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EAR_basic_template.yaml
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EAR_basic_template.yaml
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# This is the yaml (v24.09.10) file for generating the ERGA Assembly Report (EAR) using the make_EAR.py (v24.09.10) script
# Please complete the required information pointed as <Insert ...>
# The file example/mEleMax1_example.yaml contains an example of a completed yaml file
# SAMPLE INFORMATION
ToLID: <Insert ToLID>
Species: <Insert species name>
Sex: <Insert species sex> # for example: XX, XY, X0, ZZ, ZW, unknown, NA
Submitter: <Insert submitter full name>
Affiliation: <Insert submitter affiliation>
Tags: <Insert tag> # valid tags are ERGA-BGE, ERGA-Pilot, ERGA-Community
# SEQUENCING DATA
DATA: # add below name of available data and coverage
- <Insert data type>: <insert data coverage> # if coverage is not available, leave it empty
# GENOME PROFILING DATA
PROFILING:
GenomeScope:
genomescope_summary_txt: <Insert GenomeScope results summary.txt file path>
Smudgeplot: # Smudgeplot is not mandatory (but preferred for ploidy estimation), if not available, leave it empty
smudgeplot_verbose_summary_txt: <Insert Smudgeplot results summary.txt file path>
# ASSEMBLY DATA
ASSEMBLIES:
Pre-curation:
<Insert haplotype>: # valid types are hap1, pri, collapsed
gfastats--nstar-report_txt: <Insert gfastats--nstar-report.txt full path>
busco_short_summary_txt: <Insert busco_short_summary.txt full path>
merqury_folder: <Insert Merqury results folder path>
<Insert another haplotype>: # Only if hap2 is available. Otherwise remove the <Insert another haplotype> section
gfastats--nstar-report_txt: <Insert gfastats--nstar-report.txt full path>
busco_short_summary_txt: <Insert busco_short_summary.txt full path>
merqury_folder: <Insert Merqury results folder path>
Curated:
<Insert haplotype>: # valid types are hap1, pri, collapsed
gfastats--nstar-report_txt: <Insert gfastats--nstar-report.txt full path>
busco_short_summary_txt: <Insert busco_short_summary.txt full path>
merqury_folder: <Insert Merqury results folder path>
hic_FullMap_png: <Insert pretext FullMap.png full path> # also can be a HiC full contact map PNG from higlass
hic_FullMap_link: <Insert .pretext file web link> # also can be a web folder with .mcool from higlass
blobplot_cont_png: <Insert blobplot contamination .png file full path>
<Insert haplotype>: # Only if hap2 is available. Otherwise remove the <Insert another haplotype> section
gfastats--nstar-report_txt: <Insert gfastats--nstar-report.txt full path>
busco_short_summary_txt: <Insert busco_short_summary.txt full path>
merqury_folder: <Insert Merqury results folder path>
hic_FullMap_png: <Insert pretext FullMap.png full path> # also can be a HiC full contact map PNG from higlass
hic_FullMap_link: <Insert .pretext file web link> # also can be a web folder with .mcool from higlass
blobplot_cont_png: <Insert blobplot contamination .png file full path>
# METHODS DATA
PIPELINES: # add below name of the tools used for the assembly and curation steps, with versions and key parameters selected
Assembly:
<Insert ToolA>: <Insert ToolA version>/<Insert ToolA parameter>/<Insert ToolA parameter> # First field correspond to version. Use / after each field to enter the parameters used
<Insert ToolB>: <Insert ToolB version>
Curation:
<Insert ToolX>: <Insert ToolX version> # First field correspond to version. Use / after each field to enter the parameters used
<Insert ToolY>: <Insert ToolY version>/<Insert ToolY parameter>
# CURATION NOTES
NOTES:
Obs_Haploid_num: <Insert observed haploid number> # integer
Obs_Sex: <Insert observed sex> # for example: XX, XY, X0, ZZ, ZW, unknown, NA
Interventions_per_Gb: <Insert manual intervernation during curation> # integer or empty
Contamination_notes: <Insert contamination notes> # text in quotes "", related to the decontamination process, or presence of plastids or symbionts
Other_notes: <Insert other notes> # text in quotes "", related to sample characteristics and quality, the curation process, etc