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Author SHA1 Message Date
Gregor Sturm
b00bb83532 Document params 2020-07-15 11:01:15 +02:00
Gregor Sturm
86d6daf9de Implement publish_results parameter 2020-07-15 10:55:52 +02:00
Gregor Sturm
1dc47e7cd3 Make publishDir more flexible 2020-07-15 10:16:48 +02:00
Gregor Sturm
dd34fa5853 Use moduleDir for conda env 2020-07-15 09:48:17 +02:00
Gregor Sturm
f7c42ac4fd Add tests for fastqc module 2020-07-15 09:48:14 +02:00
Gregor Sturm
167067a92e Clean up module file 2020-07-15 09:47:41 +02:00
Harshil Patel
a5306b33da
Merge pull request #39 from grst/document-module-standards 
Document preliminary module structure
 2020-07-14 18:53:24 +01:00
JoseEspinosa
c485d56972 Indentation error in yml 2020-07-14 18:00:23 +02:00
JoseEspinosa
562fc74550 Indentation error in yml 2020-07-14 17:57:42 +02:00
JoseEspinosa
39b9ca205c Correcting path to test data 2020-07-14 17:42:03 +02:00
JoseEspinosa
b38135ff6b Moving bedtools/intersectbed to bedtools/intersect 2020-07-14 17:40:17 +02:00
JoseEspinosa
c059a485b9 Using bedtools{_,-}genomecov instead of genomecov alone 2020-07-14 17:31:40 +02:00
JoseEspinosa
71eaa83bf6 bedtoools/complementBed changed to bedtools/complement 2020-07-14 17:26:45 +02:00
JoseEspinosa
8c3d7aa2d8 Standardizing process names to BEDTOOLS_FOO and same with some variables 2020-07-14 17:25:32 +02:00
JoseEspinosa
99a8196776 Module bedtools-sort added 2020-07-14 17:20:12 +02:00
MaxUlysse
56ee2cc8e2 fix lint 2020-07-14 17:19:12 +02:00
MaxUlysse
1223614e15 add modules for bwa-mem2 2020-07-14 17:10:23 +02:00
JoseEspinosa
366dd1742a Merge branch 'tmp' into bedtools_dev 2020-07-14 16:49:06 +02:00
JoseEspinosa
cf9d87c977 Module bedtools-merge added 2020-07-14 16:49:06 +02:00
JoseEspinosa
708cee9cae Module bedtools-intersectbed added 2020-07-14 16:49:05 +02:00
JoseEspinosa
5f80a900e9 Changing fasta_sizes by chrom_sizes input path for genomecov 2020-07-14 16:47:27 +02:00
JoseEspinosa
f2eb3f68c0 Module bedtools-genomecov added 2020-07-14 16:47:26 +02:00
JoseEspinosa
f77a7b4ef5 Module intersectbed added 2020-07-14 16:17:23 +02:00
Gregor Sturm
7121879714
Add: All outputs should be named 2020-07-14 16:13:05 +02:00
JoseEspinosa
0ffa739cd0 Changing fasta_sizes by chrom_sizes input path for genomecov 2020-07-14 16:09:01 +02:00
JoseEspinosa
9d79d64eb9 Module genomecov added 2020-07-14 16:00:10 +02:00
JoseEspinosa
f6894c7d3a Module complementbed added 2020-07-14 15:50:35 +02:00
Gregor Sturm
8f3718795b Fix markdownlint 
Move markdownlint.yml to root directory. Like that it is automatically discovered and applied by most IDEs
 2020-07-14 12:21:33 +02:00
Gregor Sturm
fe882f1579 Add software dependencies and version string to requirements list 2020-07-14 12:07:41 +02:00
Gregor Sturm
4ee6ddc7ab Update README 2020-07-14 10:55:38 +02:00
Phil Ewels
8155270653
Merge pull request #38 from ewels/master 
Fix up cutadapt tests
 2020-07-11 17:16:26 +02:00
Phil Ewels
31c0f617b9 Fix up cutadapt tests 2020-07-11 17:14:14 +02:00
Phil Ewels
abfd112964
Merge pull request #37 from ewels/master 
Cutadapt - merge tests into one
 2020-07-11 17:09:50 +02:00
Phil Ewels
f36902b9af Cutadapt - merge tests into one 2020-07-11 17:09:06 +02:00
Phil Ewels
7ae79df07c
Merge pull request #36 from ewels/change-filestructure 
Restructure file hierarchy
 2020-07-11 14:53:33 +02:00
Phil Ewels
905e842f36 Update more paths 2020-07-11 14:36:12 +02:00
Phil Ewels
d3f3432451 Update test file imports 2020-07-11 14:33:12 +02:00
Phil Ewels
a6b2485dab Move social preview image 2020-07-11 14:28:58 +02:00
Phil Ewels
cffb8b63ab Move to new tests/ folder 2020-07-11 14:28:26 +02:00
Phil Ewels
014fef2e92 Rename tools to software 2020-07-11 14:27:21 +02:00
Phil Ewels
edd508487b
Merge pull request #35 from ewels/editor-config 
Editor config
 2020-07-11 14:20:37 +02:00
Phil Ewels
229bd5d085 Update test-datasets 2020-07-11 13:57:17 +02:00
Phil Ewels
47d55001fa Fix YAML validation errors 2020-07-11 13:54:12 +02:00
Phil Ewels
263f48d520 Fix markdownlint 2020-07-11 13:48:11 +02:00
Phil Ewels
45fb2ff4f4 Remove verbose job names 2020-07-11 13:45:08 +02:00
Phil Ewels
fc53a6f0b5 Added markdown lint config file 2020-07-11 13:44:28 +02:00
Phil Ewels
ae38a9bf41 Fix editor config styles 2020-07-11 13:42:13 +02:00
Phil Ewels
a547f27f21 New GitHub Action to lint code style 2020-07-11 13:41:31 +02:00
Phil Ewels
0241467b1e
Merge pull request #33 from nf-core/grst-patch-1 
Create .editorconfig
 2020-07-11 13:32:05 +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