mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-12-22 11:08:17 +00:00
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>
This commit is contained in:
Svyatoslav Sidorov
GitHub
parent
e0d820f9f4
commit
95dfa7bc8d
14 changed files with 294 additions and 42 deletions
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@ -19,22 +19,37 @@ process BEDTOOLS_GENOMECOV {
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}
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input:
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tuple val(meta), path(bam)
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tuple val(meta), path(intervals)
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path sizes
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val extension
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output:
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tuple val(meta), path("*.bed"), emit: bed
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tuple val(meta), path("*.${extension}"), emit: genomecov
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path "*.version.txt" , emit: version
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script:
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def software = getSoftwareName(task.process)
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def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
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if (intervals.name =~ /\.bam/) {
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"""
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bedtools \\
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genomecov \\
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-ibam $bam \\
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-ibam $intervals \\
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$options.args \\
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> ${prefix}.bed
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> ${prefix}.${extension}
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bedtools --version | sed -e "s/bedtools v//g" > ${software}.version.txt
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"""
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} else {
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"""
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bedtools \\
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genomecov \\
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-i $intervals \\
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-g $sizes \\
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$options.args \\
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> ${prefix}.${extension}
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bedtools --version | sed -e "s/bedtools v//g" > ${software}.version.txt
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"""
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}
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}
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@ -15,20 +15,26 @@ input:
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description: |
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Groovy Map containing sample information
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e.g. [ id:'test', single_end:false ]
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- bam:
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- intervals:
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type: file
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description: Input BAM file
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pattern: "*.{bam}"
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description: BAM/BED/GFF/VCF
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pattern: "*.{bam|bed|gff|vcf}"
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- sizes:
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type: file
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description: Tab-delimited table of chromosome names in the first column and chromosome sizes in the second column
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- extension:
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type: string
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description: Extension of the output file (e. g., ".bg", ".bedgraph", ".txt", ".tab", etc.) It is set arbitrarily by the user and corresponds to the file format which depends on arguments.
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output:
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- meta:
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type: map
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description: |
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Groovy Map containing sample information
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e.g. [ id:'test', single_end:false ]
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- bed:
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- genomecov:
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type: file
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description: Computed genomecov bed file
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pattern: "*.{bed}"
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description: Computed genome coverage file
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pattern: "*.${extension}"
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- version:
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type: file
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description: File containing software version
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@ -37,3 +43,4 @@ authors:
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- "@Emiller88"
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- "@sruthipsuresh"
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- "@drpatelh"
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- "@sidorov-si"
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@ -19,10 +19,11 @@ process BEDTOOLS_INTERSECT {
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}
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input:
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tuple val(meta), path(bed1), path(bed2)
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tuple val(meta), path(intervals1), path(intervals2)
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val extension
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output:
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tuple val(meta), path('*.bed'), emit: bed
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tuple val(meta), path("*.${extension}"), emit: intersect
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path '*.version.txt' , emit: version
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script:
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@ -31,10 +32,10 @@ process BEDTOOLS_INTERSECT {
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"""
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bedtools \\
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intersect \\
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-a $bed1 \\
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-b $bed2 \\
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-a $intervals1 \\
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-b $intervals2 \\
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$options.args \\
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> ${prefix}.bed
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> ${prefix}.${extension}
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bedtools --version | sed -e "s/bedtools v//g" > ${software}.version.txt
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"""
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@ -1,5 +1,5 @@
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name: bedtools_intersect
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description: allows one to screen for overlaps between two sets of genomic features.
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description: Allows one to screen for overlaps between two sets of genomic features.
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keywords:
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- bed
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- intersect
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@ -14,24 +14,27 @@ input:
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description: |
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Groovy Map containing sample information
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e.g. [ id:'test', single_end:false ]
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- bed1:
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- intervals1:
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type: file
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description: BED file, each feature in 1 is compared to 2 in search of overlaps
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pattern: "*.{bed}"
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- bed2:
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description: BAM/BED/GFF/VCF
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pattern: "*.{bam|bed|gff|vcf}"
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- intervals2:
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type: file
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description: Second bed file, used to compare to first BED file
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pattern: "*.{bed}"
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description: BAM/BED/GFF/VCF
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pattern: "*.{bam|bed|gff|vcf}"
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- extension:
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type: value
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description: Extension of the output file. It is set by the user and corresponds to the file format which depends on arguments (e. g., ".bed", ".bam", ".txt", etc.).
