Renaming rules#154
Open
KasperThystrup wants to merge 5 commits into
Open
Conversation
* Implemented f strings for input/output/logs of all rules * Removed underscores from all database names as these would bring confusion to the snakemake solver * Standardized output file naming conventions for all relevant rules * Standardized log file naming conventions for all rules * Added screening/examples folder for the templates not being used * Changed assemblers keyword to match the assembler wildcard * Changed assembly input and output names * Commented out bowtie as it was not tied to anything. * Made two output from sistr temp, to highlight them despite them not being tied up to anything.
* Polished rule naming for rules, to clarify their main tool * Removed custom from rule names
All rules have now been reorganized into: * analysis.smk -> All types of analysis which are not dependent on single reads or paired reads * Piared_Reads.smk -> all types of analysis which uses read1 and read2 as input * databases.smk -> all database creation rules
Major polishing and rule restructuring
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
1 participant
Add this suggestion to a batch that can be applied as a single commit.This suggestion is invalid because no changes were made to the code.Suggestions cannot be applied while the pull request is closed.Suggestions cannot be applied while viewing a subset of changes.Only one suggestion per line can be applied in a batch.Add this suggestion to a batch that can be applied as a single commit.Applying suggestions on deleted lines is not supported.You must change the existing code in this line in order to create a valid suggestion.Outdated suggestions cannot be applied.This suggestion has been applied or marked resolved.Suggestions cannot be applied from pending reviews.Suggestions cannot be applied on multi-line comments.Suggestions cannot be applied while the pull request is queued to merge.Suggestion cannot be applied right now. Please check back later.
Read #153
I mistakenly pulled the wrong direction