diff --git a/bio/bazam/meta.yaml b/bio/bazam/meta.yaml index 2abe5a5d517..1d2414bdd40 100644 --- a/bio/bazam/meta.yaml +++ b/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). diff --git a/bio/bedtools/bamtobed/meta.yaml b/bio/bedtools/bamtobed/meta.yaml index f8d341ee131..aa6e3825954 100644 --- a/bio/bedtools/bamtobed/meta.yaml +++ b/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. diff --git a/bio/bedtools/complement/meta.yaml b/bio/bedtools/complement/meta.yaml index b4b4f672f68..49a49a8da1a 100644 --- a/bio/bedtools/complement/meta.yaml +++ b/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. \ No newline at end of file diff --git a/bio/bedtools/coveragebed/meta.yaml b/bio/bedtools/coveragebed/meta.yaml index a4f2fd51749..796e3f7adde 100644 --- a/bio/bedtools/coveragebed/meta.yaml +++ b/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. diff --git a/bio/bedtools/genomecov/meta.yaml b/bio/bedtools/genomecov/meta.yaml index 91964b73cf9..ec4adb83bf4 100644 --- a/bio/bedtools/genomecov/meta.yaml +++ b/bio/bedtools/genomecov/meta.yaml @@ -7,5 +7,13 @@ authors: input: - BED/GFF/VCF files grouped by chromosome and genome file (`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. diff --git a/bio/bedtools/intersect/meta.yaml b/bio/bedtools/intersect/meta.yaml index 4b0befbd2a7..1f1199ae75c 100644 --- a/bio/bedtools/intersect/meta.yaml +++ b/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. diff --git a/bio/bedtools/merge/meta.yaml b/bio/bedtools/merge/meta.yaml index 4bf4fe8c164..ad55dd81827 100644 --- a/bio/bedtools/merge/meta.yaml +++ b/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. \ No newline at end of file diff --git a/bio/bedtools/slop/meta.yaml b/bio/bedtools/slop/meta.yaml index 94af30007ec..189dce5872a 100644 --- a/bio/bedtools/slop/meta.yaml +++ b/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. \ No newline at end of file diff --git a/bio/bedtools/sort/meta.yaml b/bio/bedtools/sort/meta.yaml index 9fb3b62532f..2be2c129a6b 100644 --- a/bio/bedtools/sort/meta.yaml +++ b/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.