millironx/nf-core_modules
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1315 commits 30 branches 0 tags 142 MiB
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18 commits

Author SHA1 Message Date
Harshil Patel
65a3422686
Add default publish_dir for index processes (#428) 2021-04-10 20:49:09 +01:00
Harshil Patel
dce27b8102
Update functions.nf to be more flexible for publishing by meta keys (#423) 
* Update functions.nf

* Replace saveAs line in module main script

* Add spacing for ECLint
 2021-04-09 17:23:56 +01:00
Harshil Patel
242fdb2f73
Version bumps and minor module updates (#406) 
* Version bumps and minor module updates

* Fix Pangolin tests

* Fix SPAdes tests

* stageAs @phue
 2021-04-06 13:38:41 +01:00
Jose Espinosa-Carrasco
ee90e7af77
Add default output dir for modules that create indices, updated (#336) 
* 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
Jose Espinosa-Carrasco
572abb00b3
Remove def from module options definition in main (#270) 
* 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
34e451dd2e rsem - add build info for mulled container 2021-02-03 11:04:59 +00:00
drpatelh
26e04dd298 rsem - add build info for mulled container 2021-02-03 11:04:51 +00:00
Edmund Miller
d76638d6f8
style(#77): Fix editorconfig errors 2020-12-17 17:50:24 -06:00
Harshil Patel
b236d0c834
Update main.nf 2020-12-17 10:24:01 +00:00
drpatelh
047dbde0af Add singularity containers for rnaseq pipeline modules 2020-12-13 23:41:53 +00:00
drpatelh
e5c7ecc89c Use STAR to build initial index for RSEM 2020-11-30 11:29:24 +00:00
drpatelh
a3f46865ff Remove Singularity image path 2020-11-12 14:55:16 +00:00
drpatelh
14525ed50d Remove functions file 2020-10-14 18:29:50 +01:00
drpatelh
6bb3d5caea Update container 2020-10-12 16:20:35 +01:00
drpatelh
64377d4035 Bug fixes 2020-10-12 16:20:22 +01:00
Harshil Patel
fb44f36f66
Update main.nf 2020-09-16 19:08:24 +01:00
drpatelh
cbf8329ffd Add new modules 2020-09-10 16:09:54 +01:00