CI
6f2f840fd9
Build pipeline: viash-hub.biobox.main-zp6tq
Source commit: 7f8bcc2b3e
Source message: BD rhapsody sequence analysis (#96)
* wip
* fix test
* add help
* update 2.2 args
* fix bug
* extend test data
* output separate files
* analyse missing args
* tweaks to test
* fix script
* fix test
* fix test
* move small reference
* wip generate wta test data
* don't forget about umi in r1
* remove unneeded pkg
* load reference in memory just once
* fix random choices
* extend test
* add abc immunediscoverypanel
* wip abc testing code
* fix abc test; need unique instrument, run and flowcell ids for each sample
* add smk data
* add entry to changelog
* remove old test file
* adapt test for missing read
* update description
* add comment
* ensure cwl files are absolute
* Apply suggestions from code review
Co-authored-by: Dries Schaumont <5946712+DriesSchaumont@users.noreply.github.com>
* fix suggestion
* newer pipelines have docker requirements as a hint instead of a strict requirement
* rename str to content
* remove deleted resources
* fix containers
* fix script
* fix suggestion
* fix suggestion...
* fix test
* fix component name
* fix test
* apply suggestions
* fix test
* added note
* fix changelog
* fix changelog again
* splitting hairs here
---------
Co-authored-by: Dries Schaumont <5946712+DriesSchaumont@users.noreply.github.com>
438 lines
13 KiB
YAML
438 lines
13 KiB
YAML
name: "bedtools_intersect"
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namespace: "bedtools"
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version: "main"
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authors:
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- name: "Theodoro Gasperin Terra Camargo"
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roles:
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- "author"
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- "maintainer"
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info:
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links:
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email: "theodorogtc@gmail.com"
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github: "tgaspe"
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linkedin: "theodoro-gasperin-terra-camargo"
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organizations:
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- name: "Data Intuitive"
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href: "https://www.data-intuitive.com"
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role: "Bioinformatician"
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argument_groups:
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- name: "Inputs"
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arguments:
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- type: "file"
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name: "--input_a"
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alternatives:
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- "-a"
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description: "The input file (BED/GFF/VCF/BAM) to be used as the -a file.\n"
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info: null
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example:
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- "input_a.bed"
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must_exist: true
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create_parent: true
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required: true
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direction: "input"
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multiple: false
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multiple_sep: ";"
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- type: "file"
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name: "--input_b"
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alternatives:
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- "-b"
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description: "The input file(s) (BED/GFF/VCF/BAM) to be used as the -b file(s).\n"
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info: null
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example:
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- "input_b.bed"
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must_exist: true
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create_parent: true
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required: true
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direction: "input"
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multiple: true
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multiple_sep: ";"
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- name: "Outputs"
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arguments:
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- type: "file"
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name: "--output"
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description: "The output BED file. \n"
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info: null
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example:
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- "output.bed"
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must_exist: true
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create_parent: true
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required: true
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direction: "output"
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multiple: false
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multiple_sep: ";"
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- name: "Options"
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arguments:
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- type: "boolean_true"
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name: "--write_a"
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alternatives:
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- "-wa"
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description: "Write the original A entry for each overlap."
