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  • 26d206cca3
         Merge branch 'master' into new-module/EMBOSS_SEQRET new-module/EMBOSS_SEQRET Simon Pearce 2022-10-02 15:43:08 +0100
  • eca9a1a7e2
         Update main.nf Simon Pearce 2022-10-02 15:42:54 +0100
  • d2676d6ec3
         Remove md5 test for gff format Thomas A. Christensen II 2022-10-01 13:38:26 -0500
  • c9889866a9
         add FCS adaptor (#2033) Daniel Straub 2022-09-30 22:39:55 +0200
  • 4eed099a12
         Bump HISAT2 version to 2.2.1 in all modules (#2139) Harshil Patel 2022-09-30 20:34:06 +0100
  • ef585046a0
         feat added vcflib/vcfbreakmulti module (#2134) Lucpen 2022-09-30 16:57:18 +0200
  • 03de60e6fa
         Add CHECKM/QA (#2137) James A. Fellows Yates 2022-09-30 15:50:47 +0200
  • 31c0b49f65
         Explicitly name the output files to avoid the gzi index being flown through the output channel (#2136) Matthieu Muffato 2022-09-30 13:31:48 +0100
  • ebc466caac
         Update busco input type (#2135) Mahesh Binzer-Panchal 2022-09-29 22:35:51 +0200
  • e9e77700d0
         Improve description Thomas A. Christensen II 2022-09-29 19:22:46 +0000
  • f275be88dd
         Update modules/emboss/seqret/main.nf Thomas A. Christensen II 2022-09-29 19:13:32 +0000
  • 82f85ed4bb
         Update test assertions Thomas A. Christensen II 2022-07-18 10:15:08 -0500
  • 3f0523ef88
         Add test workflows Thomas A. Christensen II 2022-07-18 10:02:33 -0500
  • 8c1b2a34f2
         Add smart format selection to module Thomas A. Christensen II 2022-07-18 09:56:46 -0500
  • 09f9a09304
         Update meta for seqret Thomas A. Christensen II 2022-07-18 09:37:10 -0500
  • 8ab1f2a184
         Flesh out module code Thomas A. Christensen II 2022-07-14 19:14:56 -0500
  • c7a5ae140b
         Initial nf-core modules emboss/seqret Thomas A. Christensen II 2022-07-14 18:40:58 -0500
  • 96602d03fa
         Update Merqury version and sha (#2132) master Mahesh Binzer-Panchal 2022-09-29 15:23:58 +0200
  • 504028346b
         samtools fasta module (#2128) Priyanka Surana 2022-09-29 08:10:44 +0100
  • b3e322064e
         [POC] Get subworkflows working again - bam_stats_samtools (#2097) Harshil Patel 2022-09-28 19:20:20 +0100
  • bfbdc4f79b
         Update cores specification in TrimGalore module (#2127) Harshil Patel 2022-09-28 14:47:27 +0100
  • 0ab15c5ee9
         Update checkM version and add support for pre-defined database (#2125) James A. Fellows Yates 2022-09-28 14:48:18 +0200
  • 3d7ce93630
         add stub and the option to compress output for vep (#2111) Ramprasad Neethiraj 2022-09-28 14:34:41 +0200
  • e9bc33485e
         bugfix: when there is a single input file, stageAs("?/*) returns the path directly, not in a list (#2114) Matthieu Muffato 2022-09-28 13:28:52 +0100
  • 83b05a8dc0
         add qname feature to samtools/view (#2115) Priyanka Surana 2022-09-28 13:04:41 +0100
  • b5aa12ad3b
         new module: samtools/getrg (#2123) Matthias De Smet 2022-09-28 14:00:10 +0200
  • 33d9ce79c1
         Remove jinja tags from workflow (#2124) Phil Ewels 2022-09-28 12:42:09 +0200
  • 0bdd589163
         New Module: endorspy (#1916) Aida Andrades Valtueña 2022-09-28 11:28:11 +0200
  • ee5f59705f
         Adding new module gfaffix (#1149) Michael L Heuer 2022-09-28 03:23:18 -0500
  • f434d0c671
         Adding stubs to PicardLiftovervcf, GATK4_mergevcfs and filterMutectCalls (#1621) Lucpen 2022-09-28 09:50:11 +0200
  • ec22f9a907
         [bug] pin bioperl version in Prokka module (#1307) Robert A. Petit III 2022-09-27 18:34:23 -0600
  • 786279b473
         New Module: NextGenMap (#1938) Chase Mateusiak 2022-09-27 14:44:47 -0500
  • a0443e2c54
