149 commits

This branch

This branch

All branches

Author	SHA1	Message	Date
James Fellows Yates	e3be393f16	Fix broken json	2022-03-24 14:18:15 +01:00
James A. Fellows Yates	edce6603ef	Merge branch 'dev' into nf-core-template-merge-2.3.2	2022-03-24 14:10:58 +01:00
sofstam	3ff54e620e	Add centrifuge classification	2022-03-24 13:02:25 +01:00
nf-core-bot	feeb8ba8dd	Template update for nf-core/tools version 2.3.2	2022-03-24 11:48:43 +00:00
nf-core-bot	6b939e6728	Template update for nf-core/tools version 2.3.1	2022-03-23 13:57:56 +00:00
James A. Fellows Yates	038a8d106a	Fix test with correct URL	2022-03-23 11:25:47 +01:00
James Fellows Yates	48b6ef508d	Update path to samplesheet	2022-03-23 10:06:01 +01:00
James Fellows Yates	358b89a4c6	Linting	2022-03-21 20:30:29 +01:00
James Fellows Yates	81bfb629ca	Add working basic test to begin	2022-03-21 20:28:09 +01:00
James A. Fellows Yates	cd9e3c604c	Merge pull request #30 from nf-core/database-untar ... Adds ability to conditionally untar databases TAR files that contain DB directories	2022-03-21 19:56:22 +01:00
James A. Fellows Yates	3079f16861	Merge branch 'dev' into database-untar	2022-03-21 19:55:36 +01:00
James Fellows Yates	07eed435c6	Replace set with explicity assignment	2022-03-21 19:54:51 +01:00
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