rename_submitted: Renames submitted contig files to NML LabWare numbers...
In phac-nml/wade: Executes molecular typing on contig assemblies
View source: R/Rename_Submitted.R
rename_submitted R Documentation
Renames submitted contig files to NML LabWare numbers
2024-01-26, Walter Demczuk & Shelley Peterson
Description
This script makes a new LabWareUpload_metrics_SUBMITTED.csv with submitted lab nos replaced with LabWare nos.
Usage
rename_submitted(Org_id, curr_work_dir)
Arguments
curr_work_dir
Start up directory from pipeline project to locate system file structure
Org_code
Organism to query: GAS, PNEUMO or GONO
Details
Copies Contig Assemblies and VCF files from submitted IRIDA sample no to LabWare No.
Reads in a list of new LabWare Nos. and submitted genome sample numbers from list.csv
Makes a new LabWareUpload_metrics_SUBMITTED.csv with subm.lab.nos replaced with LabWare Nos.
Input:
SampleNo Variable
LabWare id Submitted id in IRIDA
SampleNo is new LabWare No
Variable is the submitted IRIDA sample id.
Value
A table frame containing the results of the query
phac-nml/wade documentation built on March 16, 2024, 8:32 a.m.
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View source: R/Rename_Submitted.R
| rename_submitted | R Documentation |
Renames submitted contig files to NML LabWare numbers 2024-01-26, Walter Demczuk & Shelley Peterson
Description
This script makes a new LabWareUpload_metrics_SUBMITTED.csv with submitted lab nos replaced with LabWare nos.
Usage
rename_submitted(Org_id, curr_work_dir)
Arguments
curr_work_dir |
Start up directory from pipeline project to locate system file structure |
Org_code |
Organism to query: GAS, PNEUMO or GONO |
Details
Copies Contig Assemblies and VCF files from submitted IRIDA sample no to LabWare No. Reads in a list of new LabWare Nos. and submitted genome sample numbers from list.csv Makes a new LabWareUpload_metrics_SUBMITTED.csv with subm.lab.nos replaced with LabWare Nos.
Input: SampleNo Variable LabWare id Submitted id in IRIDA
SampleNo is new LabWare No Variable is the submitted IRIDA sample id.
Value
A table frame containing the results of the query
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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