Hi,
I have a problem with the output of rcorrector which I would like to wrap. The input are single-end or paired-end fastq file/s and the output is the name (name of the input file) of the files plus ".cor.fq" so for example:
input: sample_R1.fastq, sample_R2.fastq
output: sample_R1.cor.fq, sample_R2.cor.fq
How can I catch the output? something like:
<data name="output1" format="fastq" label="${tool.name} on ${on_string}: R1"> <discover_datasets pattern="$input1_cor"/> </data>
<data name="output2" format="fastq" label="${tool.name} on ${on_string}: R2"> <discover_datasets pattern="$input2_cor"/> <filter>library['lib'] == 'paired'</filter> </data>
but $input is the complete path ...
Has anyone an idea?
Cheer Jochen