flowcraft.generator.components.downloads module

class flowcraft.generator.components.downloads.ReadsDownload(**kwargs)[source]

Bases: flowcraft.generator.process.Process

Process template interface for reads downloading from SRA and NCBI

This process is set with:

  • input_type: accessions
  • output_type fastq
Attributes:
template_str

Class property that returns a populated template string

Methods

get_user_channel(self, input_channel[, …]) Returns the main raw channel for the process
render(template, context) Wrapper to the jinja2 render method from a template file
set_channels(self, \*\*kwargs) General purpose method that sets the main channels
set_main_channel_names(self, input_suffix, …) Sets the main channel names based on the provide input and output channel suffixes.
set_param_id(self, param_id) Sets the param_id for the process, which will be used to render the template.
set_secondary_channel(self, source, channel_list) General purpose method for setting a secondary channel
update_attributes(self, attr_dict) Updates the directives attribute from a dictionary object.
update_main_forks(self, sink) Updates the forks attribute with the sink channel destination
update_main_input  
class flowcraft.generator.components.downloads.FasterqDump(**kwargs)[source]

Bases: flowcraft.generator.process.Process

Process template for fasterq-dump

This process is set with:

  • input_type: accessions
  • output_type fastq
Attributes:
template_str

Class property that returns a populated template string

Methods

get_user_channel(self, input_channel[, …]) Returns the main raw channel for the process
render(template, context) Wrapper to the jinja2 render method from a template file
set_channels(self, \*\*kwargs) General purpose method that sets the main channels
set_main_channel_names(self, input_suffix, …) Sets the main channel names based on the provide input and output channel suffixes.
set_param_id(self, param_id) Sets the param_id for the process, which will be used to render the template.
set_secondary_channel(self, source, channel_list) General purpose method for setting a secondary channel
update_attributes(self, attr_dict) Updates the directives attribute from a dictionary object.
update_main_forks(self, sink) Updates the forks attribute with the sink channel destination
update_main_input