Jose Espinosa-Carrasco
ee90e7af77
Add default output dir for modules that create indices, updated ( #336 )
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* Add default output dir for modules that create indices
* Change path for index module test output
* Fix bowtie2/align tests
* Fixing bowtie/align tests
* Fix genomegenerate test
* Fixing README linting
2021-03-23 17:55:01 +00:00
Patrick Hüther
8a44258548
remove params section from meta.yml ( #282 )
2021-03-19 13:16:50 +01:00
Jose Espinosa-Carrasco
572abb00b3
Remove def from module options definition in main ( #270 )
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* Remove def from module options definition in main
* Fix bismark_deduplicate tests
* Fix bwameth_align tests
* Fixing gatk4 conda tests ("=" instead of ':' in build id)
* Same as previous commit (Fix gatk4 test)
* Fix qualimap bamqc test (no md5 check for pngs)
* Fix seqkit split2 tests. Changed to new test data
* Fix samtools tests. Some were missing initOptions include
* Removing TOOL SUBTOOL template module since now it is included on tools repo
2021-03-15 12:16:43 +00:00
drpatelh
dcc580e4fb
Remove Conda build ids for all modules
2021-02-16 23:58:23 +00:00
drpatelh
673d463208
bowtie - add mulled build info
2021-02-03 11:33:31 +00:00
drpatelh
a536c85ec0
bowtie - add build to conda definition
2021-02-03 08:49:18 +00:00
drpatelh
f84e5b59ca
Rename bowtie_index to bowtie_build
2021-02-01 17:53:31 +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
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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
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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
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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
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Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2020-12-18 08:16:18 +01:00
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
kevinmenden
f35850bf14
bowtie bam output
2020-12-16 11:02:58 +01:00
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
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Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2020-12-09 15:45:05 +01:00
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
