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abacas
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abricate
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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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adapterremoval
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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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allelecounter
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ampir
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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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amplify/predict
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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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amps
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amrfinderplus
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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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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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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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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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Add manual version definition for artic modules (#1867)
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2022-07-12 11:33:51 +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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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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Fix bakta: variable in main.nf (#2050)
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2022-09-13 13:03:21 +02:00 |
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bamaligncleaner
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bamcmp
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Update manual versioning (#1813)
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2022-06-27 10:35:41 +02:00 |
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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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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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bandage/image
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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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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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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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bismark
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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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Improve descriptions for modules with missing
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2022-07-06 12:03:08 +02:00 |
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bowtie2
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Improve descriptions for modules with missing
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2022-07-06 12:03:08 +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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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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bwamem2
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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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bwameth
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cat
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bugfix: when there is a single input file, stageAs("?/*) returns the path directly, not in a list (#2114)
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2022-09-28 13:28:52 +01:00 |
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cellranger
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Fixes incorrectly quoted tags (#2113)
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2022-09-27 20:37:56 +01:00 |
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centrifuge
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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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checkm/lineagewf
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Update checkM version and add support for pre-defined database (#2125)
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2022-09-28 14:48:18 +02:00 |
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chromap
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clonalframeml
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cmseq/polymut
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Update manual versioning (#1813)
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2022-06-27 10:35:41 +02:00 |
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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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removed extra ) in the version strings (#1850)
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2022-07-05 15:24:08 +02:00 |
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controlfreec
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cooler
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csvtk
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custom
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Fix broken Quast module and bump MultiQC version in dumpsoftwareversions (#2108)
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2022-09-27 09:35:52 +01:00 |
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cutadapt
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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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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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dedup
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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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deeparg
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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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deepbgc
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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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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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Deepvariant - Update main.nf (#2110)
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2022-09-27 15:34:10 +02:00 |
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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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dragonflye
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dshbio
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Update dsh-bio to 2.1 (#2100)
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2022-09-26 10:41:33 +01:00 |
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ectyper
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eido
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Fixes incorrectly quoted tags (#2113)
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2022-09-27 20:37:56 +01:00 |
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elprep
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emboss/seqret
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Add smart format selection to module
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2022-09-29 14:25:40 -05:00 |
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emmtyper
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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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add stub and the option to compress output for vep (#2111)
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2022-09-28 14:34:41 +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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Make epang output meta with the jplace channel (#2073)
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2022-09-16 10:22:50 +02:00 |
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expansionhunter
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Improve descriptions for modules with missing
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2022-07-06 12:03:08 +02:00 |
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faqcs
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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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Improve descriptions for modules with missing
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2022-07-06 12:03:08 +02:00 |
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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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fastqscan
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fasttree
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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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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
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gamma/gamma
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Update manual versioning (#1813)
