Checks for succesfull loading of module and logging versions used to file.

In the rnaseq_parser only one batch of data can be added at the same time, should be possible to add data from multiple batches

add SP(species) and ASsembly (AS) to dict for completeness please.

According to perldoc you should catch all of your system calls with a check of $? if you want your programs to exit nicely if the shell gives an error. Example below.

#set -x or && could be used. Here both are used. 
my $indexcmd = "set -x && bgzip -c $invcf > $outvcf && tabix -p vcf $outvcf";
        my $ret = `$indexcmd`;
        $? == 0 or die "system cmd `$indexcmd` failed: $ret\n exit code: $?";

Example of affected scripts (not exhaustive ):

• createBWAandSAMtoolsIndices.pl
• per_folder/index_creator.pl
• createLocalRealignmentIntervals.pl
• runpindel.pl
• maybe every perl script that contains system().

Long commandline options for tortilla.sh don't work when converting CRAM to BAM. (The short version of the commandline opts work fine.)

module load ngs-utils
tortilla.sh --cramToBam -i /groups/umcg-gd/tmp06/cramToBam/Pieter
/apps/software/ngs-utils/18.11.2/CramConversion.sh: illegal option -- -
/apps/software/ngs-utils/18.11.2/CramConversion.sh: illegal option -- c
inputFolder=/groups/umcg-gd/tmp06/cramToBam/Pieter
workDir=/groups/umcg-gd/tmp06/cramToBam/Pieter/BAM
reference=amToBam
starting to convert /groups/umcg-gd/tmp06/cramToBam/Pieter/[some_sample].merged.dedup.bam.cram
amToBam: No such file or directory

Hello.

I am having a problem on using prepareGenFromBeagle4 for a pipeline for ShapeIt.
I have downloaded libboost and but it seems that in makefile of prepareGenFromBeagle4, the path for this library is hard-coded for your machine. So, I have changed it, to work on mine too.
The only problem now is that I cant find the folder "/apps/software/Boost/1.60.0-foss-2015b-Python-2.7.9/include/ " and I have no idea how to create it.

It will be useful to include a manual for this application or make paths work on every machine.