Svyatoslav Sidorov
95dfa7bc8d
Enhance bedtools ( #557 )
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* hifiasm copied from fastqc
* hifiasm tests init from fastqc
* meta.yml init; test.yml and main.nf for printing version
* Add hifiasm version printing
* Removed spaced on an empty line
* Reverted hifiasm from main
* hifiasm copied from fastqc
* hifiasm tests init from fastqc
* meta.yml init; test.yml and main.nf for printing version
* Add hifiasm version printing
* Removed spaced on an empty line
* Reverted hifiasm from main
* Generalized intersect and genomecov
* Finished subtract and tests for intersect and genomecov
* Finished up meta YAMLs
* Replaced functions.nf in subtract
* do not add "." in prefix when suffix is set (#550 )
when using the suffix option in the fastqc module it gets added with a "." to the ${meta.id}, this leads to sample name clashing when passing the fastqc output of raw and processed files suffixed with "trim" or "clean" to multiqc.
I suggest to remove the "." this would also be more consistent with the prefix def in most of the other nf-core modules.
##' Ref:
https://nfcore.slack.com/archives/CJRH30T6V/p1625129138043900
* Modules TLC (#551 )
* Modules TLC
* Fix all the tests
* Fix linting failures (#552 )
* Modules TLC
* Fix all the tests
* Fix linting failures
* Soft-link build files to bypass lint error
* Update software/rseqc/junctionannotation/main.nf
* Fix rsem (#555 )
* bump bcftools filter
* fix bcftools
* rsem/preparereference
* added calculateexpression
* meta.yml and pytest_software
* paired end
* add test.yml
* fix rseqc/junctionsaturation (#553 )
* bump bcftools filter
* junctionsaturation meta.yml and test
* pytest config entry
* bump bcftools version down again
* fix test
* fix bcftools
* Adapt linting action (#556 )
* bump bcftools filter
* fix bcftools
* adapt module linting
* Update software/bedtools/genomecov/main.nf
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
* Update software/bedtools/genomecov/main.nf
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
* Update software/bedtools/genomecov/main.nf
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
* Update software/bedtools/genomecov/main.nf
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
* Update software/bedtools/genomecov/meta.yml
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
* Update software/bedtools/genomecov/meta.yml
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
* Update software/bedtools/genomecov/meta.yml
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
* Update software/bedtools/genomecov/meta.yml
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
* Update software/bedtools/genomecov/meta.yml
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
* Update software/bedtools/intersect/main.nf
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
* Update software/bedtools/genomecov/main.nf
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
* Update software/bedtools/genomecov/main.nf
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
* Update software/bedtools/intersect/main.nf
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
* Update software/bedtools/intersect/main.nf
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
* Update software/bedtools/intersect/main.nf
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
* Update software/bedtools/intersect/meta.yml
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
* Update software/bedtools/intersect/meta.yml
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
* Update software/bedtools/intersect/meta.yml
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
* Update software/bedtools/intersect/meta.yml
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
* Update software/bedtools/intersect/meta.yml
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
* Update software/bedtools/subtract/main.nf
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
* Update software/bedtools/subtract/main.nf
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
* Update software/bedtools/subtract/meta.yml
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
* Update software/bedtools/subtract/meta.yml
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
* Update tests/software/bedtools/genomecov/main.nf
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
* Update tests/software/bedtools/genomecov/main.nf
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
* Update tests/software/bedtools/intersect/main.nf
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
* Update tests/software/bedtools/intersect/main.nf
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
* Fixed variable names in intersect and genomecov
Co-authored-by: Sviatoslav Sidorov <sviatoslav.sidorov@crick.ac.uk>
Co-authored-by: riederd <dietmar.rieder@i-med.ac.at>
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
Co-authored-by: Kevin Menden <kevin.menden@t-online.de>
2021-07-07 09:44:09 +01:00
Jose Espinosa-Carrasco
95e02f913f
Update comments with new style ( #497 )
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* 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
466ab67808
Fixes for nanoseq modules ( #479 )
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* Fix minimap2 index module
* Fix minimap2 index tests
* Fix graphmap2 index module
* Fix graphmap2 module
* Fix ECLint
* Fix bedtools bamtobed module
