upgrade fastqc #242

See merge request !30

calcul cpm for each sample one by one

See merge request !29

delete unused library

reorder kept_contigs and idxstat

Upgrade cutadapt to 5.0

See merge request !28

#242 fastqc

See merge request !27

delete unused library

reorder kept_contigs and idxstat

doc update (generalisation and correction of script example, remove 6B in singularity command for checkm2 db and specification for samplesheet in case of flowcell if the assembly is used as input)