handling existence of replicates

replicates are appended together

Input check has a new parameter that allows the merging ("appending") of reads in the python dictionary only when cellranger is used ... as this problem we were facing only when using it.

changed order to ensure cellranger is tried

reverted script to allow the use of techinal replicates for all aligners

if a sample is defined multiple times, it will only append the file to the dictionary instead of raising an error

instead of using only the first elements of the input array, it now joins the filenames in a single string usig whitespaces.

This would make it possible to use it when more replicates are available

We may want to add a checking so it complains when not using paired end data.

added a comment explaining why this channel mapping is still necessary

add changed code line as backup

nf-core lint wants it deleted

fixed with nf-core lint

fixed with nf-core lint

flattens reads array as it is expected my the module

removing redudancy spotted

This reverts commit 5c2a21a.