96 commits

Author	SHA1	Message	Date
Phil Ewels	ae38a9bf41	Fix editor config styles	2020-07-11 13:42:13 +02:00
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
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
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