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Author SHA1 Message Date
Phil Ewels
cb89722ea8
Merge pull request #34 from luslab/feat-mod-umitools 
Added Umi-tools module covering the dedup function
 2020-07-11 13:31:40 +02:00
Phil Ewels
81b1d6081c
Merge pull request #31 from FelixKrueger/hisat2 
Added HISAT2 module and test workflow
 2020-07-11 13:29:02 +02:00
Phil Ewels
7ef2a97882
Update tools/hisat2/main.nf 2020-07-11 13:28:41 +02:00
Phil Ewels
23c2fd8520
Apply suggestions from code review 2020-07-11 13:27:56 +02:00
Phil Ewels
edda7433d3
Merge pull request #30 from FelixKrueger/bowtie2 
Added Bowtie2 module and test workflow
 2020-07-11 13:27:20 +02:00
Phil Ewels
2fee617b5b
Update tools/bowtie2/main.nf 2020-07-11 13:27:05 +02:00
Phil Ewels
ccea438b49
Update tools/bowtie2/main.nf 2020-07-11 13:26:50 +02:00
Phil Ewels
a1ff2bd677
Merge pull request #29 from FelixKrueger/multiqc 
Added DSL2 module for MultiQC
 2020-07-11 13:26:01 +02:00
Phil Ewels
5aaacf8173
Update tools/multiqc/main.nf 2020-07-11 13:25:51 +02:00
Phil Ewels
36c4cfb3b0
Merge pull request #28 from FelixKrueger/trim_galore 
Added functional Trim Galore module
 2020-07-11 13:24:09 +02:00
Phil Ewels
c627da09cc
Merge pull request #27 from FelixKrueger/fastqc 
FastQC module is working and now accepting arguments
 2020-07-11 13:23:41 +02:00
Phil Ewels
05c6d2557d
Merge pull request #24 from FelixKrueger/fastq_screen 
Added FastQ Screen module
 2020-07-11 13:23:03 +02:00
Phil Ewels
89cfc271dd
Merge pull request #22 from Jeremy1805/master 
Added the bwa short alignment (bwa mem) module
 2020-07-11 13:21:34 +02:00
Phil Ewels
8b6065764e Merge branch 'master' into tcoffee_dev 2020-07-11 13:12:17 +02:00
Phil Ewels
dce77ce3f1 Merge branch 'master' of github.com:nf-core/modules 2020-07-11 13:08:33 +02:00
Phil Ewels
21711813c1
Merge pull request #18 from annacprice/shovill 
initial commit of shovill
 2020-07-11 13:00:43 +02:00
Harshil Patel
f422384e4d
Merge pull request #13 from MaxUlysse/dev 
Add social preview image
 2020-07-10 11:34:30 +01:00
Chris Cheshire
cad6c7d781 luslab-umitools | Corrections to hash checking 2020-06-29 10:37:53 +01:00
Chris Cheshire
128fd6fc76 luslab-umitools | Rudimentary hash checking of files 2020-06-26 11:24:05 +01:00
Chris Cheshire
3d81018c79 luslab-umitools | Updated doc file 2020-06-26 09:10:19 +01:00
Chris Cheshire
0da0f15998 luslab-umitools | Dropped process_name param 2020-06-26 09:06:37 +01:00
Chris Cheshire
afb1adebb6 luslab-umitools | Added index output from module 2020-06-26 09:04:15 +01:00
Chris Cheshire
3e26c218c2 luslab-umitools | Combined bam/bai into single channel + clean up 2020-06-26 08:36:11 +01:00
Chris Cheshire
cb58bea33f luslab-umitools | Changed all tabs to 4-space 2020-06-26 08:23:16 +01:00
Chris Cheshire
a905c05147 luslab-umitools | Changed all tabs to 4-space 2020-06-26 08:22:43 +01:00
Chris Cheshire
16c9c12eee luslab-umitools | Changed from shell to script inline with best practice 2020-06-26 08:19:54 +01:00
Chris Cheshire
723279c25e luslab-umitools | Simplified docker file 2020-06-26 08:17:45 +01:00
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
Gregor Sturm
d25e5bf402
Update .editorconfig 
Co-authored-by: Phil Ewels <phil.ewels@scilifelab.se>
 2020-06-15 16:47:42 +02:00
Gregor Sturm
a2824cc580
Update .editorconfig 
Co-authored-by: Phil Ewels <phil.ewels@scilifelab.se>
 2020-06-15 16:27:20 +02:00
Gregor Sturm
bc1f77f0f9
Create .editorconfig 2020-06-15 15:57:51 +02:00
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
3520cfea42 Merge remote-tracking branch 'origin/feat-mod-umitools' into feat-mod-umitools 2020-06-03 18:41:51 +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
c09a9c7796 luslab-umitools | Added single-cell RNA-seq options and grouping option 2020-06-03 18:41:11 +02:00
Candice
addb4122fd luslab-umitools |Edited Dockerfile in umi_tools 2020-06-03 11:22:27 +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