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41 commits

Author SHA1 Message Date
Yuk Kei Wan
134c8ef6ce
add samtools merge (#296) 
* add samtools merge

* Update pytest_software.yml

* get it back to 20.11.0-edge

* Update test.yml

* Update test.yml

* Update test.yml

* Update test.yml
 2021-03-22 13:48:23 +01:00
Patrick Hüther
8a44258548
remove params section from meta.yml (#282) 2021-03-19 13:16:50 +01:00
Harshil Patel
3df3d671f2
Fix nf-core modules lint tests (#275) 
* Fix Conda definition bug

* Add process label
 2021-03-16 17:16:47 +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
phue
aafc6949d3 faidx: add process label 2021-02-17 16:56:45 +01:00
phue
3b1d126a0e add samtools/faidx + tests 2021-02-17 16:46:34 +01:00
drpatelh
dcc580e4fb Remove Conda build ids for all modules 2021-02-16 23:58:23 +00:00
drpatelh
383d35bc7d samtools - add build to conda definition 2021-02-03 09:17:38 +00:00
Harshil Patel
eb7a3861db
Update software/samtools/mpileup/meta.yml 2021-01-29 18:12:17 +00:00
JoseEspinosa
13e9f81160 Fixing lint tests 2021-01-29 18:01:58 +01:00
JoseEspinosa
22dcdc692d Adding samtools_mpileup module 2021-01-29 17:58:42 +01:00
JoseEspinosa
3eedca9bb4 Add samtools_view 2021-01-29 17:18:45 +01:00
Edmund Miller
d76638d6f8
style(#77): Fix editorconfig errors 2020-12-17 17:50:24 -06:00
drpatelh
200c946693 Add --singularity_pull_docker_container to module yml 2020-12-14 00:34:24 +00:00
drpatelh
047dbde0af Add singularity containers for rnaseq pipeline modules 2020-12-13 23:41:53 +00:00
Edmund Miller
b2cd464ad3
test(samtools): Refactor stats to use pytest-workflow 2020-11-24 21:08:34 -06:00
Edmund Miller
36bbf6baa3
test(samtools): Refactor sort to use pytest-workflow 
Pretty sure this is passing it a sorted bam though?
 2020-11-24 21:08:34 -06:00
Edmund Miller
6448638b55
test(samtools): Refactor index to use pytest-workflow 2020-11-24 21:08:34 -06:00
Edmund Miller
16cb794892
test(samtools): Refactor idxstats to use pytest-workflow 2020-11-24 21:08:34 -06:00
Edmund Miller
34d86427a6
test(samtools): Refactor flagstat to use pytest-workflow 2020-11-24 21:08:33 -06:00
drpatelh
a3f46865ff Remove Singularity image path 2020-11-12 14:55:16 +00:00
drpatelh
29f9b05433 Update docs 2020-10-15 11:13:54 +01:00
drpatelh
530789ba85 Get tests passing 2020-10-15 10:47:15 +01:00
drpatelh
14525ed50d Remove functions file 2020-10-14 18:29:50 +01:00
drpatelh
e438d026bd Unify syntax 2020-09-10 16:45:11 +01:00
drpatelh
473f1b192f Update functions script 2020-09-10 15:59:26 +01:00
Jeremy1805
789dc4f09a Changed options.publish_files definition in functions.nf/initOptions 2020-08-20 11:57:10 +01:00
drpatelh
e648dc335c Add samtools stats commands 2020-08-07 15:23:39 +01:00
drpatelh
d5b16db27d Add samtools sort 2020-08-07 15:21:28 +01:00
drpatelh
0287cad1f8 Add samtools index tests 2020-08-07 15:17:46 +01:00
drpatelh
17b5f5ef3b Get samtools idxstats tests passing 2020-08-07 15:14:45 +01:00
drpatelh
46e4d35ec3 Get samtools flagstat passing 2020-08-07 15:12:03 +01:00
drpatelh
cf5cb8945c Get samtools flagstat passing 2020-08-07 15:11:31 +01:00
drpatelh
f315a7b3c4 Hard copy files 2020-08-05 18:38:27 +01:00
drpatelh
50fce8b3cf Copy across test data and docs for samtools sort 2020-08-05 17:28:09 +01:00
drpatelh
de9d33da12 Copy across test data and docs for samtools index 2020-08-05 17:27:58 +01:00
drpatelh
137db462a7 Add samtools 2020-08-05 17:17:47 +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
d3f3432451 Update test file imports 2020-07-11 14:33:12 +02:00
Phil Ewels
014fef2e92 Rename tools to software 2020-07-11 14:27:21 +02:00