<commit_before># GGR-cwl
## CWL tools and workflows associated with the Genomics of Gene Regulation (GGR) project

[![Join the chat at https://gitter.im/alexbarrera/GGR-cwl](https://badges.gitter.im/alexbarrera/GGR-cwl.svg)](https://gitter.im/alexbarrera/GGR-cwl?utm_source=badge&utm_medium=badge&utm_campaign=pr-badge&utm_content=badge)

GGR pipelines created using the [Common Worflow Language](http://www.commonwl.org/) `draft-3` specification. 
The workflows are parametrized with values that best suit the GGR samples, 
   but they can be easily tailored for specific needs.

### [ChIP-seq](ChIP-seq_pipeline):

#### Pipelines
* [SE - Narrow](ChIP-seq_pipeline/pipeline-se-narrow.cwl)
* [SE - Narrow - w/control](ChIP-seq_pipeline/pipeline-se-narrow-with-control.cwl)
* [SE - Broad](ChIP-seq_pipeline/pipeline-se-broad.cwl)
* [SE - Broad - w/control](ChIP-seq_pipeline/pipeline-se-broad-with-control.cwl)
* [PE - Narrow](ChIP-seq_pipeline/pipeline-pe-narrow.cwl)
* [PE - Narrow - w/control](ChIP-seq_pipeline/pipeline-pe-narrow-with-control.cwl)
* [PE - Broad](ChIP-seq_pipeline/pipeline-pe-broad.cwl)
* [PE - Broad - w/control](ChIP-seq_pipeline/pipeline-pe-broad-with-control.cwl)

#### Steps
* 01 - Fastq QC step:
    * [Fastq QC step - SE](ChIP-seq_pipeline/01-qc-se.cwl)
    * [Fastq QC step - PE](ChIP-seq_pipeline/01-qc-pe.cwl)
* 02 - Trimming reads step:
    * [Trimming step - SE](ChIP-seq_pipeline/02-trim-se.cwl)
    * [Trimming step - PE](ChIP-seq_pipeline/02-trim-pe.cwl)
* 03 - Mapping step:
    * [Mapping step - SE](ChIP-seq_pipeline/03-map-se.cwl)
    * [Mapping step - PE](ChIP-seq_pipeline/03-map-pe.cwl)
* 04 - Peak calling step:
    * [Peak calling step - narrow](ChIP-seq_pipeline/04-peakcall-narrow.cwl)
    * [Peak calling step - narrow with control](ChIP-seq_pipeline/04-peakcall-narrow-with-control.cwl)
    * [Peak calling step - broad](ChIP-seq_pipeline/04-peakcall-broad.cwl)
    * [Peak calling step - broad with control](ChIP-seq_pipeline/04-peakcall-broad-with-control.cwl)
* 05 - [Quantification step](ChIP-seq_pipeline/05-quantification.cwl)


### [DNase-seq](DNase-seq_pipeline):

#### Pipelines
* [SE](DNase-seq_pipeline/pipeline-se.cwl)

#### Steps
* 01 - Mapping step:
    * 01 - [Mapping step - SE](DNase-seq_pipeline/01-map-se.cwl)
* 02 - Peak calling step:
    * 02 - [Peak calling step](DNase-seq_pipeline/02-peakcall.cwl)
* 03 - Quantification step:
    * 03 - [Quantification step](DNase-seq_pipeline/03-quantification.cwl)


### [RNA-seq](RNA-seq_pipeline):

#### Pipelines
* [PE - Unstranded](RNA-seq_pipeline/pipeline-pe-unstranded.cwl)
* [PE - Unstranded - w/sjdb](RNA-seq_pipeline/pipeline-pe-unstranded-with-sjdb.cwl)
* [PE - Stranded](RNA-seq_pipeline/pipeline-pe-stranded.cwl)
* [PE - Stranded - w/sjdb](RNA-seq_pipeline/pipeline-pe-stranded-with-sjdb.cwl)
* [PE - Revstranded](RNA-seq_pipeline/pipeline-pe-revstranded.cwl)
* [PE - Revstranded - w/sjdb](RNA-seq_pipeline/pipeline-pe-revstranded-with-sjdb.cwl)

#### Steps
* 00 - Genome files generation for STAR and RSEM:
    * 00 - [Preprocessing step](RNA-seq_pipeline/00-preprocessing.cwl)
* 01 - Fastq QC step:
    * 01 - [Fastq QC step - PE](RNA-seq_pipeline/01-qc-pe.cwl)
* 02 - Trimming reads step:
    * 02 - [Trimming step - PE](RNA-seq_pipeline/02-trim-pe.cwl)
* 03 - Mapping step:
    * 03 - [Mapping step - PE](RNA-seq_pipeline/03-map-pe.cwl)
    * 03 - [Mapping step - PE - w/sjdb](RNA-seq_pipeline/03-map-pe.cwl)
* 04 - Quantification step:
    * 04 - [Quantification step - PE - Unstranded](RNA-seq_pipeline/04-quantification-pe-unstranded.cwl)<commit_msg>Update README.md with reference to the wiki<commit_after># GGR-cwl

[![Join the chat at https://gitter.im/alexbarrera/GGR-cwl](https://badges.gitter.im/alexbarrera/GGR-cwl.svg)](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 Worflow Language](http://www.commonwl.org/) `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](https://github.com/Duke-GCB/GGR-cwl/wiki).

