Question: bowtie2 rename dataset from paired list
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brigida.rusconi • 40 wrote:
Hi,
I have a paired reads dataset list that I use for a bowtie2 workflow. I try to rename the output file with the #{input_1} option but I get an empty string for the output file. I tried to use the #{own_file} that renames according to the reference sequence and that works. I have tried different combinations of input with or without 1 or even using _2 since it is paired end fastq, but nothing worked. I looked at the wrapper and in the input section it is called input_1 so I don't understand why it is not propagating the name. Is there another way to get the identifier from the paired list to rename the output file according to the initial fastq?
Best,
Brigida
I tried the renaming with the paired and there it works. I think that in Bowtie2 it has an issue with recognizing the paired_collection. I can do the Bowtie2 with a paired_collection, but the workflow manager shows me this error when I am selecting the option "History does not include a dataset collection of the correct type or containing the correct types of datasets". Despite the error it will produce bam files for all the pairs in the collection, but I cannot get the name of each pair on the list. All the files will have an identical name e.g. Bowtie2 on data 11, data 4, and others: aligned reads (sorted BAM). This is why I need to rename them.