millironx/nf-core_modules
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Author SHA1 Message Date
FelixKrueger
684005f2cb Fixing markdown lint 2 2020-07-15 16:00:21 +01:00
FelixKrueger
4f8b7a90aa Trying to fix markdown linting 2020-07-15 15:59:17 +01:00
FelixKrueger
02156d6b0d Removing old subsampled SRR files 2020-07-15 15:48:09 +01:00
FelixKrueger
e90164dd0b Adding back tool specific input output and index files 2020-07-15 15:46:45 +01:00
FelixKrueger
1c84a234ec Adding back in all input files we had before 2020-07-15 15:12:04 +01:00
Felix Krueger
45cc9ede3e
Merge pull request #44 from drpatelh/master 
Change test directory name to input for FastQC
 2020-07-15 15:17:52 +02:00
drpatelh
532859d437 Update path 2020-07-15 14:07:19 +01:00
JoseEspinosa
7f8b8189f8 Merge remote-tracking branch 'upstream/master' into bedtools_dev 2020-07-15 15:05:26 +02:00
Harshil Patel
6028bb080b
Merge pull request #40 from grst/update-fastqc 
Update fastqc to adhere to new module guidelines
 2020-07-15 12:59:28 +01:00
Harshil Patel
741b0786f9
Merge pull request #43 from grst/update-module-requirements 
Extend and formalize module requirements
 2020-07-15 12:58:12 +01:00
Gregor Sturm
5fe7b9eb66 Update README.md 2020-07-15 13:29:21 +02:00
Gregor Sturm
a2bcb5c36a Update module according to discussion on Slack 2020-07-15 13:04:49 +02:00
Gregor Sturm
01a926866e
Update software/fastqc/test/main.nf 
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
 2020-07-15 12:48:21 +02:00
Gregor Sturm
9d7cece077
Update software/fastqc/meta.yml 
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
 2020-07-15 12:48:11 +02:00
Gregor Sturm
5a8803ee2f
Update software/fastqc/meta.yml 
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
 2020-07-15 12:48:03 +02:00
Gregor Sturm
a3db769a93
Update software/fastqc/meta.yml 
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
 2020-07-15 12:47:52 +02:00
Gregor Sturm
180310bf0a
Update software/fastqc/meta.yml 
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
 2020-07-15 12:47:42 +02:00
Gregor Sturm
6ad2b570c2
Update software/fastqc/meta.yml 
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
 2020-07-15 12:47:30 +02:00
Gregor Sturm
53897f4d97
Update software/fastqc/meta.yml 
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
 2020-07-15 12:47:19 +02:00
Gregor Sturm
450e2839d5 Extend and formalize module requirements 2020-07-15 12:44:52 +02:00
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