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Find Path Key Files
These two keyfiles are tab-separated text files which setup fastq alignment to the pangenome and which readMappings need to be aggregated when finding Paths.
FastqToMappingPlugin KeyFile Specification:
The PHG will process the following columns:
| HeaderName | Description | Required |
|---|---|---|
| cultivar | Name of the taxon to be processed. | Yes |
| flowcell_lane | Name of the flow cell this sample came from | Yes |
| filename | Name of the Fastq file to be processed | Yes |
| filename2 | Second Fastq file to be processed. If set, minimap2 will operate in paired end mode | No |
| PlateID | The id of the Plate. | No |
Note that cultivar + flowcell_lane + PlateID must be a unique value across all samples in the keyfile. If this is not, the PHG will not work correctly. After running through FastqToMapping, an additional column will be added denoting the ReadMappingID values in the DB. This is purely for reference and is not used currently in the pipeline.
Sample File:
#!txt cultivar flowcell_lane filename PlateID RecLineB1RefA1gco4_wgs wgsFlowcell RecLineB1RefA1gco4_R1.fastq wgs RecLineB1RefA1gco4_gbs gbsFlowcell RecLineB1RefA1gco4_R1_gbs.fastq gbs RecRefA1LineBgco6_wgs wgsFlowcell RecRefA1LineBgco6_R1.fastq wgs RecRefA1LineBgco6_gbs gbsFlowcell RecRefA1LineBgco6_R1_gbs.fastq gbs LineB1_wgs wgsFlowcell LineB1_R1.fastq wgs LineB1_gbs gbsFlowcell LineB1_R1_gbs.fastq gbs LineA_wgs wgsFlowcell LineA_R1.fastq wgs LineA_gbs gbsFlowcell LineA_R1_gbs.fastq gbs LineB_wgs wgsFlowcell LineB_R1.fastq wgs LineB_gbs gbsFlowcell LineB_R1_gbs.fastq gbs LineA1_wgs wgsFlowcell LineA1_R1.fastq wgs LineA1_gbs gbsFlowcell LineA1_R1_gbs.fastq gbs RecLineALineB1gco3_wgs wgsFlowcell RecLineALineB1gco3_R1.fastq wgs RecLineALineB1gco3_gbs gbsFlowcell RecLineALineB1gco3_R1_gbs.fastq gbs RecLineB1LineBgco7_wgs wgsFlowcell RecLineB1LineBgco7_R1.fastq wgs RecLineB1LineBgco7_gbs gbsFlowcell RecLineB1LineBgco7_R1_gbs.fastq gbs RefA1_wgs wgsFlowcell RefA1_R1.fastq wgs RefA1_gbs gbsFlowcell RefA1_R1_gbs.fastq gbs Ref_wgs wgsFlowcell Ref_R1.fastq wgs Ref_gbs gbsFlowcell Ref_R1_gbs.fastq gbs RecLineBLineB1gco8_wgs wgsFlowcell RecLineBLineB1gco8_R1.fastq wgs RecLineBLineB1gco8_gbs gbsFlowcell RecLineBLineB1gco8_R1_gbs.fastq gbs RecLineA1LineA1gco2_wgs wgsFlowcell RecLineA1LineA1gco2_R1.fastq wgs RecLineA1LineA1gco2_gbs gbsFlowcell RecLineA1LineA1gco2_R1_gbs.fastq gbs RecLineBLineB1gco5_wgs wgsFlowcell RecLineBLineB1gco5_R1.fastq wgs RecLineBLineB1gco5_gbs gbsFlowcell RecLineBLineB1gco5_R1_gbs.fastq gbs RecLineA1RefA1gco1_wgs wgsFlowcell RecLineA1RefA1gco1_R1.fastq wgs RecLineA1RefA1gco1_gbs gbsFlowcell RecLineA1RefA1gco1_R1_gbs.fastq gbs
Find Path Keyfile Specification
Note: This file will likely not be needed to create. FastqToMappingPlugin will export a sample keyfile given its inputs. This will probably be good enough for the majority of use cases.
The PHG will process the following columns:
| HeaderName | Description | Required |
|---|---|---|
| sampleName | Name of the taxon to be processed. | Yes |
| ReadMappingIds | ReadMappingIds in the DB. All readMappings need to be comma separated. | Yes |
| LikelyParents | List of taxon which the user believes are the likely parents for this sample. Currently this is not used. | No |
Sample File:
#!txt SampleName ReadMappingIds LikelyParents RecLineB1RefA1gco4_wgs 1 RecLineB1RefA1gco4_gbs 2 RecRefA1LineBgco6_wgs 3 RecRefA1LineBgco6_gbs 4 LineB1_wgs 5 LineB1_gbs 6 LineA_wgs 7 LineA_gbs 8 LineB_wgs 9 LineB_gbs 10 LineA1_wgs 11 LineA1_gbs 12 RecLineALineB1gco3_wgs 13 RecLineALineB1gco3_gbs 14 RecLineB1LineBgco7_wgs 15 RecLineB1LineBgco7_gbs 16 RefA1_wgs 17 RefA1_gbs 18 Ref_wgs 19 Ref_gbs 20 RecLineBLineB1gco8_wgs 21 RecLineBLineB1gco8_gbs 22 RecLineA1LineA1gco2_wgs 23 RecLineA1LineA1gco2_gbs 24 RecLineBLineB1gco5_wgs 25 RecLineBLineB1gco5_gbs 26 RecLineA1RefA1gco1_wgs 27 RecLineA1RefA1gco1_gbs 28
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