Commit graph

166 commits

Author SHA1 Message Date
James A. Fellows Yates
10502399ad
Replaced param with input val channel (#595)
* Replaced param with input val channel

* Apply suggestions from code review

Co-authored-by: Jose Espinosa-Carrasco <kadomu@gmail.com>
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>

* Apply suggestions from code review

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

* Apply suggestions from code review (missed one)

* YAML lint

Co-authored-by: Jose Espinosa-Carrasco <kadomu@gmail.com>
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-07-21 10:00:48 +02:00
Harshil Patel
e4df336294
Add hifiasm module (#596)
* Add hifiasm module

* Tidy up module

* Add pacbio files to test_data.config
2021-07-20 21:50:22 +01:00
Johnathan D
2e619add87
Add samtools ampliconclip (#590)
* created template for `samtools/ampliconclip` (#584)

* All tests passing (#584)

* Linting fixed (#584)

* Final linting fixed (#584)

* Optional output flags moved to `input` (#584)

* typo fix (#584)

* Apply suggestions from code review

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-07-20 21:31:31 +01:00
Harshil Patel
e7e30b6da6
Bump Pangolin to 3.1.7 (#593)
* 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 (#592) 2021-07-20 11:27:47 +01:00
Johnathan D
0b40798d1b
fix: lofreq/callparallel missing arg (#562) (#586)
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 (#583)
* 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 (#582)
* 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 (#581) 2021-07-16 11:54:21 +02:00
Maxime U. Garcia
b3c4667732
fix: update to gatk4.2.0.0 (#575)
* 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 (#580) 2021-07-16 11:25:22 +02:00
Maxime U. Garcia
c8877835c2
fix: update to gatk4.2.0.0 (#579) 2021-07-16 11:24:29 +02:00
Maxime U. Garcia
e7be649029
fix: update to gatk4.2.0.0 (#578) 2021-07-16 11:23:08 +02:00
Maxime U. Garcia
9fb21e1a84
fix: update to gatk4.2.0.0 (#577) 2021-07-16 11:22:01 +02:00
Maxime U. Garcia
bee23ba899
fix: update to gatk4.2.0.0 (#576) 2021-07-16 11:18:27 +02:00
Harshil Patel
e937c7950a
Rename software/ directory to modules/ to re-organise module structure (#567)
* 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