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databio / dnameth_pipelines

PEP-compatible pipelines for DNA methylation data (RRBS, WGBS)
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Need monadic handling of input_to_fastq return type #42

Open vreuter opened 5 years ago

vreuter commented 5 years ago

Right now, paired_end mode seems to assume that the return type from ngstk.input_to_fastq will be a Sequence: https://github.com/databio/dnameth_pipelines/commit/9b457e482c9f40409095c8b291975a5e9869c54d

But link isn't reflected in the implementation of ngstk.input_to_fastq: https://github.com/databio/pypiper/blob/dev/pypiper/ngstk.py#L384-L457

Then, seemingly, indexing the first element of the unaligned_fastq is just grabbing the first character of a filepath:

### Adapter trimming:  (04-16 13:44:05) elapsed: 0.0 _TIME_

> `python -u /sfs/qumulo/qhome/vpr9v/code/dnameth_pipelines/src/tools/detect_quality_code.py -f /`

Traceback (most recent call last):
  File "/sfs/qumulo/qhome/vpr9v/code/dnameth_pipelines/src/tools/detect_quality_code.py", line 62, in <module>
    txt = open(opts.filename)
IOError: [Errno 21] Is a directory: '/'
vreuter commented 5 years ago

https://github.com/databio/pypiper/commit/7ca1f598ca9c13304498d802e7131589a3a65769 https://github.com/databio/pypiper/commit/1390a24314e499ca328cab76e6917e9dbd173447 https://github.com/databio/pypiper/commit/15c20e05881598c3af395a790e03f9b20ff8dfa7