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Author SHA1 Message Date
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
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
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