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info: null
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direction: "input"
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- type: "boolean_true"
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name: "--write_b"
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alternatives:
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- "-wb"
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description: "Write the original B entry for each overlap. \nUseful for knowing\
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\ _what_ A overlaps. Restricted by -f and -r.\n"
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info: null
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direction: "input"
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- type: "boolean_true"
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name: "--left_outer_join"
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alternatives:
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- "-loj"
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description: "Perform a \"left outer join\". That is, for each feature in A report\
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\ each overlap with B. \nIf no overlaps are found, report a NULL feature for\
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\ B.\n"
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info: null
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direction: "input"
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- type: "boolean_true"
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name: "--write_overlap"
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alternatives:
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- "-wo"
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description: "Write the original A and B entries plus the number of base pairs\
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\ of overlap between the two features.\n- Overlaps restricted by -f and -r.\
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\ \n Only A features with overlap are reported.\n"
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info: null
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direction: "input"
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- type: "boolean_true"
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name: "--write_overlap_plus"
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alternatives:
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- "-wao"
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description: "Write the original A and B entries plus the number of base pairs\
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\ of overlap between the two features.\n- Overlaps restricted by -f and -r.\
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\ \n However, A features w/o overlap are also reported with a NULL B feature\
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\ and overlap = 0.\n"
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info: null
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direction: "input"
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- type: "boolean_true"
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name: "--report_A_if_no_overlap"
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alternatives:
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- "-u"
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description: "Write the original A entry _if_ no overlap is found. \n- In other\
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\ words, just report the fact >=1 hit was found.\n- Overlaps restricted by -f\
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\ and -r. \n"
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info: null
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direction: "input"
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- type: "boolean_true"
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name: "--number_of_overlaps_A"
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alternatives:
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- "-c"
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description: "For each entry in A, report the number of overlaps with B.\n- Reports\
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\ 0 for A entries that have no overlap with B.\n- Overlaps restricted by -f\
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\ and -r.\n"
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info: null
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direction: "input"
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- type: "boolean_true"
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name: "--report_no_overlaps_A"
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alternatives:
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- "-v"
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description: "Only report those entries in A that have _no overlaps_ with B.\n\
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- Similar to \"grep -v\" (an homage).\n"
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info: null
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direction: "input"
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- type: "boolean_true"
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name: "--uncompressed_bam"
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alternatives:
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- "-ubam"
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description: "Write uncompressed BAM output. Default writes compressed BAM."
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info: null
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direction: "input"
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- type: "boolean_true"
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name: "--same_strand"
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alternatives:
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- "-s"
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description: "Require same strandedness. That is, only report hits in B.\nthat\
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\ overlap A on the _same_ strand.\n- By default, overlaps are reported without\
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\ respect to strand.\n"
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info: null
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direction: "input"
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- type: "boolean_true"
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name: "--opposite_strand"
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alternatives:
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- "-S"
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description: "Require different strandedness. That is, only report hits in B\n\
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that overlap A on the _opposite_ strand.\n- By default, overlaps are reported\
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\ without respect to strand.\n"
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info: null
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direction: "input"
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- type: "double"
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name: "--min_overlap_A"
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alternatives:
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- "-f"
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description: "Minimum overlap required as a fraction of A.\n- Default is 1E-9\
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\ (i.e., 1bp).\n- FLOAT (e.g. 0.50)\n"
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info: null
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example:
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- 0.5
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required: false
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direction: "input"
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multiple: false
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multiple_sep: ";"
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- type: "double"
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name: "--min_overlap_B"
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alternatives:
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- "-F"
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description: "Minimum overlap required as a fraction of B.\n- Default is 1E-9\
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\ (i.e., 1bp).\n- FLOAT (e.g. 0.50)\n"
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info: null
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example:
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- 0.5
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required: false
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direction: "input"
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multiple: false
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multiple_sep: ";"
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- type: "boolean_true"
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name: "--reciprocal_overlap"
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alternatives:
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- "-r"
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description: "Require that the fraction overlap be reciprocal for A AND B.\n-\
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\ In other words, if -f is 0.90 and -r is used, this requires\nthat B overlap\
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\ 90% of A and A _also_ overlaps 90% of B.\n"
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info: null
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direction: "input"
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- type: "boolean_true"
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name: "--either_overlap"
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alternatives:
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- "-e"
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description: "Require that the minimum fraction be satisfied for A OR B.\n- In\
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\ other words, if -e is used with -f 0.90 and -F 0.10 this requires\nthat either\
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\ 90% of A is covered OR 10% of B is covered.\nWithout -e, both fractions would\
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\ have to be satisfied.\n"
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info: null
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direction: "input"
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- type: "boolean_true"
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name: "--split"
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description: "Treat \"split\" BAM or BED12 entries as distinct BED intervals."
