/OSG-GEM

Permalink
OSG-GEM/osg-gem.conf.example
Newer
Older
Raw Normal view History
100644 56 lines (37 sloc) 952 Bytes
Apr 2, 2016 @rynge Added conf file and initial support for hisat2
1
2 [reference]
3
May 11, 2016 @wpoehlm Added Test Input Files
4 reference_prefix = chr21-GRCh38
Apr 2, 2016 @rynge Added conf file and initial support for hisat2
5
6 [inputs]
7
Aug 8, 2016 @rynge Added support for multiple inputs and a GEM merge at the end. Simplie…
8 #
9 # List the inputs to process. Each line can either be a pair
10 # of forward and reverse files, separated by a space:
11 #
12 # input1 = forward.fastq.gz reverse.fastq.gz
13 #
14 # or a single SRR number. Example:
15 #
16 # input2 = DRR046893
17 #
Feb 21, 2017 @wpoehlm Added support for single end reads. User may select single or paired …
18 # or a single fastq file for single end reads. Example:
19 # input3 = SRR4343300.fastq.gz
Aug 8, 2016 @rynge Added support for multiple inputs and a GEM merge at the end. Simplie…
20
21 input1 = ./Test_data/TEST_1.fastq.gz ./Test_data/TEST_2.fastq.gz
Feb 21, 2017 @wpoehlm Added support for single end reads. User may select single or paired …
22 #input1 = ./Test_data/SRR4343300.fastq.gz
23 #input2 = SRR4343300
Dec 5, 2016 @wpoehlm Update osg-gem.conf.example
24 #input2 = DRR046893
Apr 2, 2016 @rynge Added conf file and initial support for hisat2
25
Feb 21, 2017 @wpoehlm Added support for single end reads. User may select single or paired …
26
Apr 2, 2016 @rynge Added conf file and initial support for hisat2
27 [config]
28
Feb 21, 2017 @wpoehlm Added support for single end reads. User may select single or paired …
29
Oct 31, 2016 @rynge Added option to control memory allocation
30 # Memory available to the jobs. This should be roughly 2X the
31 # size of the reference genome, rounded up whole GB
Dec 5, 2016 @wpoehlm Update osg-gem.conf.example
32 memory = 4 GB
Oct 31, 2016 @rynge Added option to control memory allocation
33
Feb 21, 2017 @wpoehlm Added support for single end reads. User may select single or paired …
34 # Reads are single end
35 single = False
36
37 # Reads are paired end
38 paired = True
39
Apr 2, 2016 @rynge Added conf file and initial support for hisat2
40 # process using TopHat2
41 tophat2 = False
42
43 # process using Hisat2
44 hisat2 = True
45
May 4, 2017 @wpoehlm Added support for STAR read alignment software
46 # process using STAR
47 star = False
48
Apr 2, 2016 @rynge Added conf file and initial support for hisat2
49 # process using Cufflinks
May 11, 2016 @wpoehlm Added Test Input Files
50 cufflinks = False
Apr 2, 2016 @rynge Added conf file and initial support for hisat2
51
52 # process using StringTie
May 11, 2016 @wpoehlm Added Test Input Files
53 stringtie = True
Apr 2, 2016 @rynge Added conf file and initial support for hisat2
54
Feb 21, 2017 @wpoehlm Added support for single end reads. User may select single or paired …
55