Chase Clark

`Let us dissect the above command:` doesn't match the commands above it in: https://github.com/KwanLab/Autometa/blob/main/docs/source/step-by-step-tutorial.rst#7-binning

Move unrelated files out of Nextflow pipeline directory

1

`/Autometa/workflows/` is a Nextflow/nf-core specific directory, the following files should probably find another home. It may confuse future contributors https://github.com/KwanLab/Autometa/blob/main/workflows/autometa-large-data-mode.sh https://github.com/KwanLab/Autometa/blob/main/workflows/autometa.sh https://github.com/KwanLab/Autometa/blob/main/workflows/autometa_flagged.sh

Add helpful error message

1

https://github.com/KwanLab/Autometa/blob/baf61c04dddf5b33bb825dba2841de1e38dffefe/autometa/validation/datasets.py#L47 Currently the error has to be traced back to the code: ``` Traceback (most recent call last): File "/home/chase/miniconda3/envs/autometa/bin/autometa-download-dataset", line 8, in sys.exit(main()) File "/home/chase/miniconda3/envs/autometa/lib/python3.10/site-packages/autometa/validation/datasets.py", line 197, in main...

Pipeline fails if number of splits is greater than number of input contigs

2

e.g. Input parameter is set to `--num_splits 12` but only 8 contigs are in the input ``` Error executing process > 'AUTOMETA:PRODIGAL (Annotating mock_metagenome)' Caused by: Process `AUTOMETA:PRODIGAL (Annotating mock_metagenome)`...

The *versioned* docker images for the "mock" test run aren't available on dockerhub so the pipeline fails. It might be easier to just change the nextflow module for those to...

The number of cpus is already passed to the alignment step (see `${task.cpus}`) so pass it to the build step as well ``` $ bowtie2-build --help | grep "threads" --threads...

Notes on how to upgrade to current nf-core standards

1

nf-core updated and their module format changed a pretty decent amount. At first I was really confused trying to figure out what changed but I think the changes, while a...

Create nextflow process to hmmpress marker hmms

1

One thing I wanted to note is that currently this only works with docker as executor (ie not with conda only) because the MARKERS process requires hmmpress'ed files. @Sidduppal This...

Small test datasets to sanity check/attempt to break code

6

We have some synthetic and simulated datasets. It would be nice to have some additional ultra-small test datasets to sanity-check code. e.g. metagenome.fna files other (not-comprehensive) examples: - [ ]...

This might only be important with quite large metagenomes and even then probably will still not be the slow step even if uneven. Currently, when running in parallel, the input...