Fix #91

[bricoletc]

#91 spotted a problem with nested if/else conditionals for including config files. This showed the regexp
we had for spotting these conditionals was incomplete, which I fixed, with added unit test.

This part of the code, where python syntax is 'glued' with snakemake syntax, is tricky to get right- I anticipate more edge cases exist, but I think we should wait to see them in real files rather than try and anticipate them all.

[codecov]

Codecov Report

Merging #92 (2bf6f60) into master (50cb371) will decrease coverage by 0.10%.
The diff coverage is 75.00%.

@@            Coverage Diff             @@
##           master      #92      +/-   ##
==========================================
- Coverage   98.18%   98.07%   -0.11%     
==========================================
  Files          11       11              
  Lines         882      884       +2     
  Branches      161      162       +1     
==========================================
+ Hits          866      867       +1     
- Misses          8        9       +1     
  Partials        8        8              

Flag	Coverage Δ
unittests	98.07% <75.00%> (-0.11%)	⬇️

Flags with carried forward coverage won't be shown. Click here to find out more.

Impacted Files	Coverage Δ
snakefmt/formatter.py	99.00% <75.00%> (-0.50%)	⬇️

[bricoletc]

Update; #93 raises concerned related to this, which should be addressed in this PR too, will update it as explore fixes.

[mbhall88]

Awesome work @bricoletc!

I agree, there are likely all sorts of weird edge cases, but worry about them when/if they arise.

[Smeds]

The latest commit gives me some strange results. Example

if config["programs"]["Trimming"] == "Cutadapt":

    include: "../rules/Fastq/Cutadapt_trimming.smk"


elif config["programs"]["Trimming"] == "Fastp":

    include: "../rules/Fastq/Fastp_trimming.smk"


else:

    include: "../rules/Fastq/move_fastq.smk"


# include: "../rules/CNV/ONCOCNV.smk"
# include: "../rules/CNV/cnvkit.smk"
# include: "../rules/QC/check_coverage.smk"
# include: "../rules/VCF_fix/Collect_results_DNA.smk" #Change folder!
# include: "../rules/Mutect2/Mutect2.smk"


if config["programs"]["Duplicates"] == "fgbio":

    include: "../rules/Alignment/fgbio.smk"


else:
    if config["programs"]["markduplicate"] == "GPU":

        include: "../rules/Alignment/GPU_alignment.smk"


    else:

        include: "../rules/Alignment/bwa-mem.smk"
        include: "../rules/Alignment/MarkDuplicates.smk"

Snakefmt wants to make the following modifications

  if config["programs"]["Trimming"] == "Cutadapt":
  
      include: "../rules/Fastq/Cutadapt_trimming.smk"
  
  
  elif config["programs"]["Trimming"] == "Fastp":
  
      include: "../rules/Fastq/Fastp_trimming.smk"
  
  
  else:
  
      include: "../rules/Fastq/move_fastq.smk"
  
  
- # include: "../rules/CNV/ONCOCNV.smk"
+     # include: "../rules/CNV/ONCOCNV.smk"
? ++++
- # include: "../rules/CNV/cnvkit.smk"
+     # include: "../rules/CNV/cnvkit.smk"
? ++++
- # include: "../rules/QC/check_coverage.smk"
+     # include: "../rules/QC/check_coverage.smk"
? ++++
- # include: "../rules/VCF_fix/Collect_results_DNA.smk" #Change folder!
+     # include: "../rules/VCF_fix/Collect_results_DNA.smk" #Change folder!
? ++++
- # include: "../rules/Mutect2/Mutect2.smk"
+     # include: "../rules/Mutect2/Mutect2.smk"
? ++++
  
  
- if config["programs"]["Duplicates"] == "fgbio":
+     if config["programs"]["Duplicates"] == "fgbio":
? ++++
  
      include: "../rules/Alignment/fgbio.smk"
  
  
  else:
      if config["programs"]["markduplicate"] == "GPU":
  
          include: "../rules/Alignment/GPU_alignment.smk"
  
  
      else:
  
          include: "../rules/Alignment/bwa-mem.smk"
          include: "../rules/Alignment/MarkDuplicates.smk"

[bricoletc]

Nice edge case spotted @Smeds , here's commit 01c1f87 to fix that.

[Smeds]

Nice=)