Fix/Create mock data subworkflow

[chasemc]

Part of but does-not-fix:

mention
#152

[chasemc]

PR allows creating mock contigs from an input set of Genbank assembly accessions. Also creates two minimal reports at end showing the binning results- one colored by genus (parsed from name) and one by assembly accession.

Example output:
mock_data_reports.zip

[chasemc]

Notes:
Mock data reports should write out to the main output folder.

To run the pipeline with mock data set the parameter --mock_test true

[chasemc]

A couple of things to fix (or not) before merging in (@WiscEvan I don't think I'll have time to do these today)

1. This process needs a docker image. @ajlail98 could maybe look around to find one?
   

   Autometa/modules/local/get_genomes_for_mock.nf

   Line 10 in 0ec0087

   // TODO: Docker image for emboss or another seqsplitter/python script

2. This one also:
   

   Autometa/modules/local/mock_data_reporter.nf

   Lines 14 to 15 in b73850e

   	// container TODO: The R "Rocker" Docker images don't have ps which is required by Nextflow so this may have to be a custom image?
   	// docker build https://gist.githubusercontent.com/chasemc/818111640daae05beb2b070641aa33fb/raw/09107704fa60a6311fb09542c8b99b848e168ea3/Dockerfile --tag mock_data_reporter

   
   I have an example there but it has to be built first. Maybe that's okay if the mock_data is only going to be used by developers, where instructions to build the image first could be provided
   Note: that dockerfile is a modified version of:
   https://github.com/rocker-org/rocker/blob/master/r-rmd/Dockerfile
   where procps is also installed (required by Nextflow), so the Rocker project license would have to be included

3. Last- just a note that when I happened to run this with "GCF_013307045.1" it failed because of no markers found. May be worth looking into

[evanroyrees]

📝 I've added a tag to the GET_GENOMES_FOR_MOCK process in get_genomes_for_mock.nf so the user can easily tell how many genomes are being fetched for the mock community.

Runtime Note

• I built the docker image jason-c-kwan/autometa:dev (docker build . -t jason-c-kwan/autometa:dev) prior to running:

nextflow run . -profile docker -params-file "nf-params.json" --mock_test true --input .

nf-params.json

{
    "autometa_image_tag": "dev"
}

---

Dockerfiles

I've also added dockerfiles for the processes you've mentioned. I was not sure where to put these. I've opted to place them in a $HOME/Autometa/docker/modules sub-directory. If you have guidance on where these should be placed, feel free to move them.. If you make these changes, the Makefile command modules-images will need to be updated to conform to these updated paths.

i.e. to build all autometa nextflow modules docker images from Makefile

make modules-images

A couple of things to fix (or not) before merging in

1. This process needs a docker image.
   modules/local/get_genomes_for_mock.nf)

• 🐳 Docker image for get_genomes_for_mock.nf can be built with docker/modules/get_genomes_for_mock.Dockerfile

2. This one also:
   

   Autometa/modules/local/mock_data_reporter.nf

   Lines 14 to 15 in b73850e

   	// container TODO: The R "Rocker" Docker images don't have ps which is required by Nextflow so this may have to be a custom image?
   	// docker build https://gist.githubusercontent.com/chasemc/818111640daae05beb2b070641aa33fb/raw/09107704fa60a6311fb09542c8b99b848e168ea3/Dockerfile --tag mock_data_reporter

   I have an example there but it has to be built first. Maybe that's okay if the mock_data is only going to be used by developers, where instructions to build the image first could be provided
   Note: that dockerfile is a modified version of:
   https://github.com/rocker-org/rocker/blob/master/r-rmd/Dockerfile
   where procps is also installed (required by Nextflow), so the Rocker project license would have to be included

I've used conda to create the R env

• 🐳 Docker image for mock_data_reporter.nf can be built with docker/modules/mock_data_reporter.Dockerfile

[evanroyrees]

I've added Dockerfiles for the respective Autometa nextflow modules images to docker/modules... I'm not sure if this is appropriate with the nf-core team, but everything seems to be working.

NOTE: The "beeswarm" plots contents are appearing in the mock report, but their axes titles are not... This doesn't appear to be a breaking issue, so I'm going to approve and merge.

👍