snakecharm

snakecharm copied to clipboard

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...

iromeo

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

iromeo

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...

iromeo

Snakemake wrappers resolve/completion

10

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...

iromeo

Features/#464 module resolve

2

`module` name resolve was fixed

dakochik

In the following example: ``` # Snakefile module A: snakefile: "a_file.smk" use rule * from A as snakefile_* ``` ``` # foo.smk module A: snakefile: "b_file.smk" use rule * from...

dakochik

In the following example: ``` # Snakefile rule A: input: "input_file_A" ``` ``` # boo.smk include: "Snakefile" use rule A as boo_A with: input: "boo_input_file_A" ``` Gutter icon for the...

dakochik

In the following example: ``` # Snakefile rule A: input: "input_file_A" ``` ``` # boo.smk module SNKFILE: snakefile: "Snakefile" ``` ``` # foo.smk include: "boo.smk" use rule A from SNKFILE...

dakochik

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

iromeo

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:...

iromeo