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GGR-cwl
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CWL tools and workflows for GGR
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# GGR-cwl [](https://gitter.im/alexbarrera/GGR-cwl?utm_source=badge&utm_medium=badge&utm_campaign=pr-badge&utm_content=badge) CWL tools and workflows associated with the Genomics of Gene Regulation (GGR) project GGR pipelines created using the [Common Workflow Language](http://www.commonwl.org/) `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](https://github.com/Duke-GCB/GGR-cwl/wiki). If you need help navigating the files generated by the pipelines, have a look at the [processed files cheatsheet](v1.0/processed_output_files_help.tsv). ## [ChIP-seq](v1.0/ChIP-seq_pipeline): ### Pipelines * [SE](v1.0/ChIP-seq_pipeline/pipeline-se.cwl) * [SE - w/control](v1.0/ChIP-seq_pipeline/pipeline-se-with-control.cwl) * [PE](v1.0/ChIP-seq_pipeline/pipeline-pe.cwl) * [PE - w/control](v1.0/ChIP-seq_pipeline/pipeline-pe-with-control.cwl) ### Steps * 01 - Fastq QC step: * [Fastq QC step - SE](v1.0/ChIP-seq_pipeline/01-qc-se.cwl) * [Fastq QC step - PE](v1.0/ChIP-seq_pipeline/01-qc-pe.cwl) * 02 - Trimming reads step: * [Trimming step - SE](v1.0/ChIP-seq_pipeline/02-trim-se.cwl) * [Trimming step - PE](v1.0/ChIP-seq_pipeline/02-trim-pe.cwl) * 03 - Mapping step: * [Mapping step - SE](v1.0/ChIP-seq_pipeline/03-map-se.cwl) * [Mapping step - PE](v1.0/ChIP-seq_pipeline/03-map-pe.cwl) * 04 - Peak calling step: * [Peak calling step](v1.0/ChIP-seq_pipeline/04-peakcall.cwl) * [Peak calling step - with control](v1.0/ChIP-seq_pipeline/04-peakcall-with-control.cwl) * 05 - Quantification step: * [Quantification step](v1.0/ChIP-seq_pipeline/05-quantification.cwl) * [Quantification step - with control](v1.0/ChIP-seq_pipeline/05-quantification-with-control.cwl) ## [DNase-seq](v1.0/DNase-seq_pipeline): ### Pipelines * [SE](v1.0/DNase-seq_pipeline/pipeline-se.cwl) ### Steps * 01 - Mapping step: * 01 - [Mapping step - SE](v1.0/DNase-seq_pipeline/01-map-se.cwl) * 02 - Peak calling step: * 02 - [Peak calling step](v1.0/DNase-seq_pipeline/02-peakcall.cwl) * 03 - Quantification step: * 03 - [Quantification step](v1.0/DNase-seq_pipeline/03-quantification.cwl) ## [RNA-seq](v1.0/RNA-seq_pipeline): ### Pipelines * [SE - Unstranded](v1.0/RNA-seq_pipeline/pipeline-se-unstranded.cwl) * [SE - Unstranded - w/sjdb](v1.0/RNA-seq_pipeline/pipeline-se-unstranded-with-sjdb.cwl) * [SE - Stranded](v1.0/RNA-seq_pipeline/pipeline-se-stranded.cwl) * [SE - Stranded - w/sjdb](v1.0/RNA-seq_pipeline/pipeline-se-stranded-with-sjdb.cwl) * [SE - Revstranded](v1.0/RNA-seq_pipeline/pipeline-se-revstranded.cwl) * [SE - Revstranded - w/sjdb](v1.0/RNA-seq_pipeline/pipeline-se-revstranded-with-sjdb.cwl) * [PE - Unstranded](v1.0/RNA-seq_pipeline/pipeline-pe-unstranded.cwl) * [PE - Unstranded - w/sjdb](v1.0/RNA-seq_pipeline/pipeline-pe-unstranded-with-sjdb.cwl) * [PE - Stranded](v1.0/RNA-seq_pipeline/pipeline-pe-stranded.cwl) * [PE - Stranded - w/sjdb](v1.0/RNA-seq_pipeline/pipeline-pe-stranded-with-sjdb.cwl) * [PE - Revstranded](v1.0/RNA-seq_pipeline/pipeline-pe-revstranded.cwl) * [PE - Revstranded - w/sjdb](v1.0/RNA-seq_pipeline/pipeline-pe-revstranded-with-sjdb.cwl) ### Steps * 00 - Genome files generation for STAR and RSEM: * 00 - [Preprocessing