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info: null
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direction: "input"
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- type: "file"
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name: "--genome"
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alternatives:
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- "-g"
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description: "Provide a genome file to enforce consistent chromosome \nsort order\
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\ across input files. Only applies when used \nwith -sorted option.\n"
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info: null
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example:
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- "genome.txt"
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must_exist: true
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create_parent: true
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required: false
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direction: "input"
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multiple: false
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multiple_sep: ";"
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- type: "boolean_true"
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name: "--nonamecheck"
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description: "For sorted data, don't throw an error if the file \nhas different\
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\ naming conventions for the same chromosome \n(e.g., \"chr1\" vs \"chr01\"\
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).\n"
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info: null
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direction: "input"
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- type: "boolean_true"
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name: "--sorted"
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description: "Use the \"chromsweep\" algorithm for sorted (-k1,1 -k2,2n) input.\n"
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info: null
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direction: "input"
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- type: "string"
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name: "--names"
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description: "When using multiple databases, provide an alias \nfor each that\
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\ will appear instead of a fileId when \nalso printing the DB record.\n"
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info: null
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required: false
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direction: "input"
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multiple: false
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multiple_sep: ";"
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- type: "boolean_true"
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name: "--filenames"
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description: "When using multiple databases, show each complete filename instead\
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\ of a fileId when also printing the DB record."
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info: null
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direction: "input"
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- type: "boolean_true"
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name: "--sortout"
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description: "When using multiple databases, sort the output DB hits for each\
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\ record."
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info: null
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direction: "input"
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- type: "boolean_true"
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name: "--bed"
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description: "If using BAM input, write output as BED."
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info: null
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direction: "input"
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- type: "boolean_true"
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name: "--header"
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description: "Print the header from the A file prior to results."
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info: null
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direction: "input"
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- type: "boolean_true"
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name: "--no_buffer_output"
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alternatives:
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- "--nobuf"
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description: "Disable buffered output. Using this option will cause each line\n\
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of output to be printed as it is generated, rather than saved\nin a buffer.\
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\ This will make printing large output files \nnoticeably slower, but can be\
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\ useful in conjunction with\nother software tools and scripts that need to\
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\ process one\nline of bedtools output at a time.\n"
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info: null
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direction: "input"
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- type: "integer"
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name: "--io_buffer_size"
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alternatives:
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- "--iobuf"
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description: "Specify amount of memory to use for input buffer.\nTakes an integer\
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\ argument. Optional suffixes K/M/G supported.\nNote: currently has no effect\
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\ with compressed files. \n"
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info: null
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required: false
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direction: "input"
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multiple: false
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multiple_sep: ";"
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resources:
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- type: "bash_script"
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path: "script.sh"
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is_executable: true
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description: "bedtools intersect allows one to screen for overlaps between two sets\
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\ of genomic features. \nMoreover, it allows one to have fine control as to how\
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\ the intersections are reported. \nbedtools intersect works with both BED/GFF/VCF\
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\ and BAM files as input.\n"
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test_resources:
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- type: "bash_script"
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path: "test.sh"
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is_executable: true
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info: null
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status: "enabled"
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requirements:
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commands:
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- "ps"
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keywords:
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- "feature intersection"
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- "BAM"
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- "BED"
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- "GFF"
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- "VCF"
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license: "GPL-2.0, MIT"
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references:
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doi:
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- "10.1093/bioinformatics/btq033"
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links:
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repository: "https://github.com/arq5x/bedtools2"
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documentation: "https://bedtools.readthedocs.io/en/latest/content/tools/intersect.html"
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runners:
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- type: "executable"
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id: "executable"
