Explore Workflows

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

Path: definitions/subworkflows/phase_vcf.cwl

Branch/Commit ID: 735be84cdea041fcc8bd8cbe5728b29ca3586a21

Cell Ranger ATAC Count Counts reads from a single scATAC-Seq library

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

Path: workflows/cellranger-atac-count.cwl

Branch/Commit ID: 7030da528559c7106d156284e50ff0ecedab0c4e

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

Path: definitions/pipelines/alignment_wgs_mouse.cwl

Branch/Commit ID: 22fce2dbdada0c4135b6f0677f78535cf980cb07

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

Path: cwltool/schemas/v1.0/v1.0/count-lines1-wf.cwl

Branch/Commit ID: 7c7615c44b80f8e76e659433f8c7875603ae0b25

Modified original [BioWardrobe's](https://biowardrobe.com) [PubMed ID:26248465](https://www.ncbi.nlm.nih.gov/pubmed/26248465) **RNA-Seq** basic analysis for a **pair-end** experiment. A corresponded input [FASTQ](http://maq.sourceforge.net/fastq.shtml) file has to be provided. Current workflow should be used only with the single-end RNA-Seq data. It performs the following steps: 1. Trim adapters from input FASTQ files 2. Use STAR to align reads from input FASTQ files according to the predefined reference indices; generate unsorted BAM file and alignment statistics file 3. Use fastx_quality_stats to analyze input FASTQ files and generate quality statistics files 4. Use samtools sort to generate coordinate sorted BAM(+BAI) file pair from the unsorted BAM file obtained on the step 1 (after running STAR) 5. Generate BigWig file on the base of sorted BAM file 6. Map input FASTQ files to predefined rRNA reference indices using Bowtie to define the level of rRNA contamination; export resulted statistics to file 7. Calculate isoform expression level for the sorted BAM file and GTF/TAB annotation file using GEEP reads-counting utility; export results to file

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

Path: workflows/trim-rnaseq-pe-dutp.cwl

Branch/Commit ID: ebbf23764ede324cabc064bd50647c1f643726fa

Deprecated. Single-cell Differential Expression =============================================== Runs differential expression analysis for a subset of cells between two selected conditions.

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

Path: workflows/sc_diff_expr.cwl

Branch/Commit ID: 7030da528559c7106d156284e50ff0ecedab0c4e

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

Path: definitions/pipelines/aml_trio_cle.cwl

Branch/Commit ID: 42c66dd24ce5026d3f717214ddb18b7b4fae93cf

Runs RNA-Seq BioWardrobe basic analysis with pair-end data file.

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

Path: workflows/rnaseq-pe.cwl

Branch/Commit ID: ca2dbb71d0537b1d93a8bd44719250cf8949b157

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

Path: tests/wf/mut3.cwl

Branch/Commit ID: 49cd284a8fc7884de763573075d3e1d6a4c1ffdd

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

Path: tests/wf/count-lines1-wf.cwl

Branch/Commit ID: 5ae5798f1c0c8d2178986b77cfd74edff510877a