simplifying code and adding resources.yml #10
Conversation
antgonza
changed the title
antgonza
changed the title
lucaspatel
left a comment
lucaspatel
left a comment
There was a problem hiding this comment.
Some minor concerns about testing but otherwise looks good to me.
| cd ../step-2/${sample_name}_split | ||
| # making a copy of the small_LCG before they are removed | ||
| mkdir -p {{output}}/step-2/${sample_name}_small_LCG | ||
| find . -maxdepth 1 -type f -size -512k -print0 | xargs -0 -r cp -t ../${sample_name}_small_LCG |
There was a problem hiding this comment.
So small_LCG is defined by files in size < 512kb? Probably important to note in the documentation for the PacBio workflow.
There was a problem hiding this comment.
I was expecting small_LCG to be defined by total genome size
There was a problem hiding this comment.
by file size for now. Can be optimized, they are proportational to total genome size.
There was a problem hiding this comment.
approximate 515,000 bases (half a million), because one character takes one byte approximately.
| else: | ||
| full = full.concat(loaded) | ||
|
|
||
| with h5py.File(f"{base}/{rank}", "w") as out: |
There was a problem hiding this comment.
Not sure if I'm reading this right, but wouldn't these lines here indicate that you will write full to out on every iteration of the loop, thus rewriting the same path over and over?
|
|
||
| @click.command() | ||
| @click.option("--base", type=click.Path(exists=True), required=True) | ||
| def biom_merge(base): |
There was a problem hiding this comment.
This seems like a lot of logic to merge some BIOM. Is this borrowed from qp-woltka? Do you have tests supporting this function in particular?
| "qiita-files@https://github.com/qiita-spots/qiita-files/archive/master.zip", | ||
| "qiita_client@https://github.com/qiita-spots/qiita_client/archive/master.zip", | ||
| "woltka@git+https://github.com/qiyunzhu/woltka.git#egg=woltka", | ||
| "micov@git+https://github.com/biocore/micov.git#egg=micov", |
There was a problem hiding this comment.
Minor but you can probably get micov from pip now.
There was a problem hiding this comment.
It would be nice if we can install from bioconda
jianshu93
left a comment
jianshu93
left a comment
There was a problem hiding this comment.
I like the database option. We will probably update it very soon. wol3 or even GTDB.
No description provided.