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output:
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- meta:
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type: map
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description: |
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Groovy Map containing sample information
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e.g. [ id:'test', single_end:false ]
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- bed:
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- intersect:
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type: file
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description: BED file with intersected intervals
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pattern: "*.{bed}"
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description: File containing the description of overlaps found between the two features
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pattern: "*.${extension}"
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- version:
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type: file
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description: File containing software version
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@ -40,3 +43,4 @@ authors:
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- "@Emiller88"
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- "@sruthipsuresh"
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- "@drpatelh"
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- "@sidorov-si"
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68
software/bedtools/subtract/functions.nf
Normal file
68
software/bedtools/subtract/functions.nf
Normal file
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@ -0,0 +1,68 @@
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//
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// Utility functions used in nf-core DSL2 module files
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//
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//
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// Extract name of software tool from process name using $task.process
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//
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def getSoftwareName(task_process) {
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return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
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}
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//
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// Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
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//
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def initOptions(Map args) {
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def Map options = [:]
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options.args = args.args ?: ''
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options.args2 = args.args2 ?: ''
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options.args3 = args.args3 ?: ''
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options.publish_by_meta = args.publish_by_meta ?: []
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options.publish_dir = args.publish_dir ?: ''
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options.publish_files = args.publish_files
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options.suffix = args.suffix ?: ''
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return options
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}
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//
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// Tidy up and join elements of a list to return a path string
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//
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def getPathFromList(path_list) {
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def paths = path_list.findAll { item -> !item?.trim().isEmpty() } // Remove empty entries
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paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
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return paths.join('/')
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}
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//
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// Function to save/publish module results
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//
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def saveFiles(Map args) {
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if (!args.filename.endsWith('.version.txt')) {
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def ioptions = initOptions(args.options)
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def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
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if (ioptions.publish_by_meta) {
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def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
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for (key in key_list) {
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if (args.meta && key instanceof String) {
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def path = key
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if (args.meta.containsKey(key)) {
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path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
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}
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path = path instanceof String ? path : ''
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path_list.add(path)
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}
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}
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}
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if (ioptions.publish_files instanceof Map) {
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for (ext in ioptions.publish_files) {
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if (args.filename.endsWith(ext.key)) {
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def ext_list = path_list.collect()
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ext_list.add(ext.value)
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return "${getPathFromList(ext_list)}/$args.filename"
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}
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}
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} else if (ioptions.publish_files == null) {
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return "${getPathFromList(path_list)}/$args.filename"
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}
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}
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}
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41
software/bedtools/subtract/main.nf
Normal file
41
software/bedtools/subtract/main.nf
Normal file
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@ -0,0 +1,41 @@
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// Import generic module functions
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include { initOptions; saveFiles; getSoftwareName } from './functions'
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params.options = [:]
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options = initOptions(params.options)
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process BEDTOOLS_SUBTRACT {
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tag "$meta.id"
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label 'process_medium'
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publishDir "${params.outdir}",
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mode: params.publish_dir_mode,
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saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
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conda (params.enable_conda ? "bioconda::bedtools=2.30.0" : null)
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if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
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container "https://depot.galaxyproject.org/singularity/bedtools:2.30.0--hc088bd4_0"
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} else {
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container "quay.io/biocontainers/bedtools:2.30.0--hc088bd4_0"
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}
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input:
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tuple val(meta), path(intervals1), path(intervals2)
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output:
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tuple val(meta), path("*.bed"), emit: bed
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path "*.version.txt" , emit: version
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script:
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def software = getSoftwareName(task.process)
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def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
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"""
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bedtools \\
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subtract \\
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-a $intervals1 \\
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-b $intervals2 \\
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$options.args \\
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> ${prefix}.bed
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bedtools --version | sed -e "s/bedtools v//g" > ${software}.version.txt
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"""
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}
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45
software/bedtools/subtract/meta.yml
Normal file
45
software/bedtools/subtract/meta.yml
Normal file
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name: bedtools_subtract
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description: Finds overlaps between two sets of regions (A and B), removes the overlaps from A and reports the remaining portion of A.
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keywords:
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- bed
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- gff
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- vcf
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- subtract
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tools:
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- bedtools:
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description: |
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A set of tools for genomic analysis tasks, specifically enabling genome arithmetic (merge, count, complement) on various file types.