         Fixes incorrectly quoted tags (#2113) James A. Fellows Yates 2022-09-27 21:37:56 +0200
  • 5da2c37458
         Teach nf-core bot to fix lint (#2109) Simon Pearce 2022-09-27 17:34:58 +0100
  • eb15df8036
         Deepvariant - Update main.nf (#2110) Maxime U. Garcia 2022-09-27 15:34:10 +0200
  • daab0a77dd
         Add HAMRONIZATION/FARGENE and updates all HARMONIZATION tools to 1.1.1 (#2107) James A. Fellows Yates 2022-09-27 15:32:18 +0200
  • 1780cf9bcf
         Add: ANGSD_DOCOUNTS (#2044) James A. Fellows Yates 2022-09-27 13:21:44 +0200
  • 82501fe6d0
         Fix broken Quast module and bump MultiQC version in dumpsoftwareversions (#2108) Harshil Patel 2022-09-27 09:35:52 +0100
  • 2a9a8763f9
         updated the version of delly (#2105) nvnieuwk 2022-09-27 08:57:36 +0200
  • 5d8edefb26
         new module gatk4/printsvevidence (#2103) nvnieuwk 2022-09-27 08:30:16 +0200
  • 77d5dd60eb
         Adding module bamtools stats (#2104) Francesco Lescai 2022-09-27 07:24:43 +0200
  • 07e2868920
         Added an output channel for the gzi index (#2036) Matthieu Muffato 2022-09-26 20:47:41 +0100
  • de7b50fdd0
         Updated dumpsoftwareversions.py to match the pipeline template (#2045) Matthieu Muffato 2022-09-26 18:45:07 +0100
  • f0a86eaf5b
         Multithreaded samtools commands (#2080) Matthieu Muffato 2022-09-26 17:44:36 +0100
  • 1d668eefa2
         Bump seqwish/induce to v0.7.6 (#2083) Simon Heumos 2022-09-26 18:01:21 +0200
  • 8e21005d53
         Add blast/tblastn module (#2092) Guoying Qi 2022-09-26 16:43:41 +0100
  • d1c8bddaaa
         fix typo in tag of genmap_mappability (#1527) JIANHONG OU 2022-09-26 11:21:45 -0400
  • e3e61068c1
         add module for seroba (#1816) Robert A. Petit III 2022-09-26 09:06:08 -0600
  • 0a59baf293
         Add args to mlst (#1962) Petros 2022-09-26 16:48:35 +0200
  • 6d6e3a018f
         add module for mykrobe predict and genotyphi parse (#1818) Robert A. Petit III 2022-09-26 08:18:04 -0600
  • 876bb807af
         Update container version (#2060) Rafal Stepien 2022-09-26 10:10:49 -0400
  • 32ad1746d1
         New module: Vsearch sintax (#2094) Jeanette Tångrot 2022-09-26 15:45:01 +0200
  • 29568f72ca
         Make stringtie/merge arguments configurable (#2049) Benedetto Polimeni 2022-09-26 15:26:53 +0200
  • 72adfbff72
         Update dsh-bio to 2.1 (#2100) Michael L Heuer 2022-09-26 04:41:33 -0500
  • 9d5ad1894b
         2012 bug related to species input in goattaxonsearch module (#2099) Alexander Ramos Díaz 2022-09-23 10:58:40 -0600
  • 09159edc9e
         Update samtools view (#2098) Priyanka Surana 2022-09-23 15:52:01 +0100
  • 402631fdaa
         Update samtools view (#2096) Priyanka Surana 2022-09-23 13:03:59 +0100
  • 0857e6c60f
         Adding gappa/examineheattree (#2084) Daniel Lundin 2022-09-22 15:51:25 +0200
  • 58ee946ca6
         gappa/examineassign: Explicitly output two optional files (#2086) Daniel Lundin 2022-09-22 15:04:32 +0200
  • 22e144dc63
         samtools markdup module (#2087) Priyanka Surana 2022-09-21 15:39:10 +0100
  • 41dfa13929
         Fix bcftools/stats module (#1953) SusiJo 2022-09-21 16:10:38 +0200
  • ab4c2e440d
         samtools collate module (#2078) Priyanka Surana 2022-09-21 14:12:59 +0100
  • d5d785b3d8
         [samtools] add optional csi output (#2064) Benedetto Polimeni 2022-09-20 22:08:29 +0200
  • c13f2274fb
         cat/fastq: update conditional (#2085) Matthias De Smet 2022-09-20 14:46:01 +0200
  • d8ba32c6b5
         Somalier relate (#2001) Ashot Margaryan 2022-09-19 13:22:24 +0200
  • 90aef30f43
         Set process label to process_single for modules with no task.cpus usage (#2076) James A. Fellows Yates 2022-09-19 11:54:47 +0200
  • 46ad627a73
