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guoyanzhao / VirusSeeker-Virome

VirusSeeker is a set of fully automated and modular software package designed for mining sequence data to identify sequences of microbial origin.
GNU General Public License v3.0
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Decouple sampledir workdir #8

Open koebbe opened 6 years ago

koebbe commented 6 years ago

This pull request separates the "sample" directory from the "work" directory. This keeps the sample directory untouched and allows multiple pipelines to be run at the same time against the same sample directory since all of the output files are placed in a separate "work" directory.

An additional (optional) parameter to the VirusSeeker_Virome_v... command is added to allow for naming of the work directory. If not included, the default name is "workdir":

Usage: perl $0 <sample_folder> <ref genome> <use checkpointing> <step_number> [workdir]
schackartk commented 2 years ago

To clarify, since this pull request has not been accepted, then currently the pipeline cannot be run concurrently on multiple files in the same input directory?

guoyanzhao commented 2 years ago

You are correct. You would need to concatenate the files into a single file for each set of  read 1 and read 2 files separately. 

On Monday, November 22, 2021, 12:15:37 PM CST, Kenneth Schackart @.***> wrote:

To clarify, since this pull request has not been accepted, then currently the pipeline cannot be run concurrently on multiple files in the same input directory?

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