Update wrapper documentation

bio/adapterremoval/meta.yaml

@@ -1,17 +1,20 @@
 name: "AdapterRemoval"
 description: rapid adapter trimming, identification, and read merging.
+url: https://adapterremoval.readthedocs.io/en/latest/
 authors:
   - Filipe G. Vieira
 input:
-  - raw fastq file with R1 reads
-  - raw fastq file with R2 reads (PE only)
+  - sample:
+    - raw fastq file with R1 reads
+    - raw fastq file with R2 reads (PE only)
 output:
-  - trimmed fastq file with R1 reads
-  - trimmed fastq file with R2 reads (PE only)
-  - fastq file with singleton reads (PE only; PE reads for which the mate has been discarded)
-  - fastq file with collapsed reads (PE only; overlapping mate-pairs which have been merged into a single read)
-  - fastq file with collapsed truncated reads (PE only; collapsed reads that were quality trimmed)
-  - fastq file with discarded reads (reads that did not pass filters)
-  - settings and stats file
+  - fq: path to single fastq file (SE only)
+  - fq1: path to fastq R1 (PE only)
+  - fq2: path to fastq R2 (PE only)
+  - singleton: fastq file with singleton reads (PE only; PE reads for which the mate has been discarded)
+  - collapsed: fastq file with collapsed reads (PE only; overlapping mate-pairs which have been merged into a single read)
+  - collapsed_trunc: fastq file with collapsed truncated reads (PE only; collapsed reads that were quality trimmed)
+  - discarded: fastq file with discarded reads (reads that did not pass filters)
+  - settings: settings and stats file
 notes: |
-  * For more information see, https://adapterremoval.readthedocs.io/en/latest/
+  * All output files, except for 'settings', must be compressed the same way (gz, or bz2).

bio/arriba/meta.yaml

@@ -1,4 +1,18 @@
 name: "arriba"
+url: https://github.com/suhrig/arriba
 description: Detect gene fusions from chimeric STAR output
 authors:
   - Jan Forster
+input:
+  - bam: Path to bam formatted alignment file from STAR
+  - genome: Path to fasta formatted genome sequence
+  - annotation: Path to GTF formatted genome annotation
+output:
+  - fusions: Path to output fusion file
+params:
+  - known_fusions: Path to known fusions file, see `official documentation on known fusions <https://arriba.readthedocs.io/en/latest/input-files/#known-fusions>`_ for more information.
+  - blacklist: Path to blacklist file, see `official documentation on blacklist <https://arriba.readthedocs.io/en/latest/input-files/#blacklist>`_ for more information.
+  - sv_file: Path to structural variations calls from WGS, see `official documentation on SV <https://arriba.readthedocs.io/en/latest/input-files/#structural-variant-calls-from-wgs>`_ for more information.
+  - extra: Other `optional parameters <https://arriba.readthedocs.io/en/latest/command-line-options/>`_
+notes: |
+  This tool/wrapper does not handle multi threading.

bio/art/profiler_illumina/meta.yaml

@@ -1,6 +1,15 @@
 name: art_profiler_illumina
+url: https://www.niehs.nih.gov/research/resources/software/biostatistics/art/index.cfm
 description: Use the art profiler to create a base quality score profile for
   Illumina read data from a fastq file.
 authors:
   - David Laehnemann
   - Victoria Sack
+input:
+  - Path to fastq-formatted input file (first place in the input list of files)
+output:
+  - Path to txt formatted profile (first place in the output list of files)
+params:
+  - Extra parameters (no keyword mapped parameter)
+notes: |
+  Your input file must have one of the following extensions: fastq, fastq.gz, fq or fq.gz

bio/assembly-stats/meta.yaml

@@ -1,12 +1,14 @@
 name: "assembly-stats"
 description: Generates report of summary statistics for a genome assembly
+url: https://github.com/sanger-pathogens/assembly-stats
 authors:
   - Pathogen Informatics, Wellcome Sanger Institute (assembly-stats tool) - https://github.com/sanger-pathogens
   - Max Cummins (Snakemake wrapper [unaffiliated with Wellcome Sanger Institute])
 input:
-  - Genomic assembly (fasta format)
+  - assembly: Genomic assembly (fasta format)
 output:
-  - Assembly statistics (format of your choosing, default = tab-delimited)
+  - assembly_stats: Assembly statistics (format of your choosing, default = tab-delimited)
+params:
+  - extra: Optional parameters, see `assembly-stats official documentation <https://github.com/sanger-pathogens/assembly-stats#usage>`_
 notes: |
-  * The `extra` param allows for additional program arguments.
-  * For more inforamtion see https://github.com/sanger-pathogens/assembly-stats
+  This tool/wrapper does not handle multi threading

