Jose Espinosa-Carrasco
95e02f913f
Update comments with new style ( #497 )
...
* Update comment style on functions.nf files
* Update test main.nf comments
* Add meta for ggread
2021-05-12 14:56:46 +01:00
Harshil Patel
d1c6082a66
Update modules required for rnaseq pipeline ( #449 )
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* Update HISAT2 build module
* Bump preseq version
* Fix tests
* Add meta.yml for preseq to fix linting
* Auto-detect --genomeSAindexNbases for smaller genomes
* Add placeholder to use human data for the tests
* Add CSI output option to samtools/index
* Fix samtools/index tests
2021-04-16 08:56:47 +01:00
Harshil Patel
dce27b8102
Update functions.nf to be more flexible for publishing by meta keys ( #423 )
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* Update functions.nf
* Replace saveAs line in module main script
* Add spacing for ECLint
2021-04-09 17:23:56 +01:00
suzannejin
d6850f8312
modified the samtools/fastq module ( #339 )
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* new module: samtools/fastq
* solve conflict: pytest_software.yml
* solve linting conflicts
* solved EditorConfig linting problem
* Module samtools/fastq:
* output compressed fastq.gz file(s)
* add if conditionals for single/paired reads
* samtools/fastq: modified test.yml
* samtools/fastq: modified main.nf to avoid duplicated part of the script section
Co-authored-by: suzannejin <suzanne.jin@crg.eu>
2021-03-23 17:43:52 +00:00
suzannejin
9115c12f88
new module: samtools/fastq ( #316 )
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* new module: samtools/fastq
* solve conflict: pytest_software.yml
* solve linting conflicts
* solved EditorConfig linting problem
2021-03-23 12:13:07 +01:00
Yuk Kei Wan
134c8ef6ce
add samtools merge ( #296 )
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* 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 )
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* 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 )
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* 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
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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
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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