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2022-06-27 10:35:41 +02:00 |
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gappa
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Adding gappa/examineheattree (#2084)
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2022-09-22 15:51:25 +02:00 |
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gatk
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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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gatk4
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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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gecco/run
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Update module: Gecco fix to no file generated if no hits found (#1930)
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2022-07-27 15:19:43 +02:00 |
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genescopefk
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Update manual versioning (#1813)
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2022-06-27 10:35:41 +02:00 |
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genmap
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Fixes incorrectly quoted tags (#2113)
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2022-09-27 20:37:56 +01:00 |
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genmod
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update options (#1959)
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2022-08-22 16:26:05 +02:00 |
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genomescope2
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Update outputs and test data set
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2022-05-11 10:42:17 +00:00 |
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genotyphi/parse
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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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genrich
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gfaffix
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Adding new module gfaffix (#1149)
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2022-09-28 10:23:18 +02:00 |
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gffread
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glimpse/chunk
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Creation of Glimpse Chunk (#1985)
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2022-09-01 10:01:49 +02:00 |
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glnexus
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goat/taxonsearch
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2012 bug related to species input in goattaxonsearch module (#2099)
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2022-09-23 10:58:40 -06:00 |
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graphmap2
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gstama
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Adjust requested ressources for gstama/merge, isoseq3/refine, lima, ultra/align (#1858)
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2022-07-07 11:10:18 +01:00 |
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gtdbtk/classifywf
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Update manual versioning (#1813)
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2022-06-27 10:35:41 +02:00 |
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gubbins
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gunc
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Fixes incorrectly quoted tags (#2113)
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2022-09-27 20:37:56 +01:00 |
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gunzip
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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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gvcftools/extractvariants
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added gvcftools/extractvariants (#1924)
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2022-07-25 13:30:35 +02:00 |
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hamronization
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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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haplocheck
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fix: stub output name
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2022-06-08 10:10:24 -03:00 |
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haplogrep2/classify
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Add haplogrep2 (#2030)
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2022-09-14 14:58:02 +02:00 |
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happy
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Update manual versioning (#1813)
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2022-06-27 10:35:41 +02:00 |
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hicap
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hifiasm
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hisat2
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Update manual versioning (#1813)
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2022-06-27 10:35:41 +02:00 |
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hmmcopy
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Fixes incorrectly quoted tags (#2113)
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2022-09-27 20:37:56 +01:00 |
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hmmer
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Fixes incorrectly quoted tags (#2113)
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2022-09-27 20:37:56 +01:00 |
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hmtnote
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Update main.nf
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2022-05-16 15:20:15 +00:00 |
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homer
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Update manual versioning (#1813)
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2022-06-27 10:35:41 +02:00 |
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hpsuissero
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Update manual versioning (#1813)
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2022-06-27 10:35:41 +02:00 |
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ichorcna
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Update manual versioning (#1813)
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2022-06-27 10:35:41 +02:00 |
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idr
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imputeme/vcftoprs
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instrain/profile
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Instrain profile (#1822)
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2022-06-30 18:44:41 +02:00 |
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iqtree
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ismapper
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isoseq3
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Adjust requested ressources for gstama/merge, isoseq3/refine, lima, ultra/align (#1858)
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2022-07-07 11:10:18 +01:00 |
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ivar
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jupyternotebook
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kaiju
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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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kallisto/index
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add stub for kallisto/index (#1944)
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2022-08-09 09:23:55 +02:00 |
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kallistobustools
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Improved kbtools/count (#1884)
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2022-07-14 14:27:56 +02:00 |
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kat/hist
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khmer
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Add khmer unique-kmers.py module (#1838)
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2022-06-30 16:23:30 +01:00 |
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kleborate
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kraken2/kraken2
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Improves kraken2 output glob (#1987)
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2022-08-31 15:42:44 +02:00 |
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krakentools
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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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krona
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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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last
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leehom
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Update manual versioning (#1813)
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2022-06-27 10:35:41 +02:00 |
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legsta
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lima