bio/bamtools/filter/meta.yaml

@@ -1,8 +1,20 @@
 name: bamtools filter
-description: Filters BAM files. For more information about bamtools see `bamtools documentation <http://stab.st-andrews.ac.uk/wiki/index.php/Bamtools>`_ and `bamtools source code <https://github.com/pezmaster31/bamtools>`_.
+url: https://github.com/pezmaster31/bamtools
+description: Filters BAM files. For more information about bamtools see `bamtools documentation <http://stab.st-andrews.ac.uk/wiki/index.php/Bamtools>`_
 authors:
   - Antonie Vietor
 input:
-  - bam files (.bam)
+  - bam files (.bam), must be in first position
 output:
-  - bam file (.bam)
+  - bam file (.bam), must be in first position
+params:
+  - tags: filtering tags
+  - min_size: minimum insert size
+  - max_size: maximum insert size
+  - min_length: minimum read length
+  - max_length: maximum read length
+  - additional_params: Other filtering and optional parameters
+notes: |
+  A complete usage documentation is available here: https://raw.githubusercontent.com/wiki/pezmaster31/bamtools/Tutorial_Toolkit_BamTools-1.0.pdf
+
+  This tool/wrapper does not handle multi threading

bio/bamtools/filter_json/meta.yaml

@@ -1,9 +1,16 @@
 name: bamtools filter with json
-description: Filters BAM files with JSON-script for filtering parameters and rules. For more information about bamtools see `bamtools documentation <http://stab.st-andrews.ac.uk/wiki/index.php/Bamtools>`_ and `bamtools source code <https://github.com/pezmaster31/bamtools>`_.
+url: https://github.com/pezmaster31/bamtools
+description: Filters BAM files with JSON-script for filtering parameters and rules. For more information about bamtools see `bamtools documentation <http://stab.st-andrews.ac.uk/wiki/index.php/Bamtools>`_
 authors:
   - Antonie Vietor
 input:
-  - bam files (.bam)
-  - json file (.json)
+  - bam files (.bam), must be in first position
 output:
-  - bam file (.bam)
+  - bam file (.bam), must be in first position
+params:
+  - json: Path to filter file, json formatted.
+  - region: see documentation for more information about multiple formats.
+notes: |
+  A complete usage documentation is available here: https://raw.githubusercontent.com/wiki/pezmaster31/bamtools/Tutorial_Toolkit_BamTools-1.0.pdf
+
+  This tool/wrapper does not handle multi threading

bio/bamtools/split/meta.yaml

@@ -1,8 +1,15 @@
 name: bamtools split
+url: https://github.com/pezmaster31/bamtools
 description: Split bam file into sub files, default by reference
 authors:
   - Patrik Smeds
 input:
-  - bam file
+  - bam file, this must be the only file in input.
 output:
-  - multiple bam file
+  - multiple bam file multiple formats.
+params:
+  - extra: Optional parameters
+notes: |
+  A complete usage documentation is available here: https://raw.githubusercontent.com/wiki/pezmaster31/bamtools/Tutorial_Toolkit_BamTools-1.0.pdf
+
+  This tool/wrapper does not handle multi threading

bio/bamtools/stats/meta.yaml

@@ -1,8 +1,15 @@
 name: bamtools stats
+url: https://github.com/pezmaster31/bamtools
 description: Use bamtools to collect statistics from a BAM file. For more information about bamtools see `bamtools documentation <http://stab.st-andrews.ac.uk/wiki/index.php/Bamtools>`_ and `bamtools source code <https://github.com/pezmaster31/bamtools>`_.
 authors:
   - Antonie Vietor
 input:
-  - bam files (.bam)
+  - bam files (.bam), must be in first position
 output:
-  - bamstats file (.bamstats)
+  - bamstats file (.bamstats), must be in first position
+params:
+  - Optional parameters as first and only value.
+notes: |
+  A complete usage documentation is available here: https://raw.githubusercontent.com/wiki/pezmaster31/bamtools/Tutorial_Toolkit_BamTools-1.0.pdf
+
+  This tool/wrapper does not handle multi threading

