User: ropolocan
ropolocan • 230
- Reputation:
- 230
- Status:
- Trusted
- Location:
- Canada
- Last seen:
- 2 days, 8 hours ago
- Joined:
- 1 year, 8 months ago
- Email:
- r***********@uleth.ca
Posts by ropolocan
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... Hello, @kamiljaron. I was not aware of BioMake; I would have to read up on it. I do not know prolog, nor have I ever used a logical programming language, but I will read more about what BioMake has to offer. ...
written 2 days ago by
ropolocan • 230
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... Thank you very much for your answer, @Sinji. I also look forward to test Nextflow. Both workflow systems/languages have so much potential. I think they could make a very important impact on bionformatics.
...
written 2 days ago by
ropolocan • 230
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... Thank you very much for your answer, @dariober.
> It seems to me that snakemake and nextflow are pretty much on a draw for all these metrics and both are pretty good (although in terms of user base and developers they are far from tools like luigi). So I think it's a difficult choice between the ...
written 2 days ago by
ropolocan • 230
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... I just read this excellent review by @Jeremy Leipzig. This article can be helpful for deciding which workflow management system is more suitable to each one's needs: https://academic.oup.com/bib/article-lookup/doi/10.1093/bib/bbw020 ...
written 3 days ago by
ropolocan • 230
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... Thanks for sharing this table, @shenwei356! It is very interesting to see that `nextflow` has stream processing, workflow versioning, and full support for SLURM, in addition to having native task support for any language. I believe `snakemake` has native task support for R now as well. Thanks again ...
written 3 days ago by
ropolocan • 230
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10 follow
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... I have seen increasing interest in workflow/pipeline management systems such as `snakemake` and `nextflow`. In my opinion, both seem very interesting and very promising. There is a very interesting review from 2016 in which `bash`, `make`, `snakemake` and `nextflow` were compared: https://www.jmazz. ...
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... Thank you for the very informative answer, Brian. Your answer is clear and I am now able to understand why one would prefer one way of sorting over the other. ...
written 8 days ago by
ropolocan • 230
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... Samtools has the options of sorting alignments by read name or by chromosomal coordinate. Why would someone choose one over the other? What are some practical aspects to consider for each sorting method for downstream applications (e.g. counting the number of hits vs. the reference genome). ...
written 8 days ago by
ropolocan • 230
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Comment:
C: Run time of processes in Galaxy
... Thank you for following up. ...
written 5 weeks ago by
ropolocan • 230
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Comment:
C: Run time of processes in Galaxy
... I saw the answer too. I don't know if it is the particular instance that I am using, but I do not see it either. ...
written 5 weeks ago by
ropolocan • 230
Latest awards to ropolocan
Appreciated
3 days ago,
created a post with more than 5 votes.
For Snakemake vs. Nextflow: strengths and weaknesses
Supporter
4 months ago,
voted at least 25 times.
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