Roman Chernyatchik

``` use rule methylome_npz_2_bismark from npz_cpg_2_bismark_cpg as methylome_npz_2_bismark_cpg with: ... # later: rules.methylome_npz_2_bismark_cpg.output.biscov ``` 

Do not show rule or checkpoint might be not defined error in input functions

1

``` def input_fun_targets_methylome_npz_paths(wildcards): return expand( rules.methylome_txt_2_npz.ouput, #

Find usages of rule doesn't find it's usages in `use` statements, e.g.: ``` # module_1.smk rule foo: #

 ``` # module_476.smk rule rule_476_M: input: "" ``` ``` # rule_476.smk module module_476: snakefile: "module_476.smk" use rule rule_476_M from module_476 as new_rule_476_M with: ```

For `use rule rule_476_M from module_476` and `use rule rule_476_M from module_476 with` we show only gutter at `rule_476_M`, so the behaviour is inconsistent. I think we should show both...

``` # a1.smk rule a: # a2.smk rule a: # b.smk rule b: input: rules.a #here multiple options should be shown ```

We have a redeclared inspection, but not clear how to find easily such redeclarations. Let's add gutters.

There are many features in snakemake and many directives (section types) in completion list, e.g.: cache, shadow, notebook,.... . Let's make completion more user friendly and help user to figure...

> Also note that the rules need to retrieve all their parameters via the params directive (except input files). It is not allowed to directly use wildcards, config or any...

Support for: Using already existing named conda environments Introduced in: snakemake 6.14.0 > specify conda environments via their name ([#1340](https://www.github.com/snakemake/snakemake/issues/1340)) ([735ab23](https://www.github.com/snakemake/snakemake/commit/735ab2301d0905ea054ad6efa3150acb296d0e78)) Documentation: https://snakemake.readthedocs.io/en/stable/snakefiles/deployment.html#using-already-existing-named-conda-environments > Note that Snakemake distinguishes file-based environments...