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Author SHA1 Message Date
James Fellows Yates
8012998542 Make parameter naming more consistent for clipmerge 2022-03-21 19:52:50 +01:00
James A. Fellows Yates
51a0acd05b
Merge pull request #27 from genomic-medicine-sweden/add_nanopore 
Add nanopore reads preprocessing with Porechop
 2022-03-21 19:41:58 +01:00
ljmesi
5b1b48e59e Update subworkflow name to be more consistent 2022-03-21 18:29:47 +01:00
ljmesi
4940ec57ff Remove unnecessary extra point 2022-03-21 18:26:26 +01:00
ljmesi
f6fe26de46 Rename shortread subworkflow to be more consistent 2022-03-21 18:25:56 +01:00
ljmesi
c97de32434 Make adapter and quality trimming optional 2022-03-21 18:17:08 +01:00
James A. Fellows Yates
631c115e10 Adds PoC of untarring system 2022-03-21 14:58:19 +00:00
James Fellows Yates
c7f022008c Start getting database prep ready 2022-03-21 15:07:59 +01:00
ljmesi
24a01529f5 Add mentioning about Nanopore reads pre-processing 2022-03-18 15:47:46 +01:00
ljmesi
d09a3c170e Add Porechop 2022-03-18 15:46:03 +01:00
ljmesi
582aaa105f Include long reads preprocessing subworkflow 2022-03-18 15:12:07 +01:00
ljmesi
1e42f1d9f2 Add long read preprocessing subworkflow 2022-03-18 15:10:44 +01:00
ljmesi
16be676d72 Add Porechop module 2022-03-18 14:34:10 +01:00
James A. Fellows Yates
b23fb927a9
Merge pull request #26 from genomic-medicine-sweden/add_nanopore 
Perform fastqc on nanopore reads before trimming
 2022-03-18 14:22:54 +01:00
Lauri Mesilaakso
0936b9b28e
Update workflows/taxprofiler.nf 
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
 2022-03-18 14:18:38 +01:00
ljmesi
c8e49c56f4 Perform fastqc on nanopore reads before trimming 2022-03-18 13:47:44 +01:00
James A. Fellows Yates
45428c2877
Merge pull request #24 from genomic-medicine-sweden/add_nanopore 
Add nanopore reads input
 2022-03-18 13:29:13 +01:00
ljmesi
2e1b6c5d0a Add info on Nanopore reads to fastq_1 column 2022-03-18 11:00:36 +01:00
ljmesi
7f7ddc9f14 Update comment 2022-03-18 10:48:06 +01:00
ljmesi
41b3d8db82 Add nanopore channel 2022-03-18 10:47:41 +01:00
ljmesi
0f0ed6cd46 Fix function name 2022-03-18 10:45:06 +01:00
James A. Fellows Yates
9fac82d342
Merge pull request #19 from nf-core/nf-core-template-merge-2.3 
Important! Template update for nf-core/tools v2.3
 2022-03-17 13:18:29 +01:00
James A. Fellows Yates
424f11f5ed
Update README.md 2022-03-17 13:16:16 +01:00
James A. Fellows Yates
ac77676d2b
Merge branch 'dev' into nf-core-template-merge-2.3 2022-03-17 13:11:34 +01:00
nf-core-bot
699d26b149 Template update for nf-core/tools version 2.3 2022-03-15 21:05:37 +00:00
James Fellows Yates
e39c6a8ccb Fix MALT multiqc report clash 2022-03-03 18:04:03 +01:00
James Fellows Yates
2c183ed2ed Add Kraken2 and MALT/run as Proof of Concept (currnetly MQC issue) 2022-03-03 17:42:02 +01:00
James Fellows Yates
278f5605ca Added database preparation and final channel for profiling 2022-02-19 12:36:08 +01:00
James Fellows Yates
cf55cc592c Get skeleton read processing to input for profiling 2022-02-18 16:51:01 +01:00
maxibor
1b893cb039 add check for fastq with fasta 2022-02-18 13:27:10 +01:00
maxibor
a6cfa0a1ba cleanup 2022-02-18 13:15:30 +01:00
maxibor
54a1a4fd45 update samplesheet specs 2022-02-18 13:11:18 +01:00
maxibor
1aba3ed01c Merge remote-tracking branch 'origin/dev' into dev 2022-02-18 11:53:52 +01:00
maxibor
f867c057a4 add more columns to samplesheet 2022-02-18 11:53:13 +01:00
James A. Fellows Yates
c68afbbf90
Update nextflow.config 2022-02-18 08:45:06 +01:00
James Fellows Yates
7321daf4f6 Update README with approximate pipeline outline 2022-02-18 08:41:34 +01:00
James Fellows Yates
12e7b428f2 initial template build from nf-core/tools, version 2.2 2022-02-18 07:55:14 +01:00