## [ChIP-seq](ChIP-seq_pipeline):

### Pipelines
* [SE - Narrow](ChIP-seq_pipeline/pipeline-se-narrow.cwl)
* [SE - Narrow - w/control](ChIP-seq_pipeline/pipeline-se-narrow-with-control.cwl)
* [SE - Broad](ChIP-seq_pipeline/pipeline-se-broad.cwl)
* [SE - Broad - w/control](ChIP-seq_pipeline/pipeline-se-broad-with-control.cwl)
* [PE - Narrow](ChIP-seq_pipeline/pipeline-pe-narrow.cwl)
* [PE - Narrow - w/control](ChIP-seq_pipeline/pipeline-pe-narrow-with-control.cwl)
* [PE - Broad](ChIP-seq_pipeline/pipeline-pe-broad.cwl)
* [PE - Broad - w/control](ChIP-seq_pipeline/pipeline-pe-broad-with-control.cwl)

### Steps
* 01 - Fastq QC step:
    * [Fastq QC step - SE](ChIP-seq_pipeline/01-qc-se.cwl)
    * [Fastq QC step - PE](ChIP-seq_pipeline/01-qc-pe.cwl)
* 02 - Trimming reads step:
    * [Trimming step - SE](ChIP-seq_pipeline/02-trim-se.cwl)
    * [Trimming step - PE](ChIP-seq_pipeline/02-trim-pe.cwl)
* 03 - Mapping step:
    * [Mapping step - SE](ChIP-seq_pipeline/03-map-se.cwl)
    * [Mapping step - PE](ChIP-seq_pipeline/03-map-pe.cwl)
* 04 - Peak calling step:
    * [Peak calling step - narrow](ChIP-seq_pipeline/04-peakcall-narrow.cwl)
    * [Peak calling step - narrow with control](ChIP-seq_pipeline/04-peakcall-narrow-with-control.cwl)
    * [Peak calling step - broad](ChIP-seq_pipeline/04-peakcall-broad.cwl)
    * [Peak calling step - broad with control](ChIP-seq_pipeline/04-peakcall-broad-with-control.cwl)
* 05 - [Quantification step](ChIP-seq_pipeline/05-quantification.cwl)


## [DNase-seq](DNase-seq_pipeline):

### Pipelines
* [SE](DNase-seq_pipeline/pipeline-se.cwl)

### Steps
* 01 - Mapping step:
    * 01 - [Mapping step - SE](DNase-seq_pipeline/01-map-se.cwl)
* 02 - Peak calling step:
    * 02 - [Peak calling step](DNase-seq_pipeline/02-peakcall.cwl)
* 03 - Quantification step:
    * 03 - [Quantification step](DNase-seq_pipeline/03-quantification.cwl)


## [RNA-seq](RNA-seq_pipeline):

### Pipelines
* [PE - Unstranded](RNA-seq_pipeline/pipeline-pe-unstranded.cwl)
* [PE - Unstranded - w/sjdb](RNA-seq_pipeline/pipeline-pe-unstranded-with-sjdb.cwl)
* [PE - Stranded](RNA-seq_pipeline/pipeline-pe-stranded.cwl)
* [PE - Stranded - w/sjdb](RNA-seq_pipeline/pipeline-pe-stranded-with-sjdb.cwl)
* [PE - Revstranded](RNA-seq_pipeline/pipeline-pe-revstranded.cwl)
* [PE - Revstranded - w/sjdb](RNA-seq_pipeline/pipeline-pe-revstranded-with-sjdb.cwl)

### Steps
* 00 - Genome files generation for STAR and RSEM:
    * 00 - [Preprocessing step](RNA-seq_pipeline/00-preprocessing.cwl)
* 01 - Fastq QC step:
    * 01 - [Fastq QC step - PE](RNA-seq_pipeline/01-qc-pe.cwl)
* 02 - Trimming reads step:
    * 02 - [Trimming step - PE](RNA-seq_pipeline/02-trim-pe.cwl)
* 03 - Mapping step:
    * 03 - [Mapping step - PE](RNA-seq_pipeline/03-map-pe.cwl)
    * 03 - [Mapping step - PE - w/sjdb](RNA-seq_pipeline/03-map-pe.cwl)
* 04 - Quantification step:
    * 04 - [Quantification step - PE - Unstranded](RNA-seq_pipeline/04-quantification-pe-unstranded.cwl)
{'fraction_non_alphanumeric': 0.15913771797336262, 'fraction_numerical': 0.023342029383495812, 'mean_word_length': 3.911665542818611, 'pattern_counts': {'":': 0, '<': 3, '<?xml version=': 0, '>': 3, 'https://': 7, 'lorem ipsum': 0, 'www.': 2, 'xml': 0}, 'pii_count': 0, 'substrings_counts': 0, 'word_list_counts': {'cursed_substrings.json': 0, 'profanity_word_list.json': 0, 'sexual_word_list.json': 0, 'zh_pornsignals.json': 0}}
{'dir': 'git-commits-cleaned', 'id': '4951516', 'n_tokens_mistral': 3011, 'n_tokens_neox': 2850, 'n_words': 464}