Paolo Di Tommaso
70daf8be30
Minor style improvents
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This commit provides a minor refactoring with som
Nextflow code style improvments:
- Replaces `.toGiga()` with `.giga`
- Replaces `tag { foo }` with `tag "$foo"`
- Move publishDir before input declarations. Directives should be
before the first input. Tho this is not enforced, it may be in
future versions.
- Replaces input `file` with `path`
- Remove unnecessary parentheses
2020-07-27 12:11:42 +02:00
Phil Ewels
6dfb9f02c9
Merge pull request #47 from stevekm/fastqc-unit-test
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move md5 function to lib dir and symlink to fastqc test dir, rename m…
2020-07-23 11:46:10 +02:00
Phil Ewels
dbf5b267b1
Fix code format linting
2020-07-23 11:43:48 +02:00
Phil Ewels
3406ed4da0
Merge branch 'master' into fastqc-unit-test
2020-07-17 16:00:59 +02:00
Phil Ewels
c2aef67408
Merge pull request #49 from ewels/fix-actions
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Fix a bunch of stuff in GitHub Actions test workflows
2020-07-17 16:00:23 +02:00
Phil Ewels
f01b3f13a6
Remove debugging statement
2020-07-17 16:00:08 +02:00
Phil Ewels
2d1252c804
FastQC tests - disable hash check
2020-07-17 11:30:28 +02:00
Phil Ewels
dcc4beacb1
Fix FastQC test
2020-07-17 11:26:50 +02:00
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
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Update module requirements with consensus from today's meeting
2020-07-16 16:54:15 +02:00
Gregor Sturm
6634a37bfd
Update README.md
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Co-authored-by: Phil Ewels <phil.ewels@scilifelab.se>
2020-07-16 16:48:47 +02:00
Gregor Sturm
f95f234562
Update README.md
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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
Stephen Kelly
846a862513
move md5 function to lib dir and symlink to fastqc test dir, rename md5 function
2020-07-16 09:17:48 -04:00
Phil Ewels
9dfafb4a19
Merge pull request #46 from stevekm/fastqc-unit-test
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
