nf-core_modules/tests/software/bedtools/subtract/main.nf
Svyatoslav Sidorov 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

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#!/usr/bin/env nextflow
nextflow.enable.dsl = 2
include { BEDTOOLS_SUBTRACT } from '../../../../software/bedtools/subtract/main.nf' addParams( options: [:] )
workflow test_bedtools_subtract {
input = [ [ id:'test_subtract' ],
file(params.test_data['sarscov2']['genome']['baits_bed'], checkIfExists: true),
file(params.test_data['sarscov2']['genome']['test_bed'], checkIfExists: true)
]
BEDTOOLS_SUBTRACT ( input )
}