Fix processing of input parameter

[skrakau]

Fixed issue #131: internally still the deprecated params.reads where processed instead of params.input (sorry! must have overseen something when merging the template).

To avoid future confusions and avoid the warning
"WARN: Access to undefined parameter input_paths -- Initialise it to a default value eg. params.input_paths = some_value"
for users when not running test profiles, I also initialised the input_paths variable again (even though it was removed from the template).

PR checklist

• This comment contains a description of changes (with reason)
• CHANGELOG.md is updated
• If you've fixed a bug or added code that should be tested, add tests!
• Documentation in docs is updated
• If necessary, also make a PR on the nf-core/mag branch on the nf-core/test-datasets repo

[d4straub]

LGTM!