Code polishing

[maxulysse]

Move existing functions from scripts to SarekUtils library:

• checkFileExtension
• checkParameterExistence
• checkParameterList
• checkReferenceMap
• checkRefExistence
• extractBams
• extractGenders
• returnFile
• returnStatus
• returnTSV

Modify function extractBams:

• take an extra parameter (somatic or germline) to return Channel with or without gender respectively

Add new function to SarekUtils:

• sarek_ascii() for fancy Ascii Art

Replace depreciated operator phase by join:

• for Channels bamsForHC and recalTables in germlineVC.nf
• for Channels duplicatesRealign and intervals in main.nf

Remove data footprint (a bam file was stored twice in the work directory for no reason like #584):

• removed files bam and bai from Process CreateRecalibrationTable
• duplicate Channel realignedBam to realignedBamToJoin
• use operator join for Channels realignedBamToJoin and recalibrationTable

[szilvajuhos]

Now I understand :) It is nice to see groovy utils growing.