bio/bbtools/bbduk/meta.yaml

@@ -1,17 +1,19 @@
 name: BBDuk
+url: https://jgi.doe.gov/data-and-tools/bbtools/bb-tools-user-guide/bbduk-guide/
 description: |
   Run BBDuk.
 authors:
   - Filipe G. Vieira
 input:
-  - raw fastq file with R1 reads
-  - raw fastq file with R2 reads (optional)
+  - sample: list of paths. Raw fastq file with R1 reads, raw fastq file with R2 reads (PE only, optional)
 output:
-  - trimmed fastq file with R1 reads
-  - trimmed fastq file with R2 reads (optional)
-  - fastq file with singleton reads (optional)
-  - fastq file with discarded reads (optional) 
-  - stats file (optonal)
+  - trimmed: trimmed fastq file with R1 reads, trimmed fastq file with R2 reads (PE only, optional)
+  - singleton: fastq file with singleton reads (optional)
+  - discarded: fastq file with discarded reads (optional)
+  - stats: stats file (optonal)
+params:
+  - extra: Optional parameters
+  - adapters: Literal adapters sequences
 notes: |
   * The `java_opts` param allows for additional arguments to be passed to the java compiler, e.g. "-XX:ParallelGCThreads=10" (not for `-XmX` or `-Djava.io.tmpdir`, since they are handled automatically).
   * The `extra` param allows for additional program arguments.

bio/bcftools/call/meta.yaml

@@ -1,5 +1,13 @@
 name: bcftools call
+url: https://samtools.github.io/bcftools/bcftools.html#call
 description: Call variants with `bcftools call <https://samtools.github.io/bcftools/bcftools.html#call>`_.
 authors:
   - Johannes Köster
   - Michael Hall
+input:
+  - pileup: Path to input pileup file.
+output:
+  - calls: Path to calling results.
+params:
+  - caller: Either `--multiallelic-caller` or `--consensus-caller`
+  - options: Optional parameters

bio/bcftools/concat/meta.yaml

@@ -1,13 +1,14 @@
 name: bcftools concat
+url: https://www.htslib.org/doc/bcftools.html#concat
 description: Concatenate vcf/bcf files with bcftools. For more information see `BCFtools documentation <https://www.htslib.org/doc/bcftools.html#concat>`_.
 authors:
   - Johannes Köster
   - Filipe G. Vieira
 input:
-  - vcf files
+  - calls: list of vcf files
 output:
-  - Concatenated VCF/BCF file
-notes: |
-  * The `uncompressed_bcf` param allows to specify that a BCF output should be uncompressed (ignored otherwise).
-  * The `extra` param alllows for additional program arguments (not `--threads, `-O/--output-type`, `-m/--max-mem`, or `-T/--temp-dir`).
-  * For more information see, https://samtools.github.io/bcftools/bcftools.html
+  - Concatenated VCF/BCF file, must be the first file in output
+params:
+  - extra: Optional parameters (not `--threads, `-O/--output-type`, `-m/--max-mem`, or `-T/--temp-dir`)
+  - uncompressed_bcf: The `uncompressed_bcf` param allows to specify that a BCF output should be uncompressed (ignored otherwise).
+  - bcftools_use_mem: The `bcftools_use_mem` param controls whether to pass the resources.mem_mb to bcftools