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documentation: https://bedtools.readthedocs.io/en/latest/content/tools/subtract.html
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input:
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- meta:
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type: map
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description: |
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Groovy Map containing sample information
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e.g. [ id:'test', single_end:false ]
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- intervals1:
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type: file
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description: BED/GFF/VCF
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pattern: "*.{bed|gff|vcf}"
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- intervals2:
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type: file
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description: BED/GFF/VCF
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pattern: "*.{bed|gff|vcf}"
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output:
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- meta:
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type: map
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description: |
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Groovy Map containing sample information
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e.g. [ id:'test', single_end:false ]
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- bed:
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type: file
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description: File containing the difference between the two sets of features
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patters: "*.bed"
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- version:
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type: file
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description: File containing software version
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pattern: "*.{version.txt}"
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authors:
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- "@sidorov-si"
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@ -86,6 +86,10 @@ bedtools/sort:
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- software/bedtools/sort/**
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- tests/software/bedtools/sort/**
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bedtools/subtract:
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- software/bedtools/subtract/**
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- tests/software/bedtools/subtract/**
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bismark/align:
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- software/bismark/align/**
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- software/bismark/genomepreparation/**
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@ -9,6 +9,19 @@ workflow test_bedtools_genomecov {
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file(params.test_data['sarscov2']['illumina']['test_paired_end_bam'], checkIfExists: true)
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]
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BEDTOOLS_GENOMECOV ( input )
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sizes = file('dummy_chromosome_sizes')
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extension = 'txt'
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BEDTOOLS_GENOMECOV ( input, sizes, extension )
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}
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workflow test_bedtools_genomecov_nonbam {
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input = [ [ id:'test'],
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file(params.test_data['sarscov2']['genome']['baits_bed'], checkIfExists: true)
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]
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sizes = file(params.test_data['sarscov2']['genome']['genome_sizes'], checkIfExists: true)
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extension = 'txt'
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BEDTOOLS_GENOMECOV ( input, sizes, extension )
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}
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@ -1,8 +1,17 @@
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- name: bedtools genomecov
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command: nextflow run ./tests/software/bedtools/genomecov -entry test_bedtools_genomecov -c tests/config/nextflow.config
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- name: bedtools genomecov test_bedtools_genomecov
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command: nextflow run tests/software/bedtools/genomecov -entry test_bedtools_genomecov -c tests/config/nextflow.config
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tags:
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- bedtools
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- bedtools/genomecov
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files:
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- path: ./output/bedtools/test_out.bed
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- path: output/bedtools/test_out.txt
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md5sum: 66083198daca6c001d328ba9616e9b53
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- name: bedtools genomecov test_bedtools_genomecov_nonbam
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command: nextflow run tests/software/bedtools/genomecov -entry test_bedtools_genomecov_nonbam -c tests/config/nextflow.config
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tags:
|
||||
- bedtools
|
||||
- bedtools/genomecov
|
||||
files:
|
||||
- path: output/bedtools/test_out.txt
|
||||
md5sum: f47b58840087426e5b643d8dfd155c1f
|
||||
|
|
|
|||
|
|
@ -10,5 +10,18 @@ workflow test_bedtools_intersect {
|
|||
file(params.test_data['sarscov2']['genome']['test2_bed'], checkIfExists: true)
|
||||
]
|
||||
|
||||
BEDTOOLS_INTERSECT ( input )
|
||||
extension = 'bed'
|
||||
|
||||
BEDTOOLS_INTERSECT ( input, extension )
|
||||
}
|
||||
|
||||
workflow test_bedtools_intersect_bam {
|
||||
input = [ [ id:'test' ],
|
||||
file(params.test_data['sarscov2']['illumina']['test_paired_end_bam'], checkIfExists: true),
|
||||
file(params.test_data['sarscov2']['genome']['baits_bed'], checkIfExists: true)
|
||||
]
|
||||
|
||||
extension = 'bam'
|
||||
|
||||
BEDTOOLS_INTERSECT ( input, extension )
|
||||
}
|
||||
|
|
|
|||
|
|
@ -1,8 +1,17 @@
|
|||
- name: bedtools intersect
|
||||
command: nextflow run ./tests/software/bedtools/intersect -entry test_bedtools_intersect -c tests/config/nextflow.config
|
||||
- name: bedtools intersect test_bedtools_intersect
|
||||
command: nextflow run tests/software/bedtools/intersect -entry test_bedtools_intersect -c tests/config/nextflow.config
|
||||
tags:
|
||||
- bedtools
|
||||
- bedtools/intersect
|
||||
files:
|
||||
- path: ./output/bedtools/test_out.bed
|
||||
md5sum: d41d8cd98f00b204e9800998ecf8427e
|
||||
- path: output/bedtools/test_out.bed
|
||||
md5sum: afcbf01c2f2013aad71dbe8e34f2c15c
|
||||
|
||||
- name: bedtools intersect test_bedtools_intersect_bam
|
||||
command: nextflow run tests/software/bedtools/intersect -entry test_bedtools_intersect_bam -c tests/config/nextflow.config
|
||||
tags:
|
||||
- bedtools
|
||||
- bedtools/intersect
|
||||
files:
|
||||
- path: output/bedtools/test_out.bam
|
||||
md5sum: 738324efe2b1e442ceb6539a630c3fe6
|
||||
|
|
|
|||
15
tests/software/bedtools/subtract/main.nf
Normal file
15
tests/software/bedtools/subtract/main.nf
Normal file
|
|
@ -0,0 +1,15 @@
|
|||
#!/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 )
|
||||
}
|
||||
8
tests/software/bedtools/subtract/test.yml
Normal file
8
tests/software/bedtools/subtract/test.yml
Normal file
|
|
@ -0,0 +1,8 @@
|
|||
- name: bedtools subtract test_bedtools_subtract
|
||||
command: nextflow run tests/software/bedtools/subtract -entry test_bedtools_subtract -c tests/config/nextflow.config
|
||||
tags:
|
||||
- bedtools
|
||||
- bedtools/subtract
|
||||
files:
|
||||
- path: output/bedtools/test_subtract.bed
|
||||
md5sum: 63513c4dc69e8b481ce3b4b2a9f24259
|
||||
Loading…
Reference in a new issue