Explore Workflows

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

Path: tests/wf/scatterfail.cwl

Branch/Commit ID: 49cd284a8fc7884de763573075d3e1d6a4c1ffdd

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

Path: testdata/count-lines7-wf_v1_2.cwl

Branch/Commit ID: c1875d54dedc41b1d2fa08634dcf1caa8f1bc631

Creates indices for: * [STAR](https://github.com/alexdobin/STAR) v2.5.3a (03/17/2017) PMID: [23104886](https://www.ncbi.nlm.nih.gov/pubmed/23104886) * [bowtie](http://bowtie-bio.sourceforge.net/tutorial.shtml) v1.2.0 (12/30/2016) It performs the following steps: 1. `STAR --runMode genomeGenerate` to generate indices, based on [FASTA](http://zhanglab.ccmb.med.umich.edu/FASTA/) and [GTF](http://mblab.wustl.edu/GTF2.html) input files, returns results as an array of files 2. Outputs indices as [Direcotry](http://www.commonwl.org/v1.0/CommandLineTool.html#Directory) data type 3. Separates *chrNameLength.txt* file from Directory output 4. `bowtie-build` to generate indices requires genome [FASTA](http://zhanglab.ccmb.med.umich.edu/FASTA/) file as input, returns results as a group of main and secondary files

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

Path: workflows/genome-indices.cwl

Branch/Commit ID: 5561f7ee11dd74848680351411a19aa87b13d27b

Differential gene expression analysis ===================================== Differential gene expression analysis based on the negative binomial distribution Estimate variance-mean dependence in count data from high-throughput sequencing assays and test for differential expression based on a model using the negative binomial distribution. DESeq1 ------ High-throughput sequencing assays such as RNA-Seq, ChIP-Seq or barcode counting provide quantitative readouts in the form of count data. To infer differential signal in such data correctly and with good statistical power, estimation of data variability throughout the dynamic range and a suitable error model are required. Simon Anders and Wolfgang Huber propose a method based on the negative binomial distribution, with variance and mean linked by local regression and present an implementation, [DESeq](http://bioconductor.org/packages/release/bioc/html/DESeq.html), as an R/Bioconductor package DESeq2 ------ In comparative high-throughput sequencing assays, a fundamental task is the analysis of count data, such as read counts per gene in RNA-seq, for evidence of systematic changes across experimental conditions. Small replicate numbers, discreteness, large dynamic range and the presence of outliers require a suitable statistical approach. [DESeq2](http://www.bioconductor.org/packages/release/bioc/html/DESeq2.html), a method for differential analysis of count data, using shrinkage estimation for dispersions and fold changes to improve stability and interpretability of estimates. This enables a more quantitative analysis focused on the strength rather than the mere presence of differential expression.

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

Path: workflows/deseq.cwl

Branch/Commit ID: 730b40bc403263b724399a952c0f3e2d28f13519

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

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

Branch/Commit ID: c6cced7a2e6389d2eb43342e702677ccb7c7497c

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

Path: cwltool/schemas/v1.0/v1.0/scatter-valuefrom-wf1.cwl

Branch/Commit ID: b82ce7ae901a54c7a062fd5eefd8d5ceb5a4d684

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

Path: tests/scatter-wf1.cwl

Branch/Commit ID: a5073143db4155e05df8d2e7eb59d9e62acd65a5

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

Path: task_types/tt_blastp_wnode_struct.cwl

Branch/Commit ID: 55b6ee46b0c9fb1c9949cd0888b388c6f11b73b1

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

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

Branch/Commit ID: bfe56f3138e9e6fc0b9b8c06447553d4cea03d59

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

Path: tests/io-int-default-tool-and-wf.cwl

Branch/Commit ID: e62f99dd79d6cb9c157cceb458f74200da84f6e9