bio/bcftools/filter/meta.yaml

@@ -1,14 +1,17 @@
 name: bcftools filter
+url: https://samtools.github.io/bcftools/bcftools.html#filter
 description: filter vcf/bcf file.
 authors:
   - Patrik Smeds
   - Nikos Tsardakas Renhuldt
 input:
-  - VCF/BCF file
+  - VCF/BCF file, must be the first in the input list
 output:
-  - Filtered VCF/BCF file
+  - Filtered VCF/BCF file, must be the only output
+params:
+  - extra: Optional parameters (not `--threads, `-O/--output-type`, `-m/--max-mem`, or `-T/--temp-dir`)
+  - filter: Filters, see `official bcftools expressions <https://samtools.github.io/bcftools/bcftools.html#expressions>`_ for more information.
+  - uncompressed_bcf: The `uncompressed_bcf` param allows to specify that a BCF output should be uncompressed (ignored otherwise).
+  - bcftools_use_mem: The `bcftools_use_mem` param controls whether to pass the resources.mem_mb to bcftools
 notes: |
-  * The `uncompressed_bcf` param allows to specify that a BCF output should be uncompressed (ignored otherwise).
-  * The `bcftools_use_mem` param controls whether to pass the resources.mem_mb to bcftools
-  * The `extra` param allows for additional program arguments (not `--threads, `-O/--output-type`, `-m/--max-mem`, or `-T/--temp-dir`).
-  * For more information see, https://samtools.github.io/bcftools/bcftools.html
+  * For more information see `tutorial <https://samtools.github.io/bcftools/howtos/filtering.html>`_

bio/bcftools/index/meta.yaml

@@ -1,4 +1,13 @@
 name: bcftools index
-description: Index vcf/bcf file. For more information see `BCFtools documentation <https://www.htslib.org/doc/bcftools.html#index>`_.
+url: https://samtools.github.io/bcftools/bcftools.html#index
+description: Index vcf/bcf file.
 authors:
   - Jan Forster
+input:
+  - Path to a VCF/BCF file, must be the first element of the input list.
+output:
+  - Path to the index.
+params:
+  - extra: Optional parameters
+notes: |
+  BCFTools indexes gzipped VCF files or BCF files. Raw, unzipped VCF files will raise an error.

bio/bcftools/merge/meta.yaml

@@ -1,4 +1,13 @@
 name: bcftools merge
-description: Merge vcf/bcf files with bcftools. For more information see `BCFtools documentation <https://www.htslib.org/doc/bcftools.html#merge>`_.
+url: https://samtools.github.io/bcftools/bcftools.html#index
+description: Merge vcf/bcf files with bcftools.
 authors:
   - Patrik Smeds
+intpu:
+  - calls: List of paths to VCF/BCF files.
+output:
+  - Merged VCF/BCF file, must be the first element in the output file list.
+params:
+  - Optional parameters, must be the first and only value in snakemake's params.
+notes: |
+  BCFTools will take longer to merge non-gzipped VCF files.

bio/bcftools/mpileup/meta.yaml

@@ -1,4 +1,13 @@
 name: bcftools mpileup
+url: https://samtools.github.io/bcftools/bcftools.html#mpileup
 description: Generate VCF or BCF containing genotype likelihoods for one or multiple alignment (BAM or CRAM) files with `bcftools mpileup <https://samtools.github.io/bcftools/bcftools.html#mpileup>`_.
 authors:
   - Michael Hall
+input:
+  - alignments: List of paths to bam-formatted almignments
+output:
+  - pileup: Path to pileup result file
+params:
+  - options: Optional parameters
+notes: |
+  Add --regions and --samples-files through params.options

bio/bcftools/norm/meta.yaml

@@ -1,5 +1,12 @@
 name: bcftools norm
+url: https://samtools.github.io/bcftools/bcftools.html#mpileup
 description: Left-align and normalize indels, check if REF alleles match the reference, split multiallelic sites into multiple rows; recover multiallelics from multiple rows. For more information see `BCFtools documentation <https://www.htslib.org/doc/bcftools.html#norm>`_.
 authors:
   - Dayne Filer
   - Filipe G. Vieira
+input:
+  - Path to gzipped VCF or BCF, must be the first in the input file list
+output:
+  - normalized VCF/BCF
+params:
+  - Optional parameters, ust be the first and only value in snakemake's params.

