class FCSIssue

Overview

Extends GritJiraIssue with FCS-GX contamination screening submission.

Collects the assembly FASTA paths (primary, haplotigs, hap1, hap2) from the specimen YAML and submits the gx_map_wrapper.bash pipeline to LSF.

Defined in:

submit_fcs.cr

Instance Method Summary

Instance methods inherited from class GritJiraIssue

curated_dir : String curated_dir, curation_pretext(fasta, output, no_email = false) : String curation_pretext, decon_file : String decon_file, get_json : JSON::Any get_json, get_token : String get_token, get_yaml : YAML::Any get_yaml, geval_db : String geval_db, hic_read_dir : Array(YAML::Any) | Array(String) hic_read_dir, json : JSON::Any json, merged : Bool merged, ont_read_dir : String | Nil ont_read_dir, pacbio_read_dir : String | Nil pacbio_read_dir, pretext_dir : String pretext_dir, projects : Array(YAML::Any) projects, release_version : Int32 release_version, sample_dot_version : String sample_dot_version, sample_version : String sample_version, scientific_name : String scientific_name, taxonomy : String taxonomy, telomer : String telomer, tol_id : String tol_id, working_dir : String working_dir, yaml : YAML::Any yaml

Constructor methods inherited from class GritJiraIssue

new(name : String, merged : Bool = false) new

Instance Method Detail

def decon_dir : String #

Returns the parent directory of the first assembly file, used as the output directory for contamination screening results.


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def files : Array(String) #

Returns the list of assembly FASTA paths present in the specimen YAML. Checks for primary, haplotigs, hap1, and hap2 keys.


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def submit_to_lsf : Nil #

Submits the FCS-GX contamination screening pipeline to LSF. Builds a bsub command with the decon directory, taxonomy ID, and all existing assembly FASTA files as inputs.


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