yaml_content='''# This is the yaml file for generating the ERGA Assembly Report (EAR) using the make_EAR.py script (https://github.com/ERGA-consortium/EARs)
# Please complete the required information pointed as #<Insert ...>
# The file [example]rCarCar2_EAR.yaml contains an example of a completed yaml file (https://github.com/ERGA-consortium/EARs)
# GENERAL INFORMATION
ToLID: #<Insert ToLID>
Species: #<Insert species name>
Sex: <Insert species sex> # for example: XX, XY, ZZ, ZW, unknown, NA...
Submitter: #<Insert submitter full name>
Affiliation: #<Insert affiliation>
Tag: #<Insert tag> # valid tags are ERGA-Pilot, ERGA-BGE, ERGA-Satellite
# SEQUENCING DATA
DATA:
- hic: '''
ifhic_coverage!=0:
yaml_content+=f'''{hic_coverage} # this is an estimate of the coverage of the Hi-C data
'''
else:
yaml_content+=f''':#<insert data coverage> # if coverage is not available, leave it empty
'''
yaml_content+=f''' - hifi/illumina #<select data type>: {kmer_coverage} # this is an estimate of the coverage based on the kmer coverage computed by genomescope2
pipeline: [<Insert ToolA_v1.2.3|ParamX|ParamY>, <Insert ToolB_v2.3.4>] # valid input is empty or between brackets ToolName followed by _v followed by versionNumber followed by | followed by keyToolParameter
hap1: # this name was autocompleted by GEP, check the correct naming, valid types are hap1, pri, collapsed
hic_FullMap_link: # Upload the file {results_folder}/1_evaluation/{asmID}/HiC_MAPS/{asmID}.asm1.HiC.COMBINED.FILTERED.pretext to the web and insert the link here
blobplot_cont_png: #<Insert blobplot contamination .png file full path>
'''
if (row['ALT_asm']!="None")and(notpd.isna(row['ALT_asm'])):
yaml_content+=f''' hap2: # this name was autocompleted by GEP, check the correct naming
hic_FullMap_link: # Upload the file {results_folder}/1_evaluation/{asmID}/HiC_MAPS/{asmID}.asm2.HiC.COMBINED.FILTERED.pretext to the web and insert the link here
blobplot_cont_png: #<Insert blobplot contamination .png file full path>