Andrea Telatin

Help running in offline cluster

3

I need to run *mag* in offline mode and I tried with: ```bash nextflow run $NF/nextflow/nf-core-mag-1.0.0/workflow/main.nf \ --reads '$INPUT/reads/*_R{1,2}.fq.gz' \ --busco_reference $DB/bacteria_odb9.tar.gz \ --outdir out \ --cat_db $DB/CAT_prepare_20190108.tar.gz \ --kraken2_db...

Make a versioned release

2

Hello there, thanks for this tool! I was wondering if you plan to make a release, to make it easier to make analyses reproducible. Best

Hi, thanks for the tool. This is just to fix a typo that ends in the logs :) Cheers

I'd like to run bamsnap with a custom reference (assembly output). This works disabling the "gene" track with: ``` bamsnap -draw coordinates bamplot coverage base \ -out test.png -bam aln.bam...

Help understanding why SALMON_INDEX fails

7

### Description of the bug SALMON_INDEX fails with `exit status: 1`, but if I inspect the folders I see both the `salmon` index subdirectory created and populated, the `version.yaml` file....

Documentation URL broken

1

Hi there! I noticed that the Wiki (section: API) brings to this URI [https://pezmaster31.github.com/bamtools/annotated.html](https://pezmaster31.github.com/bamtools/annotated.html) that does not resolve. Cheers Andrea

update reverseComplement() for FASTQ entries

1

When revcompl a FASTQ sequence, quality should be reversed

[feature request] Option to save (un)classified reads

1

Kraken2 allows for `--unclassified-out FILE` (and `--classified-out FILE`) and this can be handy in contamination removal steps, and could benefit from the architecture of Sepia that could allow filtering multiple...

As mentioned in #7

helper tool [suggestion]

1

Hi, if can be of help for others, I made a tool to generate the Excel file from the command line: https://github.com/quadram-institute-bioscience/start-asap/ It's easily installable via Miniconda with `conda install...