step](v1.0/RNA-seq_pipeline/00-preprocessing.cwl) * 01 - Fastq QC step: * 01 - [Fastq QC step - SE](v1.0/RNA-seq_pipeline/01-qc-se.cwl) * 01 - [Fastq QC step - PE](v1.0/RNA-seq_pipeline/01-qc-pe.cwl) * 02 - Trimming reads step: * 02 - [Trimming step - SE](v1.0/RNA-seq_pipeline/02-trim-se.cwl) * 02 - [Trimming step - PE](v1.0/RNA-seq_pipeline/02-trim-pe.cwl) * 03 - Mapping step: * 03 - [Mapping step - SE](v1.0/RNA-seq_pipeline/03-map-se.cwl) * 03 - [Mapping step - SE - w/sjdb](v1.0/RNA-seq_pipeline/03-map-se-with-sjdb.cwl) * 03 - [Mapping step - PE](v1.0/RNA-seq_pipeline/03-map-pe.cwl) * 03 - [Mapping step - PE - w/sjdb](v1.0/RNA-seq_pipeline/03-map-pe-with-sjdb.cwl) * 04 - Quantification step: * 04 - [Quantification step - SE - Unstranded](v1.0/RNA-seq_pipeline/04-quantification-se-unstranded.cwl) * 04 - [Quantification step - SE - Stranded](v1.0/RNA-seq_pipeline/04-quantification-se-stranded.cwl) * 04 - [Quantification step - SE - Revstranded](v1.0/RNA-seq_pipeline/04-quantification-se-revstranded.cwl) * 04 - [Quantification step - PE - Unstranded](v1.0/RNA-seq_pipeline/04-quantification-pe-unstranded.cwl) * 04 - [Quantification step - PE - Stranded](v1.0/RNA-seq_pipeline/04-quantification-pe-stranded.cwl) * 04 - [Quantification step - PE - Revstranded](v1.0/RNA-seq_pipeline/04-quantification-pe-revstranded.cwl) ## [ATAC-seq](v1.0/ATAC-seq_pipeline): ### Pipelines * [SE](v1.0/ATAC-seq_pipeline/pipeline-se.cwl) * [SE - Blacklist Removal](v1.0/ATAC-seq_pipeline/pipeline-se-blacklist-removal.cwl) * [PE](v1.0/ATAC-seq_pipeline/pipeline-pe.cwl) * [PE - Blacklist Removal](v1.0/ATAC-seq_pipeline/pipeline-pe-blacklist-removal.cwl) ### Steps * 01 - Fastq QC step: * [Fastq QC step - SE](v1.0/ATAC-seq_pipeline/01-qc-se.cwl) * [Fastq QC step - PE](v1.0/ATAC-seq_pipeline/01-qc-pe.cwl) * 02 - Trimming reads step: * [Trimming step - SE](v1.0/ATAC-seq_pipeline/02-trim-se.cwl) * [Trimming step - PE](v1.0/ATAC-seq_pipeline/02-trim-pe.cwl) * 03 - Mapping step: * [Mapping step - SE](v1.0/ATAC-seq_pipeline/03-map-se.cwl) * [Mapping step - SE - Blacklist Removal](v1.0/ATAC-seq_pipeline/03-map-se-blacklist-removal.cwl) * [Mapping step - PE](v1.0/ATAC-seq_pipeline/03-map-pe.cwl) * [Mapping step - PE - Blacklist Removal](v1.0/ATAC-seq_pipeline/03-map-pe-blacklist-removal.cwl) * 04 - Peak calling step: * [Peak calling step - SE](v1.0/ATAC-seq_pipeline/04-peakcall-se.cwl) * [Peak calling step - PE](v1.0/ATAC-seq_pipeline/04-peakcall-pe.cwl) * 05 - Quantification step: * [Quantification step](v1.0/ATAC-seq_pipeline/05-quantification.cwl) ## [STARR-seq](v1.0/STARR-seq_pipeline): ### Pipelines * [PE](v1.0/STARR-seq_pipeline/pipeline-pe.cwl) * [PE - UMIs](v1.0/STARR-seq_pipeline/pipeline-pe-umis.cwl) ### Steps * 01 - Fastq QC step: * [Fastq QC step - PE](v1.0/STARR-seq_pipeline/01-qc-pe.cwl) * 02 - Trimming reads step: * [Trimming step - PE](v1.0/STARR-seq_pipeline/02-trim-pe.cwl) * 03 - Mapping step: * [Mapping step - PE](v1.0/STARR-seq_pipeline/03-map-pe.cwl) * [Mapping step - PE - UMIs](v1.0/STARR-seq_pipeline/03-map-pe-umis.cwl) * 04 - Quantification step: * [Quantification step](v1.0/STARR-seq_pipeline/04-quantification.cwl) ---------------------------------------------------------------------------------------------------------- ##### 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 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.
