Chris Cheshire
|
436d6a6292
|
luslab-umitools | Updating module definition
|
2020-06-18 16:54:14 +01:00 |
|
Chris Cheshire
|
1cbfd0d125
|
luslab-umitools | Changed sample file names
|
2020-06-18 16:14:26 +01:00 |
|
Chris Cheshire
|
ceb1a6ef1a
|
luslab-umitools | Cleaned up sample file names
|
2020-06-18 15:44:27 +01:00 |
|
Chris Cheshire
|
9092ae8c01
|
luslab-umitools | Cleaned up docker files and removed groovy dependancy
|
2020-06-18 15:40:24 +01:00 |
|
Candice
|
6ecf54d73c
|
luslab-umitools | Added SAM/BAM options and group/dedup options
|
2020-06-04 17:01:46 +02:00 |
|
Candice
|
c5e958cc4f
|
luslab-umitools | Added Nextflow config file
|
2020-06-04 17:00:25 +02:00 |
|
Candice
|
064bd11ebf
|
luslab-umitools | Added single-cell RNA-seq options and grouping option
|
2020-06-03 18:41:34 +02:00 |
|
Candice
|
1508596f14
|
luslab-umitools | Edited Dockerfile in umi_tools
|
2020-06-03 18:41:34 +02:00 |
|
Candice
|
07b485eeec
|
luslab-umitools | Minor corrections to main.nf in umi_tools/dedup
|
2020-06-02 19:05:08 +02:00 |
|
Candice
|
08d26794b5
|
luslab-umitools | Created yml file for dedup in umi_tools
|
2020-06-02 19:02:18 +02:00 |
|
Candice
|
3aace7c0c2
|
luslab-umitools | Added sample_id options in dedup
|
2020-06-02 18:45:55 +02:00 |
|
Candice
|
6970d25b59
|
luslab-umitools | Added basic options to dedup tool in umi_tools
|
2020-06-02 17:23:54 +02:00 |
|
Candice
|
4656667374
|
luslab-umitools | Renamed params and changed relative paths
|
2020-06-01 16:41:47 +02:00 |
|
Candice
|
ff0265fda4
|
luslab-umitools | Added input folder in dedup/test
|
2020-06-01 16:21:29 +02:00 |
|
Candice
|
e46db6d31d
|
luslab-umitools | Created conda environment for umi_tools
|
2020-06-01 16:14:13 +02:00 |
|
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 |
|
Piotr Faba
|
c90474202c
|
update meta
|
2020-03-06 14:23:32 +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 |
|
Piotr Faba
|
88bc7dcdd8
|
the module is working in test
|
2020-03-06 10:51:46 +00:00 |
|
Piotr Faba
|
97d9ae76f0
|
add cutadapt module
|
2020-03-05 15:56:11 +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 |
|