Redirect output from MIXCR

Question

[jh]

Hi,

I am including MIXCR in a snakemake pipeline, and would like to know how to redirect the output files to a specified path. I can't seem to find this info in the documentation. https://mixcr.readthedocs.io/en/master/quickstart.html

Does anyone know?

Thanks in advance

Answer 1

[mrkt]

If your command is: mixcr analyze amplicon -s <species> \ --starting-material <startingmaterial> \ --5-end <5End> --3-end <3End> \ --adapters <adapters> \ [OPTIONS] input_file1 [input_file2] analysis_name

then set analysis_name as path/to/analysis/analysis_name

Answer 2

[mizraelson]

Just add the path as a part of the prefix for output files:

e.g.

mixcr analyze generic-tcr-amplicon \
    --species hsa \
    --rna \
    --floating-left-alignment-boundary \
    --floating-right-alignment-boundary C \
      sample_R1.fastq.gz \
      sample_R2.fastq.gz \
      /path/to/output/folder/sampleName