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1463 commits

Author SHA1 Message Date
Harshil Patel
e7e30b6da6
Bump Pangolin to 3.1.7 ()
* Bump Pangolin to 3.1.7

* Update md5sum

* Update README

* Re-word

* Re-word again

* Use channels
2021-07-20 12:25:36 +01:00
Harshil Patel
5dd049047d
Fix tyop in output for rseqc/junctionannotation () 2021-07-20 11:27:47 +01:00
Johnathan D
0b40798d1b
fix: lofreq/callparallel missing arg () ()
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-07-19 09:19:27 +01:00
Harshil Patel
2ade120249
Add --paired flag to umitools dedup and bump to 1.1.2 ()
* Add --paired flag to umitools dedup and bump to 1.1.2

* paired not paired_end

* Fix ECLint
2021-07-16 14:21:08 +01:00
Maxime U. Garcia
adfb8a3d65
fix: update samtools_merge ()
* fix: update samtools_merge

* Update modules/samtools/merge/main.nf

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-07-16 14:32:17 +02:00
Maxime U. Garcia
65ab646870
fix: update seqkit to 0.16.0 () 2021-07-16 11:54:21 +02:00
Maxime U. Garcia
b3c4667732
fix: update to gatk4.2.0.0 ()
* fix: update to gatk4.2.0.0

* fix: update md5sum
2021-07-16 11:26:28 +02:00
Maxime U. Garcia
d624336cc1
fix: update to gatk4.2.0.0 () 2021-07-16 11:25:22 +02:00
Maxime U. Garcia
c8877835c2
fix: update to gatk4.2.0.0 () 2021-07-16 11:24:29 +02:00
Maxime U. Garcia
e7be649029
fix: update to gatk4.2.0.0 () 2021-07-16 11:23:08 +02:00
Maxime U. Garcia
9fb21e1a84
fix: update to gatk4.2.0.0 () 2021-07-16 11:22:01 +02:00
Maxime U. Garcia
bee23ba899
fix: update to gatk4.2.0.0 () 2021-07-16 11:18:27 +02:00
Harshil Patel
e937c7950a
Rename software/ directory to modules/ to re-organise module structure ()
* Update README

* Rename pytest_software.yml to pytest_modules.yml

* Rename main software directory to modules

* Remove deprecated modules

* Rename tests software to modules

* Replace paths for tests in pytest_modules.yml

* Replace software with modules in Github Actions

* Replace software with modules in main.nf tests

* Rename software to modules in test.yml
2021-07-07 10:10:18 +01:00