Harshil Patel
e937c7950a
Rename software/ directory to modules/ to re-organise module structure ( #567 )
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* 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
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
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
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
38964ecfc0
Fix bedtools intersect module
2021-02-07 21:32:01 +00:00
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
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
70de0331a5
Corrected pytest and config
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
Sruthi Suresh
a984c1be7c
Added all modules with basic functionality and updated meta.yml files.
2021-01-29 23:17:44 -06:00
drpatelh
c08e6959a5
Reorganise everything
2020-08-05 16:09:25 +01:00
JoseEspinosa
a09e3a633d
I forgot to uncomment output
2020-07-16 16:38:37 +02:00
JoseEspinosa
d30089f12d
Very preliminary implementation of passing optional params to bedtools/intersect modules
2020-07-16 16:37:33 +02:00
JoseEspinosa
759dd85c92
Removing biocontainer in favor of nf-core container
2020-07-16 10:22:09 +02:00
JoseEspinosa
98c8f44130
Bedtools intersect adapted to the current module standard
2020-07-15 18:15:49 +02:00
JoseEspinosa
b38135ff6b
Moving bedtools/intersectbed to bedtools/intersect
2020-07-14 17:40:17 +02:00
