CI
3f20a97c9c
Build pipeline: viash-hub.biobox.main-tr92f
Source commit: 9f81386259
Source message: Fq subsample (#147)
304 lines
9.4 KiB
YAML
304 lines
9.4 KiB
YAML
name: "salmon_index"
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namespace: "salmon"
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version: "main"
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authors:
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- name: "Sai Nirmayi Yasa"
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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: "nirmayi@data-intuitive.com"
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github: "sainirmayi"
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linkedin: "sai-nirmayi-yasa"
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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: "Junior Bioinformatics Researcher"
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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: "--genome"
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description: "Genome of the organism to prepare the set of decoy sequences. Required\
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\ to build decoy-aware transcriptome.\n"
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info: null
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example:
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- "genome.fasta"
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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: "file"
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name: "--transcripts"
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alternatives:
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- "-t"
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description: "Transcript fasta file.\n"
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info: null
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example:
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- "transcriptome.fasta"
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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: "integer"
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name: "--kmer_len"
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alternatives:
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- "-k"
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description: "The size of k-mers that should be used for the quasi index.\n"
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info: null
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example:
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- 31
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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: "--gencode"
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description: "This flag will expect the input transcript fasta to be in GENCODE\
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\ format, and will split the transcript name at the first '|' character. These\
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\ reduced names will be used in the output and when looking for these transcripts\
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\ in a gene to transcript GTF.\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: "--features"
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description: "This flag will expect the input reference to be in the tsv file\
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\ format, and will split the feature name at the first 'tab' character. These\
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\ reduced names will be used in the output and when looking for the sequence\
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\ of the features.GTF.\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: "--keep_duplicates"
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description: "This flag will disable the default indexing behavior of discarding\
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\ sequence-identical duplicate transcripts. If this flag is passed, then duplicate\
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\ transcripts that appear in the input will be retained and quantified separately.\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: "--keep_fixed_fasta"
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description: "Retain the fixed fasta file (without short transcripts and duplicates,\
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\ clipped, etc.) generated during indexing.\n"
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info: null
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direction: "input"
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- type: "integer"
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name: "--filter_size"
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alternatives:
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- "-f"
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description: "The size of the Bloom filter that will be used by TwoPaCo during\
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\ indexing. The filter will be of size 2^{filter_size}. The default value of\
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\ -1 means that the filter size will be automatically set based on the number\
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\ of distinct k-mers in the input, as estimated by nthll.\n"
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info: null
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example:
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- -1
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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: "--sparse"
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description: "Build the index using a sparse sampling of k-mer positions This\
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\ will require less memory (especially during quantification), but will take\
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\ longer to construct and can slow down mapping / alignment.\n"
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info: null
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direction: "input"
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- type: "file"
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name: "--decoys"
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alternatives:
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- "-d"
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description: "Treat these sequences ids from the reference as the decoys that\
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\ may have sequence homologous to some known transcript. For example in case\
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\ of the genome, provide a list of chromosome names (one per line).\n"
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info: null
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example:
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- "decoys.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: "--no_clip"
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description: "Don't clip poly-A tails from the ends of target sequences.\n"
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info: null
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direction: "input"
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- type: "string"
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name: "--type"
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alternatives:
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- "-n"
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description: "The type of index to build; the only option is \"puff\" in this\
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\ version of salmon.\n"
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info: null
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example:
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- "puff"
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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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- name: "Output"
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arguments:
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- type: "file"
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name: "--index"
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alternatives:
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- "-i"
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description: "Salmon index\n"
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info: null
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example:
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- "Salmon_index"
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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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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: "Salmon is a tool for wicked-fast transcript quantification from RNA-seq\
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\ data. It can either make use of pre-computed alignments (in the form of a SAM/BAM\
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\ file) to the transcripts rather than the raw reads, or can be run in the mapping-based\
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\ mode. This component creates a salmon index for the transcriptome to use Salmon\
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\ in the mapping-based mode. It is generally recommend that you build a decoy-aware\
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\ transcriptome file. This is done using the entire genome of the organism as the\
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\ decoy sequence by concatenating the genome to the end of the transcriptome to\
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\ be indexed and populating the decoys.txt file with the chromosome names.\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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- "Transcriptome"
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- "Index"
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license: "GPL-3.0"
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references:
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doi:
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- "10.1038/nmeth.4197"
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links:
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repository: "https://github.com/COMBINE-lab/salmon"
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homepage: "https://salmon.readthedocs.io/en/latest/salmon.html"
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documentation: "https://salmon.readthedocs.io/en/latest/salmon.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: "quay.io/biocontainers/salmon:1.10.2--hecfa306_0"
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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: "docker"
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run:
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- "salmon index -v 2>&1 | sed 's/salmon \\([0-9.]*\\)/salmon: \\1/' > /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/salmon/salmon_index/config.vsh.yaml"
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runner: "executable"
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engine: "docker|native"
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output: "target/executable/salmon/salmon_index"
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executable: "target/executable/salmon/salmon_index/salmon_index"
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viash_version: "0.9.0-RC7"
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git_commit: "9f813862592fb10f8d15df59697bdaae82c7921a"
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git_remote: "https://github.com/viash-hub/biobox"
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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-RC7"
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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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