wtsi-hgi/GGR-cwl

Name: GGR-cwl

Owner: Wellcome Trust Sanger Institute - Human Genetics Informatics

Description: CWL tools and workflows for GGR

Forked from: Duke-GCB/GGR-cwl

Created: 2017-08-18 10:16:31.0

Updated: 2017-08-18 10:16:34.0

Pushed: 2017-08-18 15:04:11.0

Homepage: null

Size: 508

Language: Python

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README

GGR-cwl

CWL tools and workflows associated with the Genomics of Gene Regulation (GGR) project

GGR pipelines created using the Common Workflow Language draft-3 specification. The workflows are parametrized with values that best suit the GGR samples, but they can be easily tailored for specific needs.

For a detail User Guide to the CWL workflows, please see the wiki.

ChIP-seq:

Pipelines

• SE - Narrow
• SE - Narrow - w/control
• SE - Broad
• SE - Broad - w/control
• PE - Narrow
• PE - Narrow - w/control
• PE - Broad
• PE - Broad - w/control

Steps

• 01 - Fastq QC step:
  • Fastq QC step - SE
  • Fastq QC step - PE
• 02 - Trimming reads step:
  • Trimming step - SE
  • Trimming step - PE
• 03 - Mapping step:
  • Mapping step - SE
  • Mapping step - PE
• 04 - Peak calling step:
  • Peak calling step - narrow
  • Peak calling step - narrow with control
  • Peak calling step - broad
  • Peak calling step - broad with control
• 05 - Quantification step

DNase-seq:

Pipelines

• SE

Steps

• 01 - Mapping step:
  • 01 - Mapping step - SE
• 02 - Peak calling step:
  • 02 - Peak calling step
• 03 - Quantification step:
  • 03 - Quantification step

RNA-seq:

Pipelines

• SE - Unstranded
• SE - Unstranded - w/sjdb
• SE - Stranded
• SE - Stranded - w/sjdb
• SE - Revstranded
• SE - Revstranded - w/sjdb
• PE - Unstranded
• PE - Unstranded - w/sjdb
• PE - Stranded
• PE - Stranded - w/sjdb
• PE - Revstranded
• PE - Revstranded - w/sjdb

Steps

• 00 - Genome files generation for STAR and RSEM:
  • 00 - Preprocessing step
• 01 - Fastq QC step:
  • 01 - Fastq QC step - SE
  • 01 - Fastq QC step - PE
• 02 - Trimming reads step:
  • 02 - Trimming step - SE
  • 02 - Trimming step - PE
• 03 - Mapping step:
  • 03 - Mapping step - SE
  • 03 - Mapping step - SE - w/sjdb
  • 03 - Mapping step - PE
  • 03 - Mapping step - PE - w/sjdb
• 04 - Quantification step:
  • 04 - Quantification step - SE - Unstranded
  • 04 - Quantification step - SE - Stranded
  • 04 - Quantification step - SE - Revstranded
  • 04 - Quantification step - PE - Unstranded
  • 04 - Quantification step - PE - Stranded
  • 04 - Quantification step - PE - Revstranded

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Workflow differences legend

Depending on the experiments, there might be small differences in the workflows which will be determined by:

• All
  • Type of read:
    • SE: Single End reads
    • PE: Paired-End reads
• ChIP-seq & DNase-seq
  • Type of region targeted:
    • Narrow: Narrow (also known as Point-Source) peaks. Limited region bound (e.g. TFs).
    • Broad: Broad peaks. Wide region bound (e.g. Histone modifications)
• ChIP-seq only
  • With or without control. If a control sample is available -with-control or not.
• RNA-seq only
  • Strand specificity:
    • Unstranded: reads are not strand-specific, is not possible to know from which DNA strand they come.
    • Stranded: reads are strand-specific and can be map to the Watson and Crick strands.
    • Reverse Stranded: reads come from cDNA, which switches the mapping of the forward and reverse strand.
  • Custom SJDB: By default the STAR 2-pass mapping strategy is implemented in which a first pass of STAR is run to generate a large pool of novel splice junctions (referred as SJDB). These junctions are used to generate a genome index which is employed in the mapping step. However, this 2-pass strategy can be skipped, using a custom genome index Because typically this genome would be created with a precomputed SJDB, this option is denoted with -with-sjdb.