nf-core_modules/modules/bedtools/subtract/meta.yml

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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 08:44:09 +00:00
name: bedtools_subtract
description: Finds overlaps between two sets of regions (A and B), removes the overlaps from A and reports the remaining portion of A.
keywords:
- bed
- gff
- vcf
- subtract
tools:
- bedtools:
description: |
A set of tools for genomic analysis tasks, specifically enabling genome arithmetic (merge, count, complement) on various file types.
documentation: https://bedtools.readthedocs.io/en/latest/content/tools/subtract.html
licence: ['MIT']
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 08:44:09 +00:00
input:
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
- intervals1:
type: file
description: BED/GFF/VCF
pattern: "*.{bed|gff|vcf}"
- intervals2:
type: file
description: BED/GFF/VCF
pattern: "*.{bed|gff|vcf}"
output:
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
- bed:
type: file
description: File containing the difference between the two sets of features
patters: "*.bed"
- versions:
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 08:44:09 +00:00
type: file
description: File containing software versions
pattern: "versions.yml"
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 08:44:09 +00:00
authors:
- "@sidorov-si"