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

GGR pipelines created using the Common Workflow Language v1.0 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.

If you need help navigating the files generated by the pipelines, have a look at the processed files cheatsheet.

• SE
• SE - w/control
• PE
• PE - w/control

• 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
  • Peak calling step - with control
• 05 - Quantification step:
  • Quantification step
  • Quantification step - with control

• SE

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

• 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

• 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

• SE
• SE - Blacklist Removal
• PE
• PE - Blacklist Removal

• 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 - SE - Blacklist Removal
  • Mapping step - PE
  • Mapping step - PE - Blacklist Removal
• 04 - Peak calling step:
  • Peak calling step - SE
  • Peak calling step - PE
• 05 - Quantification step:
  • Quantification step

• PE
• PE - UMIs

• 01 - Fastq QC step:
  • Fastq QC step - PE
• 02 - Trimming reads step:
  • Trimming step - PE
• 03 - Mapping step:
  • Mapping step - PE
  • Mapping step - PE - UMIs
• 04 - Quantification step:
  • Quantification step

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 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.
• ATAC-seq only
  • Blacklist removal: whether or not to mask out blacklisted regions.