Explore Workflows

Genomic regions intersection and visualization ============================================== 1. Merges intervals within each of the filtered peaks files from ChIP/ATAC experiments 2. Overlaps merged intervals and assigns the nearest genes to them

https://github.com/datirium/workflows.git

Path: workflows/intervene.cwl

Branch/Commit ID: 30031ca5e69cec603c4733681de54dc7bffa20a3

FastQC - a quality control tool for high throughput sequence data ===================================== FastQC aims to provide a simple way to do some quality control checks on raw sequence data coming from high throughput sequencing pipelines. It provides a modular set of analyses which you can use to give a quick impression of whether your data has any problems of which you should be aware before doing any further analysis. The main functions of FastQC are: - Import of data from FastQ files (any variant) - Providing a quick overview to tell you in which areas there may be problems - Summary graphs and tables to quickly assess your data - Export of results to an HTML based permanent report - Offline operation to allow automated generation of reports without running the interactive application

https://github.com/datirium/workflows.git

Path: workflows/fastqc.cwl

Branch/Commit ID: 30031ca5e69cec603c4733681de54dc7bffa20a3

Workflow maps FASTQ files from `fastq_files` input into reference genome `reference_star_indices_folder` and insilico generated `insilico_star_indices_folder` genome (concatenated genome for both `strain1` and `strain2` strains). For both genomes STAR is run with `outFilterMultimapNmax` parameter set to 1 to discard all of the multimapped reads. For insilico genome SAM file is generated. Then it's splitted into two SAM files based on strain names and then sorted by coordinates into the BAM format. For reference genome output BAM file from STAR slignment is also coordinate sorted.

https://github.com/Barski-lab/workflows.git

Path: subworkflows/allele-alignreads-se-pe.cwl

Branch/Commit ID: afbec98437a7796a509fffbad8c3370aa099f059

https://github.com/common-workflow-language/cwltool.git

Path: cwltool/schemas/v1.0/v1.0/scatter-valuefrom-wf2.cwl

Branch/Commit ID: beab66d649dd3ee82a013322a5e830875e8556ba

https://github.com/ncbi/pgap.git

Path: task_types/tt_gcaccess_from_list.cwl

Branch/Commit ID: 49732e54e2fe2eafd2f82df3c482c73e642f6d64

https://github.com/common-workflow-language/cwl-v1.2.git

Path: tests/count-lines11-wf.cwl

Branch/Commit ID: e62f99dd79d6cb9c157cceb458f74200da84f6e9

https://github.com/common-workflow-language/cwltool.git

Path: cwltool/schemas/v1.0/v1.0/conflict-wf.cwl

Branch/Commit ID: 4a31f2a1c1163492ae37bbc748a299e8318c462c

Packed ID: collision

https://github.com/genome/analysis-workflows.git

Path: definitions/subworkflows/single_cell_rnaseq.cwl

Branch/Commit ID: 93656ed6582073e434eab168c610625a835dce37

https://github.com/common-workflow-language/common-workflow-language.git

Path: v1.0/v1.0/echo-wf-default.cwl

Branch/Commit ID: 17695244222b0301b37cb749fe4a8d89622cd1ad

https://github.com/common-workflow-language/cwltool.git

Path: cwltool/schemas/v1.0/v1.0/any-type-compat.cwl

Branch/Commit ID: 203797516329f7fb8aa5e763e6f9b331c63c3060