task: Object representing a task, which is a wiring of a module...

In mskilab/Flow: Workflow and task management for genomics pipelines.

Object representing a task, which is a wiring of a module inputs and outputs to specific entity annotations names

Description

initializing Task requires Module object (or path to module file), and values for all arguments required by Task with literals or names of columns from which to populate eventual job data. also can specify default mem for task (can be changed at job level) output is a task configuration module can also be a text based task configuration file which will have the format: MODULE_PATH ( input [(annotation)|(literal)] VALUE ... ... output ANNOTATION_NAME REGEXP_FOR_FILE

ie first row is the module path, the next rows specify whether input or output is being specified in the first column, and if input, the second column specifies whether annotation or literal and third column specifis value otherwise for output, second column specifies the name of the output annotation and the third column specifies the regexp used to query the output directory for the output file

a task object is normally instantiated from a text .task file.

It wraps together Module, FlowLiteral, FlowOutput, and FlowAnnotation objects and can also be instantiated directly from them.

The task definition file has a header, pointer to a directory containing all the code necessary to run the module + a .deploy file (a la firehose .deploy), and inputs / outputs in a standard syntax.

Here is an example of a task definition for Jeremiah Wala's Snowman rearrangement detector

#Module Snowman ('<libdir>snow.sh <libdir>snowman_150410 run -t <tumor_bam> -n <normal_bam> -e <error_rate> -p ...') ~/modules/Snowman/ input tumor_bam Tumor_clean_bam_file_wgs path input normal_bam Normal_clean_bam_file_wgs path input error_rate '0' value input cpus '1' value input analysis_id pair_id value input panel_of_normals '/xchip/gistic/Jeremiah/Projects/Lung/lung_snow24_pon.txt.gz' path input indel_mask '/xchip/gistic/Jeremiah/Projects/HengLiMask/um75-hs37d5.bed.gz' path input flags '–no-r2c-bam' value output snowman_somatic_vcf .*DATECODE.somatic.sv.vcf output snowman_germline_vcf .*DATECODE.germline.sv.vcf output snowman_somatic_indel_vcf .*DATECODE.somatic.indel.vcf output snowman_germline_indel_vcf .*DATECODE.germline.indel.vcf

Usage

Task(...)

## S4 method for signature 'Job'
task(.Object)

Arguments

...	additional FlowLiteral or Flow Annotation boject
config	path to text based ".task" task config file or Module object
mem	memory limit to task (default 4)
name	name of task
libdir	libdir library / module directory
output	FlowOutput object or list of FlowOutput object

Author(s)

Marcin Imielinski

mskilab/Flow documentation built on Dec. 12, 2024, 4:25 p.m.