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module config.models

Configuration models.

class CustomBaseModel

Base model that all other models derive from.

class InitUser

User-specific parameters for initialization.

Args:

  • author: Name of the person running the analysis.
  • email: Email address of the person running the analysis.
  • logo: Path or URL pointing to image file to be used as a logo in the run report.
  • url: A URL with additional information about the author or their affiliation.

Attributes:

  • author: Name of the person running the analysis.
  • email: Email address of the person running the analysis.
  • logo: Path or URL pointing to image file to be used as a logo in the run report.
  • url: A URL with additional information about the author or their affiliation.

class InitRun

Run-specific parameters for initialization.

Args:

  • cores: Cores to be used by the workflow engine.
  • dependency_embedding: Dependency embedding strategy to use.
  • execution_mode: Execution mode to use.
  • genome_assemblies_map: Genome assemblies mapping file.
  • profile: Snakemake profile for ZARP workflow.
  • resources_version: Version of Ensembl genome resources to use when resources are not provided.
  • rule_config: ZARP rule configuration.
  • working_directory: Root directory for all runs.
  • zarp_directory: Root directory of the ZARP repository.

Attributes:

  • cores: Cores to be used by the workflow engine.
  • dependency_embedding: Dependency embedding strategy to use.
  • execution_mode: Execution mode to use.
  • genome_assemblies_map: Genome assemblies mapping file.
  • profile: Snakemake profile for ZARP workflow.
  • resources_version: Version of Ensembl genome resources to use when resources are not provided.
  • rule_config: ZARP rule configuration.
  • working_directory: Root directory for all runs.
  • zarp_directory: Root directory of the ZARP repository.

class InitSample

Sample-specific parameters for initialization.

Args:

  • fragment_length_distribution_mean: Mean of the fragment length distribution.
  • fragment_length_distribution_sd: Standard deviation of the fragment length distribution.

Attributes:

  • fragment_length_distribution_mean: Mean of the fragment length distribution.
  • fragment_length_distribution_sd: Standard deviation of the fragment length distribution.

class InitConfig

ZARP-cli user default configuration set during initialization.

Args:

  • run: Run-specific parameters.
  • sample: Sample-specific parameters.
  • user: User-specific parameters.

Attributes:

  • run: Run-specific parameters.
  • sample: Sample-specific parameters.
  • user: User-specific parameters.

class ConfigUser

User-specific parameters.

class ConfigRun

Run-specific parameters.

Args:

  • description: Run description.
  • genome_assemblies_map: Genome assemblies mapping file.
  • identifier: Unique identifier for a run.
  • zarp_directory: Root directory of the ZARP repository.

Attributes:

  • description: Run description.
  • genome_assemblies_map: Genome assemblies mapping file.
  • identifier: Unique identifier for a run.
  • zarp_directory: Root directory of the ZARP repository.

classmethod get_identifier

get_identifier(identifier: str) → str

Get default identifier.

class ConfigSample

Sample-specific parameters.

Args:

  • adapter_3p: Tuple of adapter sequences to truncate from the 3'-ends of single-end/first and second mate libraries, respectively.
  • adapter_5p: Tuple of adapter sequences to truncate from the 5'-ends of single-end/first and second mate libraries, respectively.
  • adapter_poly_3p: Tuple of polynucleotide stretch sequences to truncate from the 3'-ends of single-end/first and second mate libraries, respectively.
  • adapter_poly_5p: Tuple of polynucleotide stretch sequences to truncate from the 3'-ends of single-end/first and second mate libraries, respectively.
  • annotations: Path to GTF file containing gene annotations for the reference_sequences.
  • read_orientation: Orientation of reads in sequencing library. Cf.
  • https: //salmon.readthedocs.io/en/latest/library_type.html.
  • reference_sequences: Path to FASTA file containing reference sequences to align reads against, typically chromosome sequences.
  • source: Origin of the sample as either a NCBI taxonomy database identifier, e.g, 9606 for humans, or the corresponding full name, e.g., "Homo sapiens".
  • star_sjdb_overhang: Overhang length for splice junctions in STAR ( parameter sjdbOverhang). Ideally the maximum read length minus 1. Lower values may result in decreased mapping accuracy, while higher values may result in longer processing times. Cf.
  • https: //github.com/alexdobin/STAR/blob/3ae0966bc604a944b1993f49aaeb597e809eb5c9/doc/STARmanual.pdf
  • salmon_kmer_size: Size of k-mers for building the Salmon index. The default value typically works fine for reads of 75 bp or longer. Consider using lower values if dealing with shorter reads. Cf.
  • https: //salmon.readthedocs.io/en/latest/salmon.html#preparing-transcriptome-indices-mapping-based-mode

Attributes:

