Commit graph

17 commits

Author SHA1 Message Date
Jose Espinosa-Carrasco
0bbd7acfc4
Fix number of cpus for modules with piped tools (#499)
* 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)
* Update functions.nf

* Replace saveAs line in module main script

* Add spacing for ECLint
2021-04-09 17:23:56 +01:00
FriederikeHanssen
555f1710e0
Update test paths in bwa mappers (#387)
* Update test paths in bwa mappers

* Fix indentation

* indices pass lcoally now

* no idea how they could ever pass before, Tests pass locally no

* Update samtools and bwamem2 versions

* Correct mulled containers + md5
2021-03-25 09:24:21 +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
81ae0089bc Fix merge conflicts 2021-02-05 10:06:39 +00:00
drpatelh
98158064a7 bwa - add build info for mulled container 2021-02-03 11:04:25 +00:00
drpatelh
dcb1dc5cd9 Remove fasta requirement from module 2021-02-02 12:34:42 +00:00
Edmund Miller
d76638d6f8
style(#77): Fix editorconfig errors 2020-12-17 17:50:24 -06:00
drpatelh
99a2364a26 Update all other modules 2020-12-14 00:05:48 +00:00
drpatelh
a3f46865ff Remove Singularity image path 2020-11-12 14:55:16 +00:00
drpatelh
1d30e2c21a Update tools not in rnaseq pipeline too 2020-10-14 18:59:25 +01:00
drpatelh
e438d026bd Unify syntax 2020-09-10 16:45:11 +01:00
drpatelh
3b1669c317 Add bwa mem 2020-08-05 17:16:08 +01:00
drpatelh
c08e6959a5 Reorganise everything 2020-08-05 16:09:25 +01:00
Paolo Di Tommaso
70daf8be30
Minor style improvents
This commit provides a minor refactoring with som
Nextflow code style improvments:
- Replaces `.toGiga()` with `.giga`
- Replaces `tag { foo }` with `tag "$foo"`
- Move publishDir before input declarations. Directives should be
  before the first input. Tho this is not enforced, it may be in
  future versions.
- Replaces input `file` with `path`
- Remove unnecessary parentheses
2020-07-27 12:11:42 +02:00
Phil Ewels
014fef2e92 Rename tools to software 2020-07-11 14:27:21 +02:00
Renamed from tools/bwa/mem/main.nf (Browse further)