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
Return to Step 3 pipeline version 0.0.40 or older