output locations etc. at end of pipeline

[ctb]

what was generated, where it is, etc.

could also be a link to the docs.

[bluegenes]

will add to the workflow docs, but should probably also print when we print workflow finished using the onsuccess snakemake command

[bluegenes]

Now, a successful run will print the directories for each tool run in the pipeline.

example:

--- Workflow executed successfully! ---

  Outputs:
	assemblyinput:  /Users/tessa/Dropbox/dib-lab/eelpond/nema_out/assembly
	get_data:  /Users/tessa/Dropbox/dib-lab/eelpond/nema_out/input_data
	salmon:  /Users/tessa/Dropbox/dib-lab/eelpond/nema_out/quant
	trimmomatic:  /Users/tessa/Dropbox/dib-lab/eelpond/nema_out/preprocess

Not quite all files produced, but I could do that if desired. Would just print a fair number of file names. Proposal: Instead, print these in a nice report using report functionality: docs: https://snakemake.readthedocs.io/en/stable/snakefiles/reporting.html example: https://snakemake.readthedocs.io/en/stable/_downloads/report.html

[ctb]

Sure! Lots of thoughts here. Quickest is: focus on making this succinct but human readable, and then provide contextual links to docs. Eg “Trinity assembler output files are in: “ then “go for explanation of this step”.

Longer term, could use papermill to run parameterized notebooks that provide summary stats on directory contents and output to HTML.

Titus Brown, [email protected]mailto:[email protected]

On Jan 21, 2019, at 2:22 PM, Tessa Pierce <[email protected]mailto:[email protected]> wrote:

Now, a successful run will print the directories for each tool run in the pipeline.

example:

--- Workflow executed successfully! ---

Outputs: assemblyinput: /Users/tessa/Dropbox/dib-lab/eelpond/nema_out/assembly get_data: /Users/tessa/Dropbox/dib-lab/eelpond/nema_out/input_data salmon: /Users/tessa/Dropbox/dib-lab/eelpond/nema_out/quant trimmomatic: /Users/tessa/Dropbox/dib-lab/eelpond/nema_out/preprocess

Not quite all files produced, but I could do that if desired. Would just print a fair number of file names. Proposal: Instead, print these in a nice report using report functionality: docs: https://snakemake.readthedocs.io/en/stable/snakefiles/reporting.html example: https://snakemake.readthedocs.io/en/stable/_downloads/report.html

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHubhttps://github.com/dib-lab/eelpond/issues/13#issuecomment-456213570, or mute the threadhttps://github.com/notifications/unsubscribe-auth/AADHSJWQA4AILafaSqw43yU3QIeNOgY0ks5vFj2WgaJpZM4aLNey.

[bluegenes]

update: turns out basic reporting is super easy to get an html via report function. Supposed to be able to print an rst too, will look into it. Will add the go <here> for docs bit to onsuccess`

ooh, papermill looks neat!