nf-core-bot
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feeb8ba8dd
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Template update for nf-core/tools version 2.3.2
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2022-03-24 11:48:43 +00:00 |
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nf-core-bot
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6b939e6728
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Template update for nf-core/tools version 2.3.1
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2022-03-23 13:57:56 +00:00 |
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James A. Fellows Yates
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038a8d106a
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Fix test with correct URL
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2022-03-23 11:25:47 +01:00 |
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James Fellows Yates
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48b6ef508d
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Update path to samplesheet
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2022-03-23 10:06:01 +01:00 |
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James Fellows Yates
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358b89a4c6
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Linting
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2022-03-21 20:30:29 +01:00 |
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James Fellows Yates
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81bfb629ca
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Add working basic test to begin
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2022-03-21 20:28:09 +01:00 |
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James A. Fellows Yates
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cd9e3c604c
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Merge pull request #30 from nf-core/database-untar
Adds ability to conditionally untar databases TAR files that contain DB directories
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2022-03-21 19:56:22 +01:00 |
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James A. Fellows Yates
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3079f16861
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Merge branch 'dev' into database-untar
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2022-03-21 19:55:36 +01:00 |
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James Fellows Yates
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07eed435c6
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Replace set with explicity assignment
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2022-03-21 19:54:51 +01:00 |
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James Fellows Yates
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8012998542
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Make parameter naming more consistent for clipmerge
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2022-03-21 19:52:50 +01:00 |
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James A. Fellows Yates
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51a0acd05b
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Merge pull request #27 from genomic-medicine-sweden/add_nanopore
Add nanopore reads preprocessing with Porechop
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2022-03-21 19:41:58 +01:00 |
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ljmesi
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5b1b48e59e
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Update subworkflow name to be more consistent
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2022-03-21 18:29:47 +01:00 |
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ljmesi
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4940ec57ff
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Remove unnecessary extra point
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2022-03-21 18:26:26 +01:00 |
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ljmesi
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f6fe26de46
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Rename shortread subworkflow to be more consistent
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2022-03-21 18:25:56 +01:00 |
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ljmesi
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c97de32434
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Make adapter and quality trimming optional
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2022-03-21 18:17:08 +01:00 |
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James A. Fellows Yates
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631c115e10
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Adds PoC of untarring system
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2022-03-21 14:58:19 +00:00 |
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James Fellows Yates
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c7f022008c
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Start getting database prep ready
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2022-03-21 15:07:59 +01:00 |
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ljmesi
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24a01529f5
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Add mentioning about Nanopore reads pre-processing
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2022-03-18 15:47:46 +01:00 |
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ljmesi
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d09a3c170e
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Add Porechop
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2022-03-18 15:46:03 +01:00 |
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ljmesi
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582aaa105f
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Include long reads preprocessing subworkflow
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2022-03-18 15:12:07 +01:00 |
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ljmesi
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1e42f1d9f2
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Add long read preprocessing subworkflow
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2022-03-18 15:10:44 +01:00 |
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ljmesi
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16be676d72
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Add Porechop module
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2022-03-18 14:34:10 +01:00 |
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James A. Fellows Yates
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b23fb927a9
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Merge pull request #26 from genomic-medicine-sweden/add_nanopore
Perform fastqc on nanopore reads before trimming
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2022-03-18 14:22:54 +01:00 |
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Lauri Mesilaakso
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0936b9b28e
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Update workflows/taxprofiler.nf
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
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2022-03-18 14:18:38 +01:00 |
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ljmesi
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c8e49c56f4
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Perform fastqc on nanopore reads before trimming
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2022-03-18 13:47:44 +01:00 |
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James A. Fellows Yates
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45428c2877
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Merge pull request #24 from genomic-medicine-sweden/add_nanopore
Add nanopore reads input
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2022-03-18 13:29:13 +01:00 |
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ljmesi
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2e1b6c5d0a
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Add info on Nanopore reads to fastq_1 column
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2022-03-18 11:00:36 +01:00 |
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ljmesi
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7f7ddc9f14
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Update comment
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2022-03-18 10:48:06 +01:00 |
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ljmesi
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41b3d8db82
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Add nanopore channel
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2022-03-18 10:47:41 +01:00 |
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ljmesi
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0f0ed6cd46
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Fix function name
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2022-03-18 10:45:06 +01:00 |
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James A. Fellows Yates
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9fac82d342
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Merge pull request #19 from nf-core/nf-core-template-merge-2.3
Important! Template update for nf-core/tools v2.3
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2022-03-17 13:18:29 +01:00 |
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James A. Fellows Yates
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424f11f5ed
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Update README.md
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2022-03-17 13:16:16 +01:00 |
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James A. Fellows Yates
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ac77676d2b
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Merge branch 'dev' into nf-core-template-merge-2.3
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2022-03-17 13:11:34 +01:00 |
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nf-core-bot
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699d26b149
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Template update for nf-core/tools version 2.3
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2022-03-15 21:05:37 +00:00 |
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James Fellows Yates
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e39c6a8ccb
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Fix MALT multiqc report clash
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2022-03-03 18:04:03 +01:00 |
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James Fellows Yates
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2c183ed2ed
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Add Kraken2 and MALT/run as Proof of Concept (currnetly MQC issue)
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2022-03-03 17:42:02 +01:00 |
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James Fellows Yates
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278f5605ca
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Added database preparation and final channel for profiling
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2022-02-19 12:36:08 +01:00 |
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James Fellows Yates
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cf55cc592c
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Get skeleton read processing to input for profiling
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2022-02-18 16:51:01 +01:00 |
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maxibor
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1b893cb039
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add check for fastq with fasta
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2022-02-18 13:27:10 +01:00 |
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maxibor
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a6cfa0a1ba
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cleanup
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2022-02-18 13:15:30 +01:00 |
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maxibor
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54a1a4fd45
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update samplesheet specs
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2022-02-18 13:11:18 +01:00 |
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maxibor
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1aba3ed01c
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Merge remote-tracking branch 'origin/dev' into dev
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2022-02-18 11:53:52 +01:00 |
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maxibor
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f867c057a4
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add more columns to samplesheet
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2022-02-18 11:53:13 +01:00 |
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James A. Fellows Yates
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c68afbbf90
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Update nextflow.config
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2022-02-18 08:45:06 +01:00 |
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James Fellows Yates
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7321daf4f6
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Update README with approximate pipeline outline
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2022-02-18 08:41:34 +01:00 |
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James Fellows Yates
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12e7b428f2
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initial template build from nf-core/tools, version 2.2
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2022-02-18 07:55:14 +01:00 |
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