multiple sample input and variable tumor/normal name

[rlancaster96]

End goal: point to a directory that contains multiple patient tumor/normal pairs as input, and output into directories unique to each patient. For example, passing to a directory that looks like this:

my_samples
   |- SAMPLEID001_TUMOR_ETC_R1.fastq.gz
   |- SAMPLEID001_TUMOR_ETC_R2.fastq.gz
   |- SAMPLEID001_NORMAL_ETC_R1.fastq.gz
   |- SAMPLEID001_NORMAL_ETC_R2.fastq.gz
   |- SAMPLEID002_TUMOR_ETC_R1.fastq.gz
   |- SAMPLEID002_TUMOR_ETC_R2.fastq.gz
   |- SAMPLEID002_NORMAL_ETC_R1.fastq.gz
   |- SAMPLEID002_NORMAL_ETC_R2.fastq.gz

and creating output like this:

my_output
   |- SAMPLEID001
      |- aligned
      |- annotated 
      |- multiqc
      |- etc
   |- SAMPLEID002
      |- aligned
      |- annotated 
      |- multiqc
      |- etc

variables defined in the params file should be:

• how tumor is denoted (eg, "T")
• how normal is denoted (eg, "N")
• input directory location
• output directory location

[rlancaster96]

Not a feature needed for current processing