* Fix tests for bedtools bamtobed module
* Add tag for graphmap2 align module
* Fix EClint
* Fix qcat module
* Add md5sum for graphmap2/align module
* Remove non-started test data file
* Remove md5sum for graphmap2 align
2021-04-30 15:57:43 +01:00
Yuk Kei Wan
3f804ee667
add bedtools bamtobed module (from nanoseq modules) ( #466 )
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* add bedtools bamtobed module
* fix erros
* fix linting problem
2021-04-30 13:20:31 +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
Patrick Hüther
8a44258548
remove params section from meta.yml ( #282 )
2021-03-19 13:16:50 +01:00
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
drpatelh
dcc580e4fb
Remove Conda build ids for all modules
2021-02-16 23:58:23 +00:00
drpatelh
0b33b6d081
Add missing build ids
2021-02-09 23:03:13 +00:00
Harshil Patel
3f431014a4
Update software/bedtools/getfasta/main.nf
2021-02-09 21:34:40 +00:00
JoseEspinosa
e118bc049a
Add bedtools getfasta module
2021-02-09 17:56:51 +01:00
Harshil Patel
46e5df2cf7
Merge pull request #151 from drpatelh/bedtools
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Follow up fixes for bedtools modules added in #79
2021-02-09 01:54:31 +00:00
JoseEspinosa
02d10c25a3
Add bedtools maskfasta module
2021-02-08 23:41:10 +01:00
drpatelh
a34d74188d
Really fix Editor Config
2021-02-07 21:49:20 +00:00
drpatelh
ef0a984cc0
Fix Editor config tests
2021-02-07 21:44:45 +00:00
drpatelh
5779b180da
Fix bedtools sort module
2021-02-07 21:32:43 +00:00
drpatelh
f3b5af4ed5
Fix bedtools slip module
2021-02-07 21:32:20 +00:00
drpatelh
38964ecfc0
Fix bedtools intersect module
2021-02-07 21:32:01 +00:00
drpatelh
a37b116186
Fix bedtools merge module
2021-02-07 21:31:39 +00:00
drpatelh
4564ef0e54
Fix bedtools genomecov module
2021-02-07 21:31:21 +00:00
drpatelh
a0c08e0c06
Fix bedtools complement module
2021-02-07 21:31:02 +00:00
drpatelh
a9102c329c
Fix bedtools complement module
2021-02-07 20:55:12 +00:00
sruthipsuresh
e360617ac6
Fixed images, genomecov
2021-01-29 23:17:44 -06:00
sruthipsuresh
e3bbbb48fc
Fixed slop file
2021-01-29 23:17:44 -06:00
sruthipsuresh
957983bd99
Fixed and tested 4 modules, keeping with fastp module syntax
2021-01-29 23:17:44 -06:00
sruthipsuresh
295fff35ec
Corrected containers and tested
2021-01-29 23:17:44 -06:00
sruthipsuresh
19b55fc67c
Fixed intersect, complement indentation issues
2021-01-29 23:17:44 -06:00
sruthipsuresh
3da39dfc88
Fixed bedtools complement module
2021-01-29 23:17:44 -06:00
sruthipsuresh
8496427c56
Update software/bedtools/complement/main.nf
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Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-01-29 23:17:44 -06:00
sruthipsuresh
fc8cdde2b4
Apply suggestions from code review
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Add all initial suggestions from review (syntax issues)
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-01-29 23:17:44 -06:00
sruthipsuresh
e5c21d15a3
Update software/bedtools/complement/main.nf
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Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-01-29 23:17:44 -06:00
sruthipsuresh
bf2703f396
Update software/bedtools/complement/main.nf
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Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-01-29 23:17:44 -06:00
sruthipsuresh
93f640154a
Update software/bedtools/complement/main.nf
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Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-01-29 23:17:44 -06:00
sruthipsuresh
ced2458d78
Update software/bedtools/complement/main.nf
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Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-01-29 23:17:44 -06:00
sruthipsuresh
29639c522f
Corrected sort
2021-01-29 23:17:44 -06:00
sruthipsuresh
70de0331a5
Corrected pytest and config
2021-01-29 23:17:44 -06:00
sruthipsuresh
2f19b4279c
All modules corrected, TODO config
2021-01-29 23:17:44 -06:00
sruthipsuresh
6e7feb9e57
Update main.nf
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Fixed prefix
2021-01-29 23:17:44 -06:00
sruthipsuresh
672f94f2af
rebased and updated all bedtools testing and modules
2021-01-29 23:17:44 -06:00
sruthipsuresh
78473edb72
Removed large testing files, will convert to updated testing
2021-01-29 23:17:44 -06:00
Sruthi Suresh
4fca435120
Fixed naming issues and links in meta.yml
2021-01-29 23:17:44 -06:00
Edmund Miller
178becdd69
style: Run yaml-lint against files
2021-01-29 23:17:44 -06:00
Edmund Miller
b16226c09c
fix(bedtools): Add header param
2021-01-29 23:17:44 -06:00
Sruthi Suresh
a984c1be7c
Added all modules with basic functionality and updated meta.yml files.
2021-01-29 23:17:44 -06:00
Sruthi Suresh
89e5473b44
Updated modules with the changed container format
2021-01-29 23:17:44 -06:00
Sruthi Suresh
6677c98b11
Updated complement and completed slop module with all parameters available.
2021-01-29 23:17:44 -06:00
Sruthi Suresh
199dfc5ea3
Added complement module with necessary test dir/parameters
2021-01-29 23:17:44 -06:00
Sruthi Suresh
709970e9af
Completed slop module for modules with test directory and updated meta.yml file
2021-01-29 23:17:44 -06:00
Sruthi Suresh
5205ce286a
Added all modules using bedtools in the enhancer transcript identification section
2021-01-29 23:17:44 -06:00
Sruthi Suresh
637b545168
Removed extraneous modules and updated removegenes module
2021-01-29 23:17:44 -06:00
