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Author SHA1 Message Date
Phil Ewels
9b4634a426 Use latest edge version of NXF for FastQC test 2020-07-17 10:35:17 +02:00
Phil Ewels
e71bb92534 Workflows - trigger on change to workflow and test data too 2020-07-16 17:14:57 +02:00
Phil Ewels
aa24c8d175 Fix a bunch of stuff in GitHub Actions test workflows 2020-07-16 17:11:34 +02:00
Gregor Sturm
2b6dc71338
Merge pull request #48 from grst/update-requirements 
Update module requirements with consensus from today's meeting
 2020-07-16 16:54:15 +02:00
Gregor Sturm
6634a37bfd
Update README.md 
Co-authored-by: Phil Ewels <phil.ewels@scilifelab.se>
 2020-07-16 16:48:47 +02:00
Gregor Sturm
f95f234562
Update README.md 
Co-authored-by: Phil Ewels <phil.ewels@scilifelab.se>
 2020-07-16 16:48:22 +02:00
Gregor Sturm
9b83ad1fe2 Update README 2020-07-16 15:42:41 +02:00
Phil Ewels
9dfafb4a19
Merge pull request #46 from stevekm/fastqc-unit-test 
add FastQC output validation and md5 checksum hash checks
 2020-07-16 15:13:44 +02:00
Stephen Kelly
4957eb98e5 update GitHub actions for Fastqc 2020-07-16 08:49:08 -04:00
Stephen Kelly
61d44c34d0 update GitHub actions for Fastqc 2020-07-16 08:31:19 -04:00
Stephen Kelly
45fbbb538c add FastQC output validation and md5 checksum hash checks 2020-07-16 08:20:37 -04:00
Harshil Patel
4ee6da3a34
Merge pull request #45 from FelixKrueger/master 
Adding back in all input files we had before
 2020-07-16 09:32:06 +01:00
FelixKrueger
9402a2efbe Still fixing linting 2020-07-16 09:06:59 +01:00
FelixKrueger
c6f73f9d56 Trying to trigger CI tests 2020-07-16 09:01:29 +01:00
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
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
Gregor Sturm
7121879714
Add: All outputs should be named 2020-07-14 16:13:05 +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