snakecharm

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``` rule: output: "foo/{sample}.{config[genome]}.out", ``` Here better highlight whole `config[genome]` as wildcard

iromeo

- [ ] Add the ability to configure new section (e.g. via YAML file & UI in plugin settings) and specify section features: * is section value accessible after `rules.rule_name.`...

dakochik

Inspection: Warn if some section name couldn't be used with project snakemake version

1

A warning that warns if some section name couldn't be used with project snakemake version (from settings), subtask of #334

iromeo

Access to input/output iterable properties by index

2

Incorrect input/output properties indexation:  So plugin ignores list of elements and counts it as one property.

dakochik

At the moment parser inserts `Py:TRIPPLE_QUOTED_STRING` instead of `Py:DOCSTRING`, see screenshot. So we get wrong highlighting.  ``` rule foo: """ doc0 """ log: "foo.log" """ doc1 """ output: touch("foo.out")...

iromeo

Add warning which detects misspelled section names, e.g we could use Levenshtein or etc distance to predict the expected section name + quick fix, subtask of #334

iromeo

Update/Install/Uninstall plugin w/o IDE restart

1

Not always work, e.g on update: ``` 2021-04-24 17:12:00,837 [ 79] INFO - #com.intellij.idea.Main - JVM: 11.0.10+9-b1341.41 (Dynamic Code Evolution 64-Bit Server VM) 2021-04-24 21:13:19,074 [14478316] INFO - lij.ide.plugins.DynamicPlugins -...

iromeo

Duplicated inspection errors:  ``` rule bams_dedup_qc_bismark2report: input: alignment_report = "bams/{sample}/{rgid_genome}_PE_report.txt", nucleotide_report="bams/{sample}/{rgid_genome}_pe.nucleotide_stats.txt", dedup_report="bams/{sample}/{rgid_genome}_pe.deduplication_report.txt" output: html="qc/bams_dedup/bismark2report/{sample}/{rgid_genome}.bismark2report.html" log: "qc/bams_dedup/bismark2report/{sample}/{rgid_genome}.bismark2report.html.log" message: "QC: Deduplicated [{wildcards.sample}] bismark2report HTML report for {wildcards.rgid_genome}" params: skip_optional_reports=True wrapper: "0.46.0/bio/bismark/bismark2report"...

iromeo

Wrappers section missing key argument false positive

1

 See https://snakemake-wrappers.readthedocs.io/en/0.64.0/wrappers/bismark/bam2nuc.html ``` bam = snakemake.input.get("bam", None) if bam: cmdline_args.append("{bam}") ... else: cmdline_args.append("--genomic_composition_only") ```

iromeo

E.g. * warn that functions / lambdas cannot be used * somehow consider it in autocompletion of `rules.` Usage example: ``` rule all: input: txt = 'out2.txt' some_var: str =...

iromeo