Explore Workflows

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Graph Name Retrieved From View
workflow graph PCA - Principal Component Analysis

Principal Component Analysis --------------- Principal component analysis (PCA) is a statistical procedure that uses an orthogonal transformation to convert a set of observations of possibly correlated variables (entities each of which takes on various numerical values) into a set of values of linearly uncorrelated variables called principal components. The calculation is done by a singular value decomposition of the (centered and possibly scaled) data matrix, not by using eigen on the covariance matrix. This is generally the preferred method for numerical accuracy.

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

Path: workflows/pca.cwl

Branch/Commit ID: 675a3ff982091faf304931e9261aacdbabf51702
workflow graph dynresreq-workflow-tooldefault.cwl

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

Path: tests/dynresreq-workflow-tooldefault.cwl

Branch/Commit ID