bio/bcftools/reheader/meta.yaml

@@ -1,4 +1,16 @@
 name: bcftools reheader
-description: Change header or sample names of vcf/bcf file. For more information see `BCFtools documentation <https://www.htslib.org/doc/bcftools.html#reheader>`_.
+url: https://samtools.github.io/bcftools/bcftools.html#mpileup
+description: Change header or sample names of vcf/bcf file.
 authors:
   - Jan Forster
+input:
+  - vcf: Path to vcf file
+  - header: Path to the new header (optional)
+  - samples: Path to the sample file (optional)
+output:
+  - reheaded vcf, must be the only output file
+params:
+  - extra: bcftools reheader optional parameters
+  - view_extra: bcftools view optional parameters
+notes: |
+  This wrapper requires at least two threads: one for bcftools reheader, one for bcftools view.

bio/bcftools/sort/meta.yaml

@@ -1,4 +1,12 @@
 name: bcftools sort
+url: https://www.htslib.org/doc/bcftools.html#sort
 description: Sort vcf/bcf file. For more information see `BCFtools documentation <https://www.htslib.org/doc/bcftools.html#sort>`_.
 authors:
   - Filipe G. Vieira
+input:
+  - VCF/BCF file, must be the first element of the input list
+output:
+  - VCF/BCF file, must be the first element of the output list
+params:
+  - extra: Optional parameters
+  - uncompressed_bcf: Boolean. Return uncompressed BCF file.

bio/bcftools/view/meta.yaml

@@ -1,14 +1,14 @@
 name: bcftools view
+url: https://samtools.github.io/bcftools/bcftools.html#view
 description: View vcf/bcf file in a different format.
 authors:
   - Johannes Köster
   - Nikos Tsardakas Renhuldt
 input:
-  - VCF/BCF file
+  - VCF/BCF file, must be the first in the input file list
 output:
-  - Filtered VCF/BCF file
-notes: |
-  * The `uncompressed_bcf` param allows to specify that a BCF output should be uncompressed (ignored otherwise).
-  * The `bcftools_use_mem` param controls whether to pass the resources.mem_mb to bcftools
-  * The `extra` param allows for additional program arguments (not `--threads, `-O/--output-type`, `-m/--max-mem`, or `-T/--temp-dir`).
-  * For more information see, https://samtools.github.io/bcftools/bcftools.html
+  - Filtered VCF/BCF file, must be the only element in the output file list
+params:
+  extra: The `extra` param allows for additional program arguments (not `--threads, `-O/--output-type`, `-m/--max-mem`, or `-T/--temp-dir`).
+  uncompressed_bcf: he `uncompressed_bcf` param allows to specify that a BCF output should be uncompressed (ignored otherwise).
+  bcftools_use_mem: The `bcftools_use_mem` param controls whether to pass the resources.mem_mb to bcftools

bio/bedtools/complement/meta.yaml

@@ -1,10 +1,13 @@
 name: bedtools complement
+url: https://bedtools.readthedocs.io/en/latest/content/tools/complement.html
 description: >
   `Bedtools complement <https://bedtools.readthedocs.io/en/latest/content/tools/complement.html>`_ maps all regions of the genome which are not covered by the input.
 authors:
   - Antonie Vietor
 input:
-  - BED/GFF/VCF files
-  - genome file (`genome file format <https://bedtools.readthedocs.io/en/latest/content/general-usage.html#genome-file-format>`_)
+  - in_file: BED/GFF/VCF files
+  - genome: genome file (`genome file format <https://bedtools.readthedocs.io/en/latest/content/general-usage.html#genome-file-format>`_)
 output:
-  - complemented BED/GFF/VCF file
+  - complemented BED/GFF/VCF file, must be the first element in the output list
+params:
+  - extra: Optional parameters

bio/bedtools/coveragebed/meta.yaml

@@ -1,6 +1,14 @@
 name: "coverageBed"
+url: https://bedtools.readthedocs.io/en/latest/content/tools/coverage.html
 description:
   Returns the depth and breadth of coverage of features from B
   on the intervals in A.
 authors:
   - Patrik Smeds
+input:
+  - a: BAM/BED/GFF/VCF file
+  - b: One or more BAM/BED/GFF/VCF file(s)
+output:
+  - Output coverage file, this must be the first element of the output file list.
+params:
+  - extra: Optional parameters, see `coverageBed official documentation <https://bedtools.readthedocs.io/en/latest/content/tools/coverage.html#usage-and-option-summary>`_ for more information.