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542 commits 30 branches 0 tags 142 MiB
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211 commits

Author SHA1 Message Date
Chris Cheshire
6d34e6964f seacr | added new line at end 2021-01-05 10:20:13 +00:00
Chris Cheshire
e25edbf7b8 seacr | Added meta file 2021-01-05 10:18:11 +00:00
Chris Cheshire
c110088b5e Updated line endings 2021-01-05 09:56:15 +00:00
Chris Cheshire
37840b3855 seacr | updated trailing whitespace 2021-01-05 09:54:44 +00:00
Chris Cheshire
9c00d1722c seacr | PR review changes 2021-01-05 09:50:47 +00:00
Chris Cheshire
7e9cbfc8d1 Merge remote-tracking branch 'nf-core/master' 2021-01-05 09:10:11 +00:00
Harshil Patel
c98f9284a2
Merge pull request #89 from KevinMenden/master 
Add bowtie module
 2020-12-18 14:56:29 +00:00
kevinmenden
32f6191ff3 editorconfig 2020-12-18 11:11:19 +01:00
kevinmenden
db0b631906 removed index from test output 2020-12-18 11:06:02 +01:00
kevinmenden
299a3fa07e adding .index back 2020-12-18 10:58:37 +01:00
kevinmenden
0be13edc52 next try at editorconfig 2020-12-18 09:52:38 +01:00
kevinmenden
07f0a2476a fixed linting errors 2020-12-18 09:50:05 +01:00
kevinmenden
0eb20c14bf fixed unaligned output 2020-12-18 09:20:35 +01:00
kevinmenden
1c89c9717b Merge branch 'master' of https://github.com/KevinMenden/modules 2020-12-18 09:16:17 +01:00
kevinmenden
f840325ead added unaligned output 2020-12-18 09:14:40 +01:00
Kevin Menden
7805d25cc5
Update software/bowtie/align/meta.yml 
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
 2020-12-18 09:13:48 +01:00
Kevin Menden
a7f1ff29d7
Update software/bowtie/align/meta.yml 
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
 2020-12-18 09:13:42 +01:00
Kevin Menden
dc4108fd9b
Update software/bowtie/align/meta.yml 
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
 2020-12-18 09:13:35 +01:00
Kevin Menden
41329b8982
Apply suggestions from code review 
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
 2020-12-18 08:16:18 +01:00
Edmund Miller
d76638d6f8
style(#77): Fix editorconfig errors 2020-12-17 17:50:24 -06:00
Chris Cheshire
6f1c66f22f Merge remote-tracking branch 'nf-core/master' 2020-12-17 14:29:20 +00:00
Chris Cheshire
b24834dfce seacr | local testing implimented 2020-12-17 14:20:24 +00:00
Chris Cheshire
74e7b5385f seacr | Added main process structure 2020-12-17 13:54:48 +00:00
Harshil Patel
b236d0c834
Update main.nf 2020-12-17 10:24:01 +00:00
kevinmenden
57ab6dbcbf groovy formatting 2020-12-17 10:24:48 +01:00
kevinmenden
d75cb75111 added singularity; edge NXF version 2020-12-17 07:33:44 +01:00
Chris Cheshire
3ff2b558e0 seacr | Added callpeak skeleton 2020-12-16 11:05:06 +00:00
kevinmenden
f35850bf14 bowtie bam output 2020-12-16 11:02:58 +01:00
drpatelh
200c946693 Add --singularity_pull_docker_container to module yml 2020-12-14 00:34:24 +00:00
drpatelh
99a2364a26 Update all other modules 2020-12-14 00:05:48 +00:00
drpatelh
047dbde0af Add singularity containers for rnaseq pipeline modules 2020-12-13 23:41:53 +00:00
drpatelh
115efec15c Update Salmon quant to use BAM input 2020-12-09 21:20:52 +00:00
drpatelh
37b8b82c98 Fix tyop 2020-12-09 21:20:26 +00:00
drpatelh
42f318fe75 Update Salmon modules 2020-12-09 21:20:11 +00:00
kevinmenden
42020ce5ac added tests for bowtie paired-end alignment; resolved index bug 2020-12-09 16:39:05 +01:00
kevinmenden
cc72028d3d output index as directory 2020-12-09 15:58:56 +01:00
Kevin Menden
560a6a578b
Apply suggestions from code review 
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
 2020-12-09 15:45:05 +01:00
Harshil Patel
79a0ce79ab
Merge pull request #82 from abhi18av/master 
Add multiqc module
 2020-12-09 11:31:07 +00:00
Abhinav Sharma
0c9f29e0a2 Give finishing touches after the review 2020-12-08 19:08:00 +05:30
Abhinav Sharma
b56a0322ab
Apply suggestions from code review by @drpatelh 
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
 2020-12-08 18:57:14 +05:30
kevinmenden
9d67da2b2c added module yml files 2020-12-08 13:40:32 +01:00
kevinmenden
508761e05c Added bowtie index and align modules 2020-12-08 12:57:00 +01:00
Harshil Patel
cd2cf9cf2f
Merge pull request #85 from nf-core/pytest-workflow-refactor 
Refactor all tests to use pytest-workflow
 2020-12-04 14:30:00 +00:00
Abhinav Sharma
3da7aec183 Update the signatures 2020-12-04 12:25:16 +05:30
Abhinav Sharma
a30df8a59b Iterate again on MultiQC 2020-12-04 12:11:17 +05:30
Abhinav Sharma
5fd3ba3ce6 Update the tests for MultiQC 2020-12-02 13:09:32 +05:30
Abhinav Sharma
4e657c82e2 Move the MultiQC test files to data folder 2020-12-01 12:27:31 +05:30
Abhinav Sharma
b43c1f3937 Refactor the multiqc test code 2020-12-01 12:19:52 +05:30
Abhinav Sharma
131609dc05 Tweak the output section to make the tests pass 2020-12-01 12:03:37 +05:30
Paolo Cozzi
835ac48565 Fixing MULTIQC module and adding tests (#1) 
* fix multiqc process

* fix multiqc tests

* move multiqc test input data into tests/data/fastqc/ folder

Move input tests data into tests/data/fastqc/ and linking those files into software/multiqc/test/input/ as stated from the project documentation

* add multiqc github workflow

* remove unused file

* generalize multiqc input data

User must collect all desidered files in a channel (as described in https://seqera.io/training/#_multiqc_report

* update meta information
 2020-12-01 12:03:37 +05:30