         Add gappa/examineassign (#2079) Daniel Lundin 2022-09-19 11:49:42 +0200
  • b6f18f8733
         eslreformat: descriptive suffix (#2081) Daniel Lundin 2022-09-19 09:49:00 +0200
  • f62e4cf5f0
         Added Somalier extract module (#1986) Ashot Margaryan 2022-09-19 08:58:17 +0200
  • 38383cfaef
         Update eido/validate module (#2071) Rafal Stepien 2022-09-16 09:00:03 -0400
  • 9764eef361
         Update eido/convert module (#2072) Rafal Stepien 2022-09-16 08:54:40 -0400
  • b98f1b77d1
         Bump bcl-convert version (#2077) Matthias De Smet 2022-09-16 14:34:52 +0200
  • 54ff289487
         Update mOTUs to remove now unused channel (#2075) James A. Fellows Yates 2022-09-16 10:23:21 +0200
  • b121596ae0
         Make epang output meta with the jplace channel (#2073) Daniel Lundin 2022-09-16 10:22:50 +0200
  • e55012ff92
         DeepBGC: tiny revisiosn (#2070) Jasmin F 2022-09-15 22:57:33 +0200
  • 8372df6fb2
         Update MOTUS/MERGE (#2068) James A. Fellows Yates 2022-09-15 19:45:43 +0200
  • d90c291f18
         epang: Missing .gz in output spec (#2069) Daniel Lundin 2022-09-15 16:31:58 +0200
  • 4963ca0570
         Add bases2fastq (#2054) Edmund Miller 2022-09-15 13:50:33 +0000
  • 513b5fcab9
         update stub for svdb/merge (#2066) Ramprasad Neethiraj 2022-09-15 14:20:09 +0200
  • 847bebc0ab
         Make hmmer/hmmalign output files with correct prefix (#2067) Daniel Lundin 2022-09-15 14:06:18 +0200
  • 4b1d4bf401
         Update MULTIQC for an additional custom config (#2063) James A. Fellows Yates 2022-09-15 13:53:15 +0200
  • 8572bc8865
         Update stub for ucsc/wigtobigwig (#2065) Ramprasad Neethiraj 2022-09-15 13:12:05 +0200
  • b63b9f752d
         Fix for nested directories in tar archive (#2062) Matthias De Smet 2022-09-15 11:32:36 +0200
  • 978087354e
         Update METAPHLAN3_METAPHLAN3 to correct module name (#2056) James A. Fellows Yates 2022-09-15 09:09:55 +0200
  • 885e724e07
         Add postprocessing option to hmmer/eslreformat (#2061) Daniel Lundin 2022-09-14 18:43:50 +0200
  • 8c0127e071
         Update container version (#2059) Rafal Stepien 2022-09-14 11:16:08 -0400
  • d7d6b8222e
         Deepbgc update versions.yml (#2058) louperelo 2022-09-14 16:15:00 +0200
  • 67652c7c4d
         add stub to picard/addorreplacereadgroups (#2057) Ramprasad Neethiraj 2022-09-14 15:44:47 +0200
  • cad9133c71
         Add haplogrep2 (#2030) Lucpen 2022-09-14 14:58:02 +0200
  • 393dbd6dda
         Update UNTAR to account for file-only or multi-directory tar archives (#2055) James A. Fellows Yates 2022-09-14 10:40:45 +0200
  • c9b29c7686
         Add eido/convert module (#2051) Rafal Stepien 2022-09-13 12:17:29 -0400
  • 2456ef7d99
         Add eido/validate module (#2048) Rafal Stepien 2022-09-13 10:27:28 -0400
  • 36bcd675ae
         Update METAPHLAN3/MERGEMETAPHLANTABLES (#2041) James A. Fellows Yates 2022-09-13 14:37:46 +0200
  • ee0346b4d1
         Update KRAKENTOOLS/COMBINEKREPORTS (#2043) James A. Fellows Yates 2022-09-13 14:31:27 +0200
  • 77a6dd3f61
         Fix bakta: variable in main.nf (#2050) Jasmin F 2022-09-13 13:03:21 +0200
  • 5587389874
         Multiqc v1.13 release update (by @robsyme) (#2047) Alexander Peltzer 2022-09-12 15:48:58 +0200
  • d75b37fef1
         Upgraded getchromsizes to support meta and output the gzi index (#2046) Matthieu Muffato 2022-09-12 13:17:13 +0100
  • 2c70c1c195
         Fix duplicated input in single-end fastp command (#2034) James A. Fellows Yates 2022-09-09 11:08:52 +0200
  • 65800cee75
         new module gatk4/collectsvevidence (#2039) nvnieuwk 2022-09-09 10:58:47 +0200
  • c736d26b7e
         bedToBigBed AutoSql option (#1981) Matthieu Muffato 2022-09-09 09:27:47 +0100