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Adjust requested ressources for gstama/merge, isoseq3/refine, lima, ultra/align (#1858)
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2022-07-07 11:10:18 +01:00 |
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lissero
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lofreq
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macrel/contigs
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macs2/callpeak
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mafft
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malt
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Update MALT to older version due to major bug in most recent version (#1796)
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2022-06-20 08:20:22 +02:00 |
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maltextract
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manta
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Reduce resource requests (#2021)
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2022-09-07 10:33:05 +02:00 |
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mapdamage2
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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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mash
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Patch mash screen
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2022-05-25 12:29:14 +00:00 |
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mashtree
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maxbin2
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maxquant/lfq
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ran prettier
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2022-05-16 14:30:40 +02:00 |
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mcroni
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Update manual versioning (#1813)
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2022-06-27 10:35:41 +02:00 |
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md5sum
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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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medaka
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megahit
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megan
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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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meningotype
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merqury
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Add Merqury (#1647)
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2022-07-14 10:38:50 +02:00 |
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merquryfk
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Update Merqury version and sha (#2132)
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2022-09-29 15:23:58 +02:00 |
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meryl
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Merge branch 'master' into meryl_unionsum
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2022-05-09 16:16:08 +02:00 |
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metabat2
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metaphlan3
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Update METAPHLAN3_METAPHLAN3 to correct module name (#2056)
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2022-09-15 09:09:55 +02:00 |
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methyldackel
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minia
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miniasm
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minimap2
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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
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Add args to mlst (#1962)
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2022-09-26 15:48:35 +01:00 |
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mobsuite/recon
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mosdepth
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Update main.nf
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2022-05-25 19:42:15 +01:00 |
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motus
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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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msisensor
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msisensor2
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Fixes incorrectly quoted tags (#2113)
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2022-09-27 20:37:56 +01:00 |
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msisensorpro
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mtnucratio
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Set process label to process_single for modules with no task.cpus usage (#2076)
|
2022-09-19 11:54:47 +02:00 |
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multiqc
|
Set process label to process_single for modules with no task.cpus usage (#2076)
|
2022-09-19 11:54:47 +02:00 |
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multivcfanalyzer
|
Fixes incorrectly quoted tags (#2113)
|
2022-09-27 20:37:56 +01:00 |
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mummer
|
Update manual versioning (#1813)
|
2022-06-27 10:35:41 +02:00 |
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muscle
|
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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mykrobe/predict
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add module for mykrobe predict and genotyphi parse (#1818)
|
2022-09-26 15:18:04 +01:00 |
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nanolyse
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nanoplot
|
Bump tool versions for modules required in viralrecon (#1859)
|
2022-07-07 14:48:04 +01:00 |
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ncbigenomedownload
|
Use a newer container version because the previous one is broken (#1933)
|
2022-08-22 11:18:09 +01:00 |
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nextclade
|
Bump tool versions for modules required in viralrecon (#1859)
|
2022-07-07 14:48:04 +01:00 |
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nextgenmap
|
New Module: NextGenMap (#1938)
|
2022-09-27 20:44:47 +01:00 |
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ngmaster
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ngscheckmate/ncm
|
NGSCheckMate doesn't generate a pdf for only one sample, made optional output (#1839)
|
2022-06-30 17:43:34 +01:00 |
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nucmer
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optitype
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pairix
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pairtools
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panaroo/run
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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
|
Update manual versioning (#1813)
|
2022-06-27 10:35:41 +02:00 |
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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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pbccs
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pbptyper
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add module for pbptyper (#2005)
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2022-09-07 15:29:03 -06:00 |
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pear
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Add new module: Pear (#1779)
|
2022-07-15 10:28:31 +02:00 |
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peddy
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phantompeakqualtools
|
Update manual versioning (#1813)
|
2022-06-27 10:35:41 +02:00 |
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phyloflash
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picard
|
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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fix(pints): Remove update check (#1989)
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2022-09-08 05:03:48 +02:00 |
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pirate
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plasmidfinder
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Update manual versioning (#1813)
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2022-06-27 10:35:41 +02:00 |
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plasmidid
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plink
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plink2
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pmdtools/filter
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porechop
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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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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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prinseqplusplus
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prodigal
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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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prokka
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[bug] pin bioperl version in Prokka module (#1307)
