Svyatoslav Sidorov
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95dfa7bc8d
|
Enhance bedtools (#557)
* 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 |
|
Patrick Hüther
|
8a44258548
|
remove params section from meta.yml (#282)
|
2021-03-19 13:16:50 +01:00 |
|
drpatelh
|
4564ef0e54
|
Fix bedtools genomecov module
|
2021-02-07 21:31:21 +00:00 |
|
sruthipsuresh
|
e360617ac6
|
Fixed images, genomecov
|
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 |
|
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
|
c485d56972
|
Indentation error in yml
|
2020-07-14 18:00:23 +02:00 |
|
JoseEspinosa
|
c059a485b9
|
Using bedtools{_,-}genomecov instead of genomecov alone
|
2020-07-14 17:31:40 +02:00 |
|
JoseEspinosa
|
5f80a900e9
|
Changing fasta_sizes by chrom_sizes input path for genomecov
|
2020-07-14 16:47:27 +02:00 |
|
JoseEspinosa
|
f2eb3f68c0
|
Module bedtools-genomecov added
|
2020-07-14 16:47:26 +02:00 |
|