docs: Documentation update (#1295)

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### Description

Follow up on #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 <[email protected]>
Co-authored-by: tdayris <[email protected]>
Co-authored-by: Johannes Köster <[email protected]>
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 <[email protected]>
Co-authored-by: Christopher Schröder <[email protected]>

bio/bazam/meta.yaml

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

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

bio/bedtools/complement/meta.yaml

@@ -5,7 +5,11 @@ url: https://bedtools.readthedocs.io/en/latest/content/tools/complement.html
 authors:
   - Antonie Vietor
 input:
-  - BED/GFF/VCF files
-  - genome file
+  - in_file: interval files (BED/GFF/VCF)
+  - genome: genome file
 output:
   - complemented BED/GFF/VCF file
+params:
+  - extra: additional program arguments (except `-i` and `-g`)
+notes: |
+  * This program/wrapper does not handle multi-threading.

bio/bedtools/coveragebed/meta.yaml

@@ -4,3 +4,12 @@ description:
 url: https://bedtools.readthedocs.io/en/latest/content/tools/coverage.html
 authors:
   - Patrik Smeds
+input:
+  - a: Path to the feature file (BAM/BED/GFF/VCF). This file is compared to `b` (see below)
+  - b: Path or list of paths to file(s) (BAM/BED/GFF/VCF).
+output:
+  - Path to the coverage file.
+params:
+  - extra: additional program arguments (except `-a` and `-b`)
+notes: |
+  * This program/wrapper does not handle multi-threading.

bio/bedtools/genomecov/meta.yaml

@@ -7,5 +7,13 @@ authors:
 input:
   - 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
   - BAM files sorted by position.
+  - ref: Path to genome file, this must come after the other files
 output:
   - genomecov (.genomecov)
+params:
+  - extra: additional program arguments
+note: |
+  * If user provides a BAM file, then no need to provide a reference genome file
+  * If user provides a BED file, then reference genome file is required
+  * BAM/GFF/VCF/BED files *must* come first. Input file order matters in this wrapper.
+  * This program/wrapper does not handle multi-threading.

bio/bedtools/intersect/meta.yaml

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

bio/bedtools/merge/meta.yaml

@@ -3,3 +3,11 @@ description: Merge entries in one or multiple BED/BAM/VCF/GFF files with bedtool
 url: https://bedtools.readthedocs.io/en/latest/content/tools/merge.html
 authors:
   - Jan Forster
+input:
+  - Path or list of paths to interval(s) file(s) (BED/GFF/VCF/BAM)
+output:
+  - Path to merged interval(s) file.
+params:
+  - extra: additional program arguments (except for `-i`)
+notes: |
+  * 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

@@ -3,3 +3,13 @@ description: Increase the size of each feature in a BED/BAM/VCF by a specified f
 url: https://bedtools.readthedocs.io/en/latest/content/tools/slop.html
 authors:
   - Jan Forster
+input:
+  - Path to an interval file (BED/GFF/VCF)
+output:
+  - Path to the expanded intervals file
+params:
+  - genome: Path to a genome file
+  - extra: additional program arguments (except for `-i` or `-g`)
+notes: |
+  * Extra parameters requires either `-b` or (`-l` and `-r`)
+  * This program/wrapper does not handle multi-threading.

bio/bedtools/sort/meta.yaml

@@ -5,8 +5,12 @@ url: https://bedtools.readthedocs.io/en/latest/content/tools/sort.html
 authors:
   - Antonie Vietor
 input:
-  - BED/GFF/VCF files
-  - optional a tab separating file that determines the sorting order and contains the chromosome names in the first column
-  - optional a fasta index file
+  - in_file: Path to interval file (BED/GFF/VCF formatted)
+  - genome: optional a tab separating file that determines the sorting order and contains the chromosome names in the first column
+  - faidx: optional a fasta index file
 output:
-  - sorted BED/GFF/VCF file
+  - Path to the sorted interval file (BED/GFF/VCF formatted)
+params:
+  - extra: additional program arguments (except for `-i`, `-g`, or `--faidx`)
+notes: |
+  * This program/wrapper does not handle multi-threading.