  • adapter_3p: Tuple of adapter sequences to truncate from the 3'-ends of single-end/first and second mate libraries, respectively.
  • adapter_5p: Tuple of adapter sequences to truncate from the 5'-ends of single-end/first and second mate libraries, respectively.
  • adapter_poly_3p: Tuple of polynucleotide stretch sequences to truncate from the 3'-ends of single-end/first and second mate libraries, respectively.
  • adapter_poly_5p: Tuple of polynucleotide stretch sequences to truncate from the 3'-ends of single-end/first and second mate libraries, respectively.
  • annotations: Path to GTF file containing gene annotations for the reference_sequences.
  • read_orientation: Orientation of reads in sequencing library. Cf.
  • https: //salmon.readthedocs.io/en/latest/library_type.html.
  • reference_sequences: Path to FASTA file containing reference sequences to align reads against, typically chromosome sequences.
  • source: Origin of the sample as either a NCBI taxonomy database identifier, e.g, 9606 for humans, or the corresponding full name, e.g., "Homo sapiens".
  • star_sjdb_overhang: Overhang length for splice junctions in STAR ( parameter sjdbOverhang). Ideally the maximum read length minus 1. Lower values may result in decreased mapping accuracy, while higher values may result in longer processing times. Cf.
  • https: //github.com/alexdobin/STAR/blob/3ae0966bc604a944b1993f49aaeb597e809eb5c9/doc/STARmanual.pdf
  • salmon_kmer_size: Size of k-mers for building the Salmon index. The default value typically works fine for reads of 75 bp or longer. Consider using lower values if dealing with shorter reads. Cf.
  • https: //salmon.readthedocs.io/en/latest/salmon.html#preparing-transcriptome-indices-mapping-based-mode

class Config

ZARP-cli main configuration.

Args:

  • ref: References to individual sequencing libraries by local file path or read archive identifiers OR paths to ZARP sample tables; see documentation for details.
  • run: Run-specific parameters.
  • sample: Sample-specific parameters.
  • user: User-specific parameters.

Attributes:

  • ref: References to individual sequencing libraries by local file path or read archive identifiers OR paths to ZARP sample tables; see documentation for details.
  • run: Run-specific parameters.
  • sample: Sample-specific parameters.
  • user: User-specific parameters.

class SampleReference

Sample reference information.

Args:

  • identifier: Read archive identifier.
  • lib_paths: Path (single-ended) or paths (paired-ended) to files containing sequencing reads.
  • name: Sample name.
  • ref: References to individual sequencing libraries by local file path or read archive identifiers OR paths to ZARP sample tables; see documentation for details.
  • table_path: Path to ZARP sample table.
  • type: Type of sample reference.

Attributes:

  • identifier: Read archive identifier.
  • lib_paths: Path (single-ended) or paths (paired-ended) to files containing sequencing reads.
  • name: Sample name.
  • ref: References to individual sequencing libraries by local file path or read archive identifiers OR paths to ZARP sample tables; see documentation for details.
  • table_path: Path to ZARP sample table.
  • type: Type of sample reference.

class Sample

Sample-specific parameters.

Args:

  • type: Type of sample, local (single/paired) or remote.
  • identifier: Read archive identifier.
  • name: Sample name; if not provided, a sample name will be set based on the input file name or read archive identifier.
  • paths: Path (single-ended) or paths (paired-ended) to files containing sequencing reads.

Attributes:

  • type: Type of sample, local (single/paired) or remote.
  • identifier: Read archive identifier.
  • name: Sample name; if not provided, a sample name will be set based on the input file name or read archive identifier.
  • paths: Path (single-ended) or paths (paired-ended) to files containing sequencing reads.

class ConfigFileContent

Snakemake configuration file content.

class ConfigFileSRA

SRA download workflow configuration file content.

Args:

  • cluster_log_dir: Path to cluster log directory.
  • log_dir: Path to log directory.
  • outdir: Path to output directory.
  • samples: Path to sample table.
  • samples_out: Path to output sample table.

Attributes:

  • cluster_log_dir: Path to cluster log directory.
  • log_dir: Path to log directory.
  • outdir: Path to output directory.
  • samples: Path to sample table.
  • samples_out: Path to output sample table.

class ConfigFileHTSinfer

HTSinfer workflow configuration file content.

Args:

  • cluster_log_dir: Path to cluster log directory.
  • log_dir: Path to log directory.
  • samples: Path to sample table.
  • outdir: Path to output directory.
  • samples_out: Path to output sample table.

Attributes:

  • cluster_log_dir: Path to cluster log directory.
  • log_dir: Path to log directory.
  • samples: Path to sample table.
  • outdir: Path to output directory.
  • samples_out: Path to output sample table.

class ConfigFileZARP

ZARP workflow configuration file content.

Args:

  • samples: Path to sample table.
  • output_dir: Path to output directory.
  • log_dir: Path to log directory.
  • cluster_log_dir: Path to cluster log directory.
  • kallisto_indexes: Path to kallisto indexes.
  • salmon_indexes: Path to Salmon indexes.
  • star_indexes: Path to STAR indexes.
  • alfa_indexes: Path to ALFA indexes.
  • rule_config: Path to ZARP rule configuration.
  • report_description: Run report description.
  • report_logo: Path or URL pointing to image file to be used as a logo for the run report.
  • report_url: URL to link to from the run report.
  • author_name: Name of the person running the analysis.
  • author_email: Email address of the person running the analysis.

Attributes:

  • samples: Path to sample table.
  • output_dir: Path to output directory.
  • log_dir: Path to log directory.
  • cluster_log_dir: Path to cluster log directory.
  • kallisto_indexes: Path to kallisto indexes.
  • salmon_indexes: Path to Salmon indexes.
  • star_indexes: Path to STAR indexes.
  • alfa_indexes: Path to ALFA indexes.
  • report_description: Run report description.
  • report_logo: Path or URL pointing to image file to be used as a logo for the run report.
  • report_url: URL to link to from the run report.
  • author_name: Name of the person running the analysis.
  • author_email: Email address of the person running the analysis.