97 commits

Author	SHA1	Message	Date
Candice	5f82d0a702	luslab-umitools | Customized Dockerfile for umi_tools	2020-06-01 16:13:30 +02:00
Candice	7cc1319801	luslab-umitools | Renamed dedup.nf to main.nf	2020-06-01 15:18:49 +02:00
Candice	e00b7bd91e	luslab-umitools | Added parameter overriding function to umi_tools	2020-06-01 15:02:21 +02:00
Candice	549f81e4ea	luslab-umitools | Created a Dockerfile for umi_tools module	2020-06-01 14:52:43 +02:00
Candice	bfdccfe1b9	luslab-umitools | Initialized test.nf	2020-06-01 14:40:50 +02:00
Candice	ab2d819df3	luslab-umitools | Renamed umi-tools.nf to dedup.nf	2020-06-01 14:40:50 +02:00
Candice	ff243acf63	luslab-umitools | Created umitool.nf file in the dedup folder	2020-06-01 14:40:50 +02:00
Candice	baa5805350	luslab-umitools | Created test.nf and test folder in umi_tools/dedup	2020-06-01 14:40:50 +02:00
FelixKrueger	a2104ca3b9	Added HISAT2 module and test workflow	2020-03-20 11:04:25 +00:00
FelixKrueger	a526551300	Added Bowtie2 module and test workflow	2020-03-19 18:13:15 +00:00
FelixKrueger	974c6168d6	Added short description of MultiQC	2020-03-18 10:06:38 +00:00
FelixKrueger	223077e5a6	MultiQC module and test workflow	2020-03-17 21:46:21 +00:00
FelixKrueger	6208ac9799	Added functional Trim Galore module	2020-03-16 17:49:39 +00:00
FelixKrueger	f8916eb9b5	FastQC module is working and now accepting arguments	2020-03-16 14:17:38 +00:00
FelixKrueger	0ceb45068e	FastQ Screen works with E coli paired-end test file	2020-03-10 22:14:25 +00:00
FelixKrueger	d9a3b02b00	Updated yaml description	2020-03-10 14:13:36 +00:00
Phil Ewels	c8ceddfe77	Tidying, add samtools and trim_galore	2020-03-06 14:33:48 +00:00
Piotr Faba	c90474202c	update meta	2020-03-06 14:23:32 +00:00
Phil Ewels	198e9a85eb	FastQC: add dockerfile and environment.yml	2020-03-06 14:04:18 +00:00
Piotr Faba	1c941ef8d6	Update test-data commit and references	2020-03-06 13:59:14 +00:00
Piotr Faba	490eca706c	single and paired end supported	2020-03-06 13:23:12 +00:00
FelixKrueger	a6f7296e22	Initial commit	2020-03-06 13:21:17 +00:00
JoseEspinosa	5f9cf40f5a	Changing publishDir to take params.outdir and modifying yml for github actions	2020-03-06 12:23:23 +01:00
Piotr Faba	88bc7dcdd8	the module is working in test	2020-03-06 10:51:46 +00:00
Jeremy1805	60f1d3b7a1	Updated tools/bwa/mem/meta.yml	2020-03-05 16:35:56 +00:00
Jeremy1805	356e23823c	Updated tools/bwa/mem/meta.yml	2020-03-05 16:31:46 +00:00
JoseEspinosa	707d2855d6	Adding tcoffee module	2020-03-05 17:18:35 +01:00
Jeremy1805	a4836ae3c3	Added tools/bwa/mem	2020-03-05 16:06:25 +00:00
Piotr Faba	97d9ae76f0	add cutadapt module	2020-03-05 15:56:11 +00:00
annacprice	e623dca3b7	initial commit of shovill	2020-03-05 09:29:23 +00:00
Maxime Garcia	48be154434	Update tools/bwa/index/meta.yml ... Co-Authored-By: Olga Botvinnik <olga.botvinnik@gmail.com>	2020-01-24 10:39:52 +01:00
MaxUlysse	7fbfd2d6cb	add samtools faidx to index fasta file	2020-01-23 11:36:21 +01:00
MaxUlysse	b8dda67338	add htslib tabix to index bgzipped vcf files	2020-01-23 11:35:49 +01:00
MaxUlysse	9db873c3bc	add gatk dict to create dictionnary from fasta file	2020-01-23 11:35:19 +01:00
MaxUlysse	a69aebd01b	fix index process	2020-01-23 10:19:00 +01:00
MaxUlysse	ad3c14a964	fix typo	2020-01-21 11:25:13 +01:00
MaxUlysse	1f46499e3b	add bwa index	2020-01-21 11:24:32 +01:00
Phil Ewels	5fbde1c69d	Fix trim galore process name	2019-12-06 11:24:07 +01:00
Phil Ewels	c77ea13d35	Fixed FastQC tests with submodule	2019-12-06 10:15:49 +01:00
Phil Ewels	93f7b26aa2	Use submodules for test data	2019-12-06 09:24:33 +01:00
Phil Ewels	e2a205c8df	Added nextflow.config files for all	2019-12-05 22:18:33 +01:00
Phil Ewels	eb41e5ebba	FastQC: actually run a test	2019-12-05 22:11:12 +01:00
Phil Ewels	acc4eb0054	GitHub actions - run nextflow in a docker image	2019-12-05 15:57:32 +01:00
Phil Ewels	af766a9cc7	Added TrimGalore	2019-12-05 15:53:38 +01:00
Phil Ewels	97fbd32644	Added samtools sort + index ... Added container to FastQC	2019-12-05 15:36:35 +01:00
Phil Ewels	5e4c023edd	Start work on FastQC module files	2019-12-05 15:18:09 +01:00
Phil Ewels	4582ab344c	Add GitHub Actions, put FastQC in to a directory	2019-12-05 14:52:43 +01:00