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feat: Mashmap #485

Merged
merged 21 commits into from
May 13, 2022
Merged

feat: Mashmap #485

merged 21 commits into from
May 13, 2022

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tdayris
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@tdayris tdayris commented May 6, 2022

Description

This PR adds MashMap, a long read aligner.

QC

For all wrappers added by this PR, I made sure that

  • there is a test case which covers any introduced changes,
  • input: and output: file paths in the resulting rule can be changed arbitrarily,
  • either the wrapper can only use a single core, or the example rule contains a threads: x statement with x being a reasonable default,
  • rule names in the test case are in snake_case and somehow tell what the rule is about or match the tools purpose or name (e.g., map_reads for a step that maps reads),
  • all environment.yaml specifications follow the respective best practices,
  • wherever possible, command line arguments are inferred and set automatically (e.g. based on file extensions in input: or output:),
  • all fields of the example rules in the Snakefiles and their entries are explained via comments (input:/output:/params: etc.),
  • stderr and/or stdout are logged correctly (log:), depending on the wrapped tool,
  • temporary files are either written to a unique hidden folder in the working directory, or (better) stored where the Python function tempfile.gettempdir() points to (see here; this also means that using any Python tempfile default behavior works),
  • the meta.yaml contains a link to the documentation of the respective tool or command,
  • Snakefiles pass the linting (snakemake --lint),
  • Snakefiles are formatted with snakefmt,
  • Python wrapper scripts are formatted with black.

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@fgvieira
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fgvieira commented May 6, 2022

It seems that MashMap has its own output format, "space-delimited with each line consisting of query name, length, 0-based start, end, strand, target name, length, start, end and mapping nucleotide identity".
Just for the sake com consistency with other read mappers, is there a way to convert this output to a SAM/BAM/CRAM?

Also, does MasMap uses any temp folder?

@tdayris
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tdayris commented May 6, 2022

Just for the sake com consistency with other read mappers, is there a way to convert this output to a SAM/BAM/CRAM?

Mashmap format to SAM/BAM/CRAM is not supported by MashMap. There is an open issue about that on their git. I'm wrapping this tool to follow Salmon guideline to create a gentrome file with decoy sequences.

Also, does MasMap uses any temp folder?

There is no official variable or command line argument to overload any default temporary directory.

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@fgvieira fgvieira merged commit c05006d into snakemake:master May 13, 2022
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2 participants