Jose Espinosa-Carrasco
0bbd7acfc4
Fix number of cpus for modules with piped tools ( #499 )
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* Split CPUs for piped commands
* Fix tests, bams no md5 check
2021-05-18 09:52:00 +02:00
Jose Espinosa-Carrasco
95e02f913f
Update comments with new style ( #497 )
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* Update comment style on functions.nf files
* Update test main.nf comments
* Add meta for ggread
2021-05-12 14:56:46 +01:00
Harshil Patel
dce27b8102
Update functions.nf to be more flexible for publishing by meta keys ( #423 )
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* Update functions.nf
* Replace saveAs line in module main script
* Add spacing for ECLint
2021-04-09 17:23:56 +01:00
Patrick Hüther
4a1571317d
update bwameth container build to match conda version ( #402 )
2021-04-06 10:45:14 +01:00
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
phue
bf0e0d857d
bwameth/align: fix fasta name retrieval
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apparently bwameth doesn't like './' in front of the filepath? I have no idea. This works however
2021-02-20 13:12:43 +01:00
phue
c67e591caf
apply suggestions from review
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thanks @drpatelh
2021-02-20 12:51:01 +01:00
phue
a963c67481
bwameth: pass genome index as directory
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instead of single files
2021-02-18 11:51:36 +01:00
phue
84a5da0d91
add bwameth/align module + tests
2021-02-17 18:23:11 +01:00
