validate all settings in the settings file before starting snakemake

[alexg9010]

If the user creates a settings file, where a the tools paragraph is actually empty like in the example below:

general:
[..]
    bowtie2:
        # set k if you want to report at most k alignments per read
        # k: 1
        # N: Sets the number of mismatches to allowed in a seed alignment during multiseed alignment. Can be set to 0 or 1. Setting this higher makes alignment slower (often much slower) but increases sensitivity. Default: 0.
        # N: 0
[...]

We get a cryptic error later in the pipeline:

message)�[0m
�[31mRuleException:
TypeError in line 174 of /gnu/store/nxk52pcmvizq6vlb4xmg2x0c3s74xprb-pigx-chipseq-0.0.42/libexec/pigx_chipseq/scripts/SnakeFunctions.py:
'NoneType' object is not iterable
  File "/gnu/store/nxk52pcmvizq6vlb4xmg2x0c3s74xprb-pigx-chipseq-0.0.42/libexec/pigx_chipseq/Rules/Mapping.py", line 220, in __rule_bowtie2
  File "/gnu/store/nxk52pcmvizq6vlb4xmg2x0c3s74xprb-pigx-chipseq-0.0.42/libexec/pigx_chipseq/scripts/SnakeFunctions.py", line 174, in join_params
  File "/gnu/store/09a5iq080g9b641jyl363dr5jkkvnhcn-python-3.8.2/lib/python3.8/concurrent/futures/thread.py", line 57, in run�[0m

We need to validate this earlier.

[rekado]

Alexander Blume (Gosdschan) <notifications@github.com> writes:

If the user creates a settings file, where a the tools paragraph is actually empty like in the example below: ``` general: [..] bowtie2: # set k if you want to report at most k alignments per read # k: 1 # N: Sets the number of mismatches to allowed in a seed alignment during multiseed alignment. Can be set to 0 or 1. Setting this higher makes alignment slower (often much slower) but increases sensitivity. Default: 0. # N: 0 [...] ``` We get a cryptic error later in the pipeline: ``` message)[0m [31mRuleException: TypeError in line 174 of /gnu/store/nxk52pcmvizq6vlb4xmg2x0c3s74xprb-pigx-chipseq-0.0.42/libexec/pigx_chipseq/scripts/SnakeFunctions.py: 'NoneType' object is not iterable File "/gnu/store/nxk52pcmvizq6vlb4xmg2x0c3s74xprb-pigx-chipseq-0.0.42/libexec/pigx_chipseq/Rules/Mapping.py", line 220, in __rule_bowtie2 File "/gnu/store/nxk52pcmvizq6vlb4xmg2x0c3s74xprb-pigx-chipseq-0.0.42/libexec/pigx_chipseq/scripts/SnakeFunctions.py", line 174, in join_params File "/gnu/store/09a5iq080g9b641jyl363dr5jkkvnhcn-python-3.8.2/lib/python3.8/concurrent/futures/thread.py", line 57, in run[0m ``` We need to validate this earlier.

We could also be a little more lenient in cases like that. Clearly, when a setting isn’t provided we should fall back to the defaults. We can accomplish this with an accessor procedure that takes a settings “path” and either returns that value or the default. If the path cannot be followed because any one of its components is invalid we fall back to the default. (A path could be specified as an array, and the accessor would be a recursive procedure popping off the head of the array as it recurses.)

…

-- Ricardo