Roman Chernyatchik issues

Results 105 issues of


                                            Roman Chernyatchik

Resolve for post-deployment scripts

See https://snakemake.readthedocs.io/en/stable/snakefiles/deployment.html#providing-post-deployment-scripts (introduced in 6.14 ) My suggestion is to implement cond file reference resolve: * resolve - resolves only to `*.yaml` * multi-resolve - also adds `*.post-deploy.sh` variant

good_for_next_release

Yaml bases resolve / completion for 'config` and `pep.config`

Yaml keys completion for `config` and `pep.config` objects (e.g. see #360 issue) Expected completion: * in python code: `config['']`, `config['key1'][""]` * in SnakemakeSL: `shell: "echo config[key1][key2]" * Completion both for...

Snakemake wrappers resolve/completion

Resolve / completion from the configured wrappers repo ``` rule samtools_sort: input: "mapped/{sample}.bam" output: "mapped/{sample}.sorted.bam" params: "-m 4G" threads: 8 wrapper: "0.0.8/bio/samtools_sort" ``` > Here, Snakemake will automatically downloads the...

codeInsight

Enable Unbound variable Inspection in python code inside SMK files.

Due to 2021.3 API changes, we had to disable the inspection. New API required to re-enable it. Test `Inspection: Unbound variable Inspection replacement` (`resources/features/highlighting/inspections/unbound_variable.feature`) temporary disabled. See 516ff9473133ad6350d5502c0018ef8f6db341ac

3rd party

Use project wide caching in wildcards collector

Use project wide caching in wildcards collector. Do not traverse all links each time, cache wildcards + update them on some events. P.S.: could be also used for other things:...

codeInsight

good_for_next_release

Insert handler for wrappers keyword args completion

Insert handler for wrappers keyword args completion E.g. before: ```shell rule foo: input: f wrapper: "0.74.0/bio/bismark/bismark_methylation_extractor" ``` After: rule foo: input: fq = "" wrapper: "0.74.0/bio/bismark/bismark_methylation_extractor" ```

codeInsight

good_for_next_release

Roman Chernyatchik

Resolve for post-deployment scripts

Yaml bases resolve / completion for 'config` and `pep.config`

Snakemake wrappers resolve/completion

Enable Unbound variable Inspection in python code inside SMK files.

Use project wide caching in wildcards collector

Insert handler for wrappers keyword args completion

Insert wrapper example as a template

Add wrapper args info into documentation popup

An Inspection that informs that some wrapper has a newer version

Refactor 'rule like' term in sources