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docker_setup_strategy: "ifneedbepullelsecachedbuild"
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- type: "nextflow"
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id: "nextflow"
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directives:
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tag: "$id"
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auto:
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simplifyInput: true
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simplifyOutput: false
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transcript: false
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publish: false
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config:
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labels:
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mem1gb: "memory = 1000000000.B"
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mem2gb: "memory = 2000000000.B"
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mem5gb: "memory = 5000000000.B"
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mem10gb: "memory = 10000000000.B"
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mem20gb: "memory = 20000000000.B"
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mem50gb: "memory = 50000000000.B"
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mem100gb: "memory = 100000000000.B"
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mem200gb: "memory = 200000000000.B"
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mem500gb: "memory = 500000000000.B"
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mem1tb: "memory = 1000000000000.B"
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mem2tb: "memory = 2000000000000.B"
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mem5tb: "memory = 5000000000000.B"
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mem10tb: "memory = 10000000000000.B"
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mem20tb: "memory = 20000000000000.B"
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mem50tb: "memory = 50000000000000.B"
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mem100tb: "memory = 100000000000000.B"
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mem200tb: "memory = 200000000000000.B"
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mem500tb: "memory = 500000000000000.B"
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mem1gib: "memory = 1073741824.B"
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mem2gib: "memory = 2147483648.B"
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mem4gib: "memory = 4294967296.B"
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mem8gib: "memory = 8589934592.B"
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mem16gib: "memory = 17179869184.B"
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mem32gib: "memory = 34359738368.B"
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mem64gib: "memory = 68719476736.B"
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mem128gib: "memory = 137438953472.B"
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mem256gib: "memory = 274877906944.B"
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mem512gib: "memory = 549755813888.B"
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mem1tib: "memory = 1099511627776.B"
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mem2tib: "memory = 2199023255552.B"
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mem4tib: "memory = 4398046511104.B"
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mem8tib: "memory = 8796093022208.B"
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mem16tib: "memory = 17592186044416.B"
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mem32tib: "memory = 35184372088832.B"
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mem64tib: "memory = 70368744177664.B"
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mem128tib: "memory = 140737488355328.B"
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mem256tib: "memory = 281474976710656.B"
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mem512tib: "memory = 562949953421312.B"
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cpu1: "cpus = 1"
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cpu2: "cpus = 2"
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cpu5: "cpus = 5"
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cpu10: "cpus = 10"
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cpu20: "cpus = 20"
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cpu50: "cpus = 50"
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cpu100: "cpus = 100"
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cpu200: "cpus = 200"
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cpu500: "cpus = 500"
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cpu1000: "cpus = 1000"
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debug: false
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container: "docker"
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engines:
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- type: "docker"
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id: "docker"
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image: "debian:stable-slim"
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target_registry: "images.viash-hub.com"
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target_tag: "main"
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namespace_separator: "/"
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setup:
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- type: "apt"
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packages:
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- "bedtools"
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- "procps"
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interactive: false
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- type: "docker"
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run:
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- "echo \"bedtools: \\\"$(bedtools --version | sed -n 's/^bedtools //p')\\\"\"\
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\ > /var/software_versions.txt\n"
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entrypoint: []
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cmd: null
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- type: "native"
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id: "native"
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build_info:
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config: "src/bedtools/bedtools_intersect/config.vsh.yaml"
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runner: "executable"
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engine: "docker|native"
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output: "target/executable/bedtools/bedtools_intersect"
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executable: "target/executable/bedtools/bedtools_intersect/bedtools_intersect"
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viash_version: "0.9.0"
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git_commit: "7f8bcc2b3e1ffaac9778b6acb42420b19660d1a1"
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git_remote: "https://x-access-token:ghs_aSDBedV4vU66pddFDN6d8UEy0ZQApn08RAsh@github.com/viash-hub/biobox"
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git_tag: "v0.2.0-3-g7f8bcc2"
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package_config:
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name: "biobox"
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version: "main"
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description: "A collection of bioinformatics tools for working with sequence data.\n"
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info: null
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viash_version: "0.9.0"
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source: "src"
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target: "target"
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config_mods:
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- ".requirements.commands := ['ps']\n"
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- ".engines += { type: \"native\" }"
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- ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
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- ".engines[.type == 'docker'].target_tag := 'main'"
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keywords:
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- "bioinformatics"
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- "modules"
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- "sequencing"
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license: "MIT"
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organization: "vsh"
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links:
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repository: "https://github.com/viash-hub/biobox"
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issue_tracker: "https://github.com/viash-hub/biobox/issues"
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