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Do checkpoint on values after Cdhit #30

See merge request !21

Conflicts:
	main.nf
	modules/read_alignment.nf
	subworkflows/hifi_reads.nf
	subworkflows/short_reads.nf

	remove workflow no longer used
	skip alignment use only for filtering when --skip_filtering
	Correct output emit by sickle

Adding possibility to give flowcell information on samplesheet

See merge request !20

# Conflicts:
#   modules/host_filter.nf
#   modules/read_alignment.nf

	Remaniment du subworkflow filtering pour ne comporte plus de process, creation du module filtering_cpm.nf contenant les process de filtrage

Conflicts:
	main.nf

	Not yet dealing with these informations

	Not yet dealing with these informations