banzai

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This is a better way to handle config settings: https://en.wikipedia.org/wiki/INI_file

jimmyodonnell

Hi there, This is a semi-automated message from a fellow bioinformatician. Through a GitHub search, I found that the following source files make use of BLAST's `-max_target_seqs` parameter: - [scripts/annotation/blast_script.sh](https://github.com/jimmyodonnell/banzai/blob/18a97e983543ffb17e2bf57896ad12ec755adb37/scripts/annotation/blast_script.sh)...

armish

Cutadapt can now operate in parallel: https://cutadapt.readthedocs.io/en/stable/changes.html#v1-15-2017-11-23 Before implementing, check the important caveats ('Multi-core support is only available on Python 3, and not yet with some command-line arguments').

jimmyodonnell

derep_fasta_hash.py appears to truncate fasta headers at 45 characters

6

1. I love your work. And your stylish Polynesian beverages. 2. The new hash option for dereplicating is working great -- esp. useful for combining datasets. But... 3. the hashes...

invertdna

Banzai without secondary indices

4

Seems like we run into an issue if you are not using secondary indices, as you need them to generate ID_COMBO in line 268 awk: illegal field $(), name "COLNUM2"...

ramongallego

document format for CSV file

3

The README mentions the need for a CSV file, but it would be useful to add an example to show the exact format for this file.

fmichonneau

Using compressed files as raw data

4

When using .gz or any other compressed fastq files as input, the script successfully find the zipped files and decompresses the first one, but then fails to use it. The...

ramongallego

logfile -- version number?

5

Hey - I think it would be a good idea to list version number/github fork/something in the banzai logfile, especially given the number of different forks and putative users at...

invertdna

and it should still work if there's only one library in the dataset

invertdna

when running the pipeline on a multi-library dataset, the current code fails when the "already peared?" option is set to YES, because the script looks for a single merged.assembled.fasta file....

invertdna