Add bandage

[sjackman]

No description provided.

[codecov-io]

Codecov Report

Merging #150 into dev will increase coverage by 0.07%.
The diff coverage is 100%.

@@            Coverage Diff             @@
##              dev     #150      +/-   ##
==========================================
+ Coverage   39.05%   39.12%   +0.07%     
==========================================
  Files          59       59              
  Lines        5654     5661       +7     
==========================================
+ Hits         2208     2215       +7     
  Misses       3446     3446

Impacted Files	Coverage Δ
flowcraft/generator/engine.py	91.33% <ø> (ø)	⬆️
...wcraft/generator/components/assembly_processing.py	100% <100%> (ø)	⬆️

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[sjackman]

This component works as is, but Bandage loads the FASTA file, whereas I would like to load the GFA file output by SPAdes. Any tips on how I can load the GFA file instead of the FASTA file?

[ODiogoSilva]

Yes @sjackman , this is a recurrent situation for us and something that you can solve using secondary links. The basic idea is that you can connect two components with any number of secondary channels that pass additional information besides the main channels. I'll walk you through briefly:

1. On the spades nextflow template, where you define the output channel for the gfa file, assign it to a channel:

file "*.gfa" optional true into assemblyGfa_{{ pid }}

2. On the spades python class, add the information that you have a secondary channel source, using the self.link_start attribute, and provide the name of the channel:

# Notice that we exclude _{{ pid }} here
self.link_start.extend(["assemblyGfa"])

3. On the bandage python class, add the information that you wish to receive a secondary channel with that name, using the link_end attribute:

self.link_end.append({
    "link": "assemblyGfa",
    "alias": "assemblyGfa"
})

4. Finally on the bandage nextflow template, you can receive the assemblyGfa channel in the input declaration:

        input:
        set sample_id, file(assembly_gfa) from {{input_channel}}
        file (assembly_gfa) from assemblyGfa_{{ pid }}

And you should have access to the Gfa file as well. With this system you can easily pass data between components, even if those components are not contiguous. For instance, if you created a pipeline like:

spades pilon bandage

the bandage component would still receive the GFA from spades!

[sjackman]

Awesome. Thank you very much for the detailed instructions, Diogo. I'd like to first merge this PR, if you would, without support for GFA. I'll submit a new PR next week to add support for GFA.

[sjackman]

Our Hackseq hackathon is wrapping up in one hour! Thank you all for being so responsive this weekend! It's been great getting these PRs merged while we hacked. I hadn't expected that.

[ODiogoSilva]

Another fine addition good to go 👍 Great job at the hackathon, I'm glad we could integrate your efforts quickly into flowcraft. These only one minor coment.

[ODiogoSilva]

Could you be more specific here on the regex pattern? This will also include dot file (.command.*) from nextflow in the publishDir.

[sjackman]

I've changed it to "*.png *.svg".

[sjackman]

Thanks for merging, Diogo!