class FCSIssue
- FCSIssue
- GritJiraIssue
- Reference
- Object
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.crInstance Method Summary
-
#submit_to_lsf : Nil
Submits the FCS-GX contamination screening pipeline to LSF.
Instance methods inherited from class GritJiraIssue
assembly_files(keys : Array(String)) : Array(String)
assembly_files,
curated_dir : String
curated_dir,
curation_pretext(fasta, output, no_email = false) : String
curation_pretext,
decon_dir : String
decon_dir,
decon_file : String
decon_file,
files : Array(String)
files,
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,
user : String
user,
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 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.