millironx/taxprofiler
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  • 98dc8014a5 Fix kraken2 module James Fellows Yates 2022-03-28 16:46:45 +0200
  • 231253227c Remove run merging for now due to complexity James Fellows Yates 2022-03-28 16:38:10 +0200
  • 0e0e8128e8 Prettier format sofstam 2022-03-28 13:43:32 +0200
  • ee53283696 Debugging comment James Fellows Yates 2022-03-28 09:13:05 +0200
  • 8dc9e583ad Debugging run merging James Fellows Yates 2022-03-27 09:30:23 +0200
  • e6e8ed7cc9 Add some debugging notes James A. Fellows Yates 2022-03-26 20:54:50 +0000
  • 622fafedc8 Prempt centrifuge database untar crash James A. Fellows Yates 2022-03-26 20:22:35 +0000
  • 120382f51d Fix input channels to kraken2 James Fellows Yates 2022-03-26 06:45:16 +0100
  • 59d3f18a75 Update nextflow_schema.json sofstam 2022-03-25 17:18:04 +0100
  • 16bdc79cc0 Apply prettier sofstam 2022-03-25 16:30:26 +0100
  • 37a70dc3e3 Merge branch 'dev' into classification_centrifuge sofstam 2022-03-25 13:48:23 +0100
  • 000f129dab
         Apply suggestions from code review James A. Fellows Yates 2022-03-25 15:32:56 +0100
  • ede362dbf9 Remove duplicate config and sync longread fastqc James Fellows Yates 2022-03-25 15:28:30 +0100
  • b763bfa2c0 More cleanup James Fellows Yates 2022-03-25 15:26:57 +0100
  • 0e6f7e2ca1 Revert "Some more cleanup" James Fellows Yates 2022-03-25 15:24:10 +0100
  • 7ddcb09a85 Some more cleanup James Fellows Yates 2022-03-25 15:22:41 +0100
  • b5f5c75504 Fix file header descriptions James Fellows Yates 2022-03-25 15:21:52 +0100
  • dfcf8f7b1a Prettier James Fellows Yates 2022-03-25 15:10:52 +0100
  • ff1f28f4f0 Update schema James Fellows Yates 2022-03-25 15:01:25 +0100
  • 4e93abc7c0 Add read improved read preprocessing James Fellows Yates 2022-03-25 14:58:06 +0100
  • fafb7e0f6f
         Update README.md James A. Fellows Yates 2022-03-24 16:59:12 +0100
  • f3c21203c8
         Merge pull request #32 from nf-core/nf-core-template-merge-2.3.2 James A. Fellows Yates 2022-03-24 15:50:38 +0100
  • 92a3c8ec8d Prettier James Fellows Yates 2022-03-24 15:40:14 +0100
  • 494c641fb8 Prettier James Fellows Yates 2022-03-24 15:37:42 +0100
  • cc9368ee52 Prettier linting and update schema James Fellows Yates 2022-03-24 15:35:09 +0100
  • 203cd2e7d3 Prettier James Fellows Yates 2022-03-24 14:31:53 +0100
  • e3be393f16 Fix broken json James Fellows Yates 2022-03-24 14:18:15 +0100
  • edce6603ef
         Merge branch 'dev' into nf-core-template-merge-2.3.2 James A. Fellows Yates 2022-03-24 14:10:58 +0100
  • 3ff54e620e Add centrifuge classification sofstam 2022-03-24 12:51:45 +0100
  • feeb8ba8dd Template update for nf-core/tools version 2.3.2 nf-core-bot 2022-03-24 11:48:43 +0000
  • 6b939e6728 Template update for nf-core/tools version 2.3.1 nf-core-bot 2022-03-23 13:57:56 +0000
  • 038a8d106a
         Fix test with correct URL James A. Fellows Yates 2022-03-23 11:25:47 +0100
  • 48b6ef508d Update path to samplesheet James Fellows Yates 2022-03-23 10:06:01 +0100
  • 358b89a4c6 Linting James Fellows Yates 2022-03-21 20:30:29 +0100
  • 81bfb629ca Add working basic test to begin James Fellows Yates 2022-03-21 20:28:09 +0100
  • cd9e3c604c
         Merge pull request #30 from nf-core/database-untar James A. Fellows Yates 2022-03-21 19:56:22 +0100
  • 3079f16861
         Merge branch 'dev' into database-untar James A. Fellows Yates 2022-03-21 19:55:36 +0100
  • 07eed435c6 Replace set with explicity assignment James Fellows Yates 2022-03-21 19:54:51 +0100
