
added sha256sum
|
2022-05-06 10:28:14 +02:00 |
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shigatyper
|
make prettier
|
2022-04-21 12:55:56 -06:00 |
|
shovill
|
Update all modules to new NF DSL2 syntax (#1099)
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2021-11-26 07:58:40 +00:00 |
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sistr
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add module for sistr (#1323)
|
2022-02-18 17:33:48 -07:00 |
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slimfastq
|
Merge remote-tracking branch 'origin' into motus_profile
|
2022-05-05 09:41:13 -04:00 |
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snapaligner
|
snapaligner: improve index detection (#1836)
|
2022-06-30 12:19:46 +02:00 |
|
snippy
|
add snippy/core module (#1855)
|
2022-09-08 06:58:10 +02:00 |
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snpdists
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Update all modules to new NF DSL2 syntax (#1099)
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2021-11-26 07:58:40 +00:00 |
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snpeff
|
DRAFT: Extend output from snpeff (#1895)
|
2022-07-16 20:08:52 +02:00 |
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snpsift/split
|
Added new module snpsift/split (#1031)
|
2021-12-17 09:08:14 +01:00 |
|
snpsites
|
Fix formatting in yaml files, add yamllint config (#1279)
|
2022-02-15 11:15:27 +00:00 |
|
somalier
|
Somalier relate (#2001)
|
2022-09-19 13:22:24 +02:00 |
|
sourmash/sketch
|
feat: add sourmash sketch (#1287)
|
2022-02-15 12:30:28 +01:00 |
|
spades
|
Bump tool versions for modules required in viralrecon (#1859)
|
2022-07-07 14:48:04 +01:00 |
|
spatyper
|
Update all modules to new NF DSL2 syntax (#1099)
|
2021-11-26 07:58:40 +00:00 |
|
sratools
|
refactor: move files to custom section
|
2022-05-11 17:33:45 +02:00 |
|
srst2/srst2
|
Merge remote-tracking branch 'origin' into motus_profile
|
2022-05-05 09:41:13 -04:00 |
|
ssuissero
|
add module for ssuisero (#1329)
|
2022-02-27 20:04:03 -07:00 |
|
stadeniolib/scramble
|
new tool: staden_io_lib (#1499)
|
2022-04-08 09:54:15 -04:00 |
|
staphopiasccmec
|
Update all modules to new NF DSL2 syntax (#1099)
|
2021-11-26 07:58:40 +00:00 |
|
star
|
Add stub star align genomegenerate (#1948)
|
2022-08-09 09:42:19 +02:00 |
|
stranger
|
add stubs for stranger (#1543)
|
2022-04-22 10:10:43 +02:00 |
|
strelka
|
Update intervals (#1278)
|
2022-02-10 10:34:22 +01:00 |
|
stringtie
|
add stub for stringtie (#1949)
|
2022-08-09 10:11:37 +02:00 |
|
subread/featurecounts
|
Update all modules to new NF DSL2 syntax (#1099)
|
2021-11-26 07:58:40 +00:00 |
|
svdb
|
update stub for svdb/merge (#2066)
|
2022-09-15 14:20:09 +02:00 |
|
svtk/standardize
|
new module: svtk/standardize (#2031)
|
2022-09-08 15:03:08 +02:00 |
|
tabix
|
Added an output channel for the gzi index (#2036)
|
2022-09-26 21:47:41 +02:00 |
|
tailfindr
|
Tailfindr (#1904)
|
2022-07-22 16:20:53 +02:00 |
|
tbprofiler/profile
|
Fix formatting in yaml files, add yamllint config (#1279)
|
2022-02-15 11:15:27 +00:00 |
|
tiddit
|
TIDDIT - add --skip_assembly when no bwa specified (#1769)
|
2022-06-13 17:02:59 +02:00 |
|
transdecoder
|
Transdecoder predict (#1251)
|
2022-02-02 09:46:07 +01:00 |
|
trimgalore
|
Update all modules to new NF DSL2 syntax (#1099)
|
2021-11-26 07:58:40 +00:00 |
|
trimmomatic
|
Trimmomatic (#1757)
|
2022-06-17 13:18:15 +00:00 |
|
ucsc
|
Update stub for ucsc/wigtobigwig (#2065)
|
2022-09-15 13:12:05 +02:00 |
|
ultra
|
New modules: ultra/index and ultra/align (#1830)
|
2022-07-04 07:46:49 +01:00 |
|
umitools
|
Fix Conda tests
|
2022-05-23 22:39:12 +01:00 |
|
unicycler
|
Update all modules to new NF DSL2 syntax (#1099)
|
2021-11-26 07:58:40 +00:00 |
|
untar
|
Fix for nested directories in tar archive (#2062)
|
2022-09-15 11:32:36 +02:00 |
|
unzip
|
Untar unzip meta (#1408)
|
2022-03-21 14:49:28 +01:00 |
|
vardictjava
|
Added java options to vardict java (#1695)
|
2022-08-10 14:13:03 +02:00 |
|
variantbam
|
Update all modules to new NF DSL2 syntax (#1099)
|
2021-11-26 07:58:40 +00:00 |
|
vcf2db
|
new module vcf2db (#1795)
|
2022-06-17 15:54:02 +02:00 |
|
vcf2maf
|
vcf2maf module with built in VEP (#1768)
|
2022-06-20 18:27:12 +02:00 |
|
vcfanno
|
small changes to vcfanno (#1804)
|
2022-06-24 08:58:26 +02:00 |
|
vcflib/vcfuniq
|
Bump tool versions for modules required in viralrecon (#1859)
|
2022-07-07 14:48:04 +01:00 |
|
vcftools
|
Update all modules to new NF DSL2 syntax (#1099)
|
2021-11-26 07:58:40 +00:00 |
|
vsearch
|
New module: Vsearch sintax (#2094)
|
2022-09-26 14:45:01 +01:00 |
|
whamg
|
New module: Whamg (#1994)
|
2022-09-02 13:33:48 +02:00 |
|
yara
|
Add samtools index to yara_mapper module (#1353)
|
2022-03-04 10:08:02 -05:00 |
b5aa12ad3b