millironx/nf-core_modules
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Author SHA1 Message Date
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
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