snakecharm

snakecharm copied to clipboard

iromeo

AttributeError: 'Checkpoint' object has no attribute 'output'

1

Checkpoint type differs from Rule type: `checkpoints.A.output.mydir` leads to `AttributeError: 'Checkpoint' object has no attribute 'output'`, should be `checkpoints.A.get(**wildcards).output.mydir` Code example: ``` import os from snakemake import shell shell.prefix('set -vexu...

iromeo

Code indentation fix in rules

19

Code indentation fix in rules for new line after: * rule name declaration * rule parameter name

iromeo

Resolve/completion for `config` attrs

1

E.g. `config[genome]` where `genome` is defined in `configfile` or in cmdline using `--config` argument. Warn only about first usage and consider defined downstream. ``` rule download_fa: output: directory("fa") shell: 'rsync...

iromeo

Fetch correct wildcards if arg value in rule is link to other section or section arg

1

Fetch correct wildcards if arg value in rule is link to other section or section arg. Support required for inspection checking undeclards wildcards and for completion/resolve ``` rule foo1: output:...

iromeo

May be caused: 1) set custom interpreter in snakemake settings (not project one) 2) updated the interpreter using terminal snakemake version 3) resolve/completion issues for interpreter sdk methods Vers: 0.10.0.SNAPSHOT...

iromeo

Snakemake adds new section names from time to time and this leads to errors like #332. In order to be more friendly to newer snakemake releases parser behavior should be...

iromeo

File `boo.smk`: ``` if condition: use rule r as rule_new1 else: use rule r as rule_new2 ``` File `foo.smk`: ``` module M: snakefile: "boo.smk" use rule * from M as...

dakochik

See https://snakemake.readthedocs.io/en/stable/snakefiles/modularization.html#meta-wrappers. E.g. smth like for wrappers - completion, resolve, documentation

iromeo

``` shell.executable("bash") rule all: input: "foo.txt" rule one: output: pipe("pipe.txt") shell: "echo test > {output}" # TODO: works OK rule two: input: pipe("pipe.txt") output: "foo.txt" shell: """ cat {input} >...

iromeo