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docs: Documentation update (snakemake#1295)
<!-- Ensure that the PR title follows conventional commit style (<type>: <description>)--> <!-- Possible types are here: https://github.com/commitizen/conventional-commit-types/blob/master/index.json --> ### Description Follow up on snakemake#392 I finally have time to continue this. This is a new chunk of 9 meta.yaml updated to explicitly give IO parameters names (if any) and updated notes. ### QC <!-- Make sure that you can tick the boxes below. --> Wrappers have not been changed. The only changes are in meta.yaml files. Most of the QC steps below do not apply here. * [X] I confirm that: For all wrappers added by this PR, * 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](https://en.wikipedia.org/wiki/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](https://stackoverflow.com/a/64594513/2352071), * 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 `Snakefile`s 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](https://docs.python.org/3/library/tempfile.html#tempfile.gettempdir); 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, * `Snakefile`s pass the linting (`snakemake --lint`), * `Snakefile`s are formatted with [snakefmt](https://github.com/snakemake/snakefmt), * Python wrapper scripts are formatted with [black](https://black.readthedocs.io). * Conda environments use a minimal amount of channels, in recommended ordering. E.g. for bioconda, use (conda-forge, bioconda, nodefaults, as conda-forge should have highest priority and defaults channels are usually not needed because most packages are in conda-forge nowadays). --------- Co-authored-by: tdayris <tdayris@gustaveroussy.fr> Co-authored-by: tdayris <thibault.dayris@gustaveroussy.fr> Co-authored-by: Johannes Köster <johannes.koester@uni-due.de> Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com> Co-authored-by: snakedeploy-bot[bot] <115615832+snakedeploy-bot[bot]@users.noreply.github.com> Co-authored-by: Felix Mölder <felix.moelder@uni-due.de> Co-authored-by: Christopher Schröder <christopher.schroeder@tu-dortmund.de>
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‎bio/bazam/meta.yaml

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@@ -4,7 +4,15 @@ url: https://github.com/ssadedin/bazam
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authors:
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- Christopher Schröder
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input:
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- BAM/CRAM file
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- reference genome
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- bam: Path to mapping file (BAM/CRAM formatted)
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- reference: Optional path to reference genome sequence (FASTA formatted). Required for CRAM input.
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output:
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- fastq file
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- reads: Path to realigned reads (single-ended or interleaved) (FASTQ formatted) *OR*
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- r1: Path to upstream reads (FASTQ formatted) *AND*
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- r2: Path to downstream reads (FASTQ formatted)
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params:
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- extra: Optional parameters passed to `bazam`
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note: |
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* Output files include either paths to both `r1` and `r2`, or a single path to `reads`.
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* This wrapper/tool does not handle multithreading.
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* The `java_opts` param allows for additional arguments to be passed to the java compiler (not for `-XmX` or `-Djava.io.tmpdir`, since they are handled automatically).

‎bio/bedtools/bamtobed/meta.yaml

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@@ -5,8 +5,10 @@ url: https://bedtools.readthedocs.io/en/latest/content/tools/bamtobed.html
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authors:
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- Filipe G. Vieira
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input:
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- BAM file
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- BAM file, this must be the first file in the input file list
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output:
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- BED file
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- BED file, this must be the first file in the output file list
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params:
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- extra: additional program arguments (except `-i`)
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notes: |
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* The `extra` param allows for additional program arguments.
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* This program/wrapper does not handle multi-threading.

‎bio/bedtools/complement/meta.yaml

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authors:
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- Antonie Vietor
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input:
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- BED/GFF/VCF files
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- genome file
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- in_file: interval files (BED/GFF/VCF)
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- genome: genome file
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output:
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- complemented BED/GFF/VCF file
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params:
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- extra: additional program arguments (except `-i` and `-g`)
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notes: |
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* This program/wrapper does not handle multi-threading.

‎bio/bedtools/coveragebed/meta.yaml

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url: https://bedtools.readthedocs.io/en/latest/content/tools/coverage.html
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authors:
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- Patrik Smeds
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input:
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- a: Path to the feature file (BAM/BED/GFF/VCF). This file is compared to `b` (see below)
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- b: Path or list of paths to file(s) (BAM/BED/GFF/VCF).
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output:
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- Path to the coverage file.
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params:
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- extra: additional program arguments (except `-a` and `-b`)
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notes: |
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* This program/wrapper does not handle multi-threading.

‎bio/bedtools/genomecov/meta.yaml

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input:
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- BED/GFF/VCF files grouped by chromosome and genome file (`genome file format <https://bedtools.readthedocs.io/en/latest/content/general-usage.html#genome-file-format>`_) OR
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- BAM files sorted by position.
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- ref: Path to genome file, this must come after the other files
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output:
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- genomecov (.genomecov)
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params:
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- extra: additional program arguments
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note: |
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* If user provides a BAM file, then no need to provide a reference genome file
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* If user provides a BED file, then reference genome file is required
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* BAM/GFF/VCF/BED files *must* come first. Input file order matters in this wrapper.
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* This program/wrapper does not handle multi-threading.

‎bio/bedtools/intersect/meta.yaml

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@@ -3,3 +3,12 @@ description: Intersect BED/BAM/VCF files with bedtools.
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url: https://bedtools.readthedocs.io/en/latest/content/tools/intersect.html
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authors:
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- Jan Forster
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input:
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- left: Path to the left region file. Each feature in left region file is compared to right region(s) file(s) in search of overlaps. (BAM/BED/GFF/VCF formatted)
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- right: Path or list of paths to region(s) file(s) (BAM/BED/GFF/VCF formatted)
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output:
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- Path to the intersection.
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params:
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- extra: additional program arguments (except `-a` (left) and `-b` (right))
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note: |
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* This program/wrapper does not handle multi-threading.

‎bio/bedtools/merge/meta.yaml

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url: https://bedtools.readthedocs.io/en/latest/content/tools/merge.html
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authors:
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- Jan Forster
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input:
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- Path or list of paths to interval(s) file(s) (BED/GFF/VCF/BAM)
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output:
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- Path to merged interval(s) file.
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params:
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- extra: additional program arguments (except for `-i`)
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notes: |
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* Warning: If multiple files are provided in input, then this wrapper requires exactly 3 threads. Else, it requires exactly one thread.

‎bio/bedtools/slop/meta.yaml

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url: https://bedtools.readthedocs.io/en/latest/content/tools/slop.html
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authors:
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- Jan Forster
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input:
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- Path to an interval file (BED/GFF/VCF)
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output:
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- Path to the expanded intervals file
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params:
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- genome: Path to a genome file
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- extra: additional program arguments (except for `-i` or `-g`)
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notes: |
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* Extra parameters requires either `-b` or (`-l` and `-r`)
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* This program/wrapper does not handle multi-threading.

‎bio/bedtools/sort/meta.yaml

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authors:
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- Antonie Vietor
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input:
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- BED/GFF/VCF files
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- optional a tab separating file that determines the sorting order and contains the chromosome names in the first column
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- optional a fasta index file
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- in_file: Path to interval file (BED/GFF/VCF formatted)
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- genome: optional a tab separating file that determines the sorting order and contains the chromosome names in the first column
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- faidx: optional a fasta index file
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output:
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- sorted BED/GFF/VCF file
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- Path to the sorted interval file (BED/GFF/VCF formatted)
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params:
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- extra: additional program arguments (except for `-i`, `-g`, or `--faidx`)
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notes: |
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* This program/wrapper does not handle multi-threading.

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