  • 8012998542 Make parameter naming more consistent for clipmerge James Fellows Yates 2022-03-21 19:52:50 +0100
  • 51a0acd05b
         Merge pull request #27 from genomic-medicine-sweden/add_nanopore James A. Fellows Yates 2022-03-21 19:41:58 +0100
  • 5b1b48e59e Update subworkflow name to be more consistent ljmesi 2022-03-21 18:29:47 +0100
  • 4940ec57ff Remove unnecessary extra point ljmesi 2022-03-21 18:26:26 +0100
  • f6fe26de46 Rename shortread subworkflow to be more consistent ljmesi 2022-03-21 18:25:56 +0100
  • c97de32434 Make adapter and quality trimming optional ljmesi 2022-03-21 18:17:08 +0100
  • 631c115e10 Adds PoC of untarring system James A. Fellows Yates 2022-03-21 14:58:19 +0000
  • c7f022008c Start getting database prep ready James Fellows Yates 2022-03-21 15:07:59 +0100
  • 24a01529f5 Add mentioning about Nanopore reads pre-processing ljmesi 2022-03-18 15:47:46 +0100
  • d09a3c170e Add Porechop ljmesi 2022-03-18 15:46:03 +0100
  • 582aaa105f Include long reads preprocessing subworkflow ljmesi 2022-03-18 15:12:07 +0100
  • 1e42f1d9f2 Add long read preprocessing subworkflow ljmesi 2022-03-18 15:10:44 +0100
  • 16be676d72 Add Porechop module ljmesi 2022-03-18 14:34:10 +0100
  • b23fb927a9
         Merge pull request #26 from genomic-medicine-sweden/add_nanopore James A. Fellows Yates 2022-03-18 14:22:54 +0100
  • 0936b9b28e
         Update workflows/taxprofiler.nf Lauri Mesilaakso 2022-03-18 14:18:38 +0100
  • c8e49c56f4 Perform fastqc on nanopore reads before trimming ljmesi 2022-03-18 13:47:44 +0100
  • 45428c2877
         Merge pull request #24 from genomic-medicine-sweden/add_nanopore James A. Fellows Yates 2022-03-18 13:29:13 +0100
  • 2e1b6c5d0a Add info on Nanopore reads to fastq_1 column ljmesi 2022-03-18 11:00:36 +0100
  • 7f7ddc9f14 Update comment ljmesi 2022-03-18 10:48:06 +0100
  • 41b3d8db82 Add nanopore channel ljmesi 2022-03-18 10:47:41 +0100
  • 0f0ed6cd46 Fix function name ljmesi 2022-03-18 10:45:06 +0100
  • 9fac82d342
         Merge pull request #19 from nf-core/nf-core-template-merge-2.3 James A. Fellows Yates 2022-03-17 13:18:29 +0100
  • 424f11f5ed
         Update README.md James A. Fellows Yates 2022-03-17 13:16:16 +0100
  • ac77676d2b
         Merge branch 'dev' into nf-core-template-merge-2.3 James A. Fellows Yates 2022-03-17 13:11:34 +0100
  • 699d26b149 Template update for nf-core/tools version 2.3 nf-core-bot 2022-03-15 21:05:37 +0000
  • e39c6a8ccb Fix MALT multiqc report clash James Fellows Yates 2022-03-03 18:04:03 +0100
  • 2c183ed2ed Add Kraken2 and MALT/run as Proof of Concept (currnetly MQC issue) James Fellows Yates 2022-03-03 17:42:02 +0100
  • 278f5605ca Added database preparation and final channel for profiling James Fellows Yates 2022-02-19 12:36:08 +0100
  • cf55cc592c Get skeleton read processing to input for profiling James Fellows Yates 2022-02-18 16:51:01 +0100
  • 1b893cb039 add check for fastq with fasta maxibor 2022-02-18 13:27:10 +0100
  • a6cfa0a1ba cleanup maxibor 2022-02-18 13:15:30 +0100
  • 54a1a4fd45 update samplesheet specs maxibor 2022-02-18 13:11:18 +0100
  • 1aba3ed01c Merge remote-tracking branch 'origin/dev' into dev maxibor 2022-02-18 11:53:52 +0100
  • f867c057a4 add more columns to samplesheet maxibor 2022-02-18 11:53:13 +0100
  • c68afbbf90
         Update nextflow.config James A. Fellows Yates 2022-02-18 08:45:06 +0100
  • 7321daf4f6 Update README with approximate pipeline outline James Fellows Yates 2022-02-18 08:41:34 +0100
  • 12e7b428f2 initial template build from nf-core/tools, version 2.2 James Fellows Yates 2022-02-18 07:55:14 +0100