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2022-09-28 01:34:23 +01:00 |
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pycoqc
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pydamage
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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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qcat
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qualimap
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Fix broken Quast module and bump MultiQC version in dumpsoftwareversions (#2108)
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2022-09-27 09:35:52 +01:00 |
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quast
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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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racon
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rapidnj
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Update manual versioning (#1813)
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2022-06-27 10:35:41 +02:00 |
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rasusa
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raven
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raxmlng
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rgi/main
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RGI/main export versions as explicit emission strings (#1909)
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2022-07-20 10:33:53 +02:00 |
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rhocall/annotate
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fix versions.yaml
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2022-06-07 14:43:35 +02:00 |
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rmarkdownnotebook
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roary
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rsem
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rseqc
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rtgtools
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new module rtgtools/pedfilter (#1777)
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2022-06-14 16:02:18 +02:00 |
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salmon
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samblaster
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samtools
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samtools fasta module (#2128)
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2022-09-29 08:10:44 +01:00 |
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scoary
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scramble
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New module: scramble (#2015)
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2022-09-07 13:19:18 +02:00 |
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seacr/callpeak
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Update manual versioning (#1813)
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2022-06-27 10:35:41 +02:00 |
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seqkit
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seqsero2
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seqtk
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Fixes incorrectly quoted tags (#2113)
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2022-09-27 20:37:56 +01:00 |
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sequenzautils
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|
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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
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add module for seroba (#1816)
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2022-09-26 16:06:08 +01:00 |
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sexdeterrmine
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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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shasum
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fix software definitions
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2022-05-06 11:07:05 +02:00 |
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shigatyper
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shovill
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sistr
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slimfastq
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Update manual versioning (#1813)
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2022-06-27 10:35:41 +02:00 |
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snapaligner
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snapaligner: improve index detection (#1836)
|
2022-06-30 12:19:46 +02:00 |
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snippy
|
add snippy/core module (#1855)
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2022-09-08 06:58:10 +02:00 |
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snpdists
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snpeff
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DRAFT: Extend output from snpeff (#1895)
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2022-07-16 20:08:52 +02:00 |
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snpsift/split
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snpsites
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somalier
|
Somalier relate (#2001)
|
2022-09-19 13:22:24 +02:00 |
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sortmerna
|
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sourmash/sketch
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spades
|
Bump tool versions for modules required in viralrecon (#1859)
|
2022-07-07 14:48:04 +01:00 |
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spatyper
|
|
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sratools
|
refactor: move files to custom section
|
2022-05-11 17:33:45 +02:00 |
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srst2/srst2
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|
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ssuissero
|
Update manual versioning (#1813)
|
2022-06-27 10:35:41 +02:00 |
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stadeniolib/scramble
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|
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staphopiasccmec
|
|
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star
|
Add stub star align genomegenerate (#1948)
|
2022-08-09 09:42:19 +02:00 |
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stranger
|
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strelka
|
Reduce resource requests (#2021)
|
2022-09-07 10:33:05 +02:00 |
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stringtie
|
Make stringtie/merge arguments configurable (#2049)
|
2022-09-26 14:26:53 +01:00 |
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subread/featurecounts
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|
|
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svdb
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update stub for svdb/merge (#2066)
|
2022-09-15 14:20:09 +02:00 |
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svtk/standardize
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new module: svtk/standardize (#2031)
|
2022-09-08 15:03:08 +02:00 |
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tabix
|
Added an output channel for the gzi index (#2036)
|
2022-09-26 21:47:41 +02:00 |
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tailfindr
|
Tailfindr (#1904)
|
2022-07-22 16:20:53 +02:00 |
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tbprofiler/profile
|
|
|
|
tiddit
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TIDDIT - add --skip_assembly when no bwa specified (#1769)
|
2022-06-13 17:02:59 +02:00 |
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transdecoder
|
|
|
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trimgalore
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Update cores specification in TrimGalore module (#2127)
|
2022-09-28 15:47:27 +02:00 |
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trimmomatic
|
Trimmomatic (#1757)
|
2022-06-17 13:18:15 +00:00 |
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ucsc
|
Set process label to process_single for modules with no task.cpus usage (#2076)
|
2022-09-19 11:54:47 +02:00 |
|
ultra
|
Adjust requested ressources for gstama/merge, isoseq3/refine, lima, ultra/align (#1858)
|
2022-07-07 11:10:18 +01:00 |
|
umitools
|
Set PYTHONHASHSEED for umitools dedup (#1932)
|
2022-08-31 14:05:12 +01:00 |
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unicycler
|
|
|
|
untar
|
Fix for nested directories in tar archive (#2062)
|
2022-09-15 11:32:36 +02:00 |
|
unzip
|
Reduce resource requests (#2021)
|
2022-09-07 10:33:05 +02:00 |
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vardictjava
|
Added java options to vardict java (#1695)
|
2022-08-10 14:13:03 +02:00 |
|
variantbam
|
Update manual versioning (#1813)
|
2022-06-27 10:35:41 +02:00 |
|
vcf2db
|
Update manual versioning (#1813)
|
2022-06-27 10:35:41 +02:00 |
|
vcf2maf
|
Update manual versioning (#1813)
|
2022-06-27 10:35:41 +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
|
Reduce resource requests (#2021)
|
2022-09-07 10:33:05 +02:00 |
|
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 |
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yara
|
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