Fastqc multiqc

[deyazoubi]

add new rule

• the rule is tested, results can be seen in stepnames 039_Fastqc

two issues have to solve

1. lines

   spike/rules/fastqc/Snakefile

   Line 17 in 7e939e2

   directory("{prefix}%s%s/{run}/determined/fastqc/Keimbahn/" % (config['dirs']['intermediate'], config['stepnames']['Fastqc']))

   and

   spike/rules/fastqc/Snakefile

   Line 40 in 7e939e2

   inp=directory("%s%s%s/{run}/determined/fastqc/Keimbahn/" % (config['dirs']['prefix'],config['dirs']['intermediate'], config['stepnames']['Fastqc'])),

   
   Sample_Project must be variable for different project

2. after solve the point 1, for AG_remke the new rule will not work
   the reason is

   spike/scripts/parse_samplesheet.py

   Line 559 in 7e939e2

   def get_samples(samplesheets, config):

   
   in this function # "only consider samples that have some spike_entity_role defined" and this not the case for AG_remke
   one solutions is

   spike/scripts/parse_samplesheet.py

   Line 571 in 9f7e583

   def get_samples_all(samplesheets, config):

[sjanssen2]

please ping me when the tests are passing