Roman Chernyatchik
Roman Chernyatchik
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...
See https://snakemake.readthedocs.io/en/stable/snakefiles/modularization.html#meta-wrappers. E.g. smth like for wrappers - completion, resolve, documentation
``` 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} >...
Seems is working: ``` shell.executable("bash") def get_params(wildcards): return {'test': 'oo', 'norm': 'oo'} rule test: output: "aa" params: unpack(get_params) shell: "echo {params}" ```
 ``` shell.executable("bash") rule all: input: 'result.r1', 'result.c1', # targeting checkpoint output overrides input 'result.c2' # TODO: works OK def rule1_input(wc): checkpoints.check1.get(**wc).output[0] return "result.r2" rule r1: input: rule1_input output: 'result.r1',...
``` def version(): return "3.3" rule rule1: # This rule creates an intermediate file. input: 'test.inter' output: 'dir/test.out' log: a='log/logfile.log' #TODO: works OK version: version() threads: 3 shell: 'if [...
Dynamic is going to be deprecated in 6.0, not sure we should add full support here. ``` shell.executable("bash") rule all: input: 'output/result.n3', output: 'output/done.txt', shell: 'echo all >> {output}' #...
Seems dynamic could be used in input section (need to check)  ``` # TODO: not an error, dynamic 1) could be in input 2) could have wildcards # will...
Some resources properties could be provided via cmdline / cluster profile, so they will be missing in code. Let's add a tab into Snakemake support settings, that allows configuring such...
Maybe better to show warning/weak warning here ``` # TODO: no undeclared error here, will be empty on runtime, maybe warning? rule a1: shell: "echo -{input}-" ``` 