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
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
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
kevinmenden
0eb20c14bf
fixed unaligned output
2020-12-18 09:20:35 +01:00
kevinmenden
f840325ead
added unaligned output
2020-12-18 09:14:40 +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
...
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
