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92 commits 30 branches 0 tags 142 MiB
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52 commits

Author SHA1 Message Date
Chris Cheshire
0f5da3bd99
review-correction | Add channels back into file 
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
 2020-06-23 09:39:46 +01:00
Chris Cheshire
aeec856fe1
review-correction | Docker file update 
Co-authored-by: Phil Ewels <phil.ewels@scilifelab.se>
 2020-06-23 09:38:09 +01:00
Chris Cheshire
fc8bc4675d
review-correction | Variable name change 
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
 2020-06-23 09:34:57 +01:00
Chris Cheshire
cdd50fdf7d
review-correction | Variable name change 
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
 2020-06-23 09:34:47 +01:00
Chris Cheshire
58d345fe81 luslab-umitools | Cleanup for submission 2020-06-19 15:55:45 +01:00
Chris Cheshire
961d12275a luslab-umitools | Cleaned dependancy file 2020-06-19 08:22:37 +01:00
Chris Cheshire
9945ac88e0 luslab-umitools | Module feature complete 2020-06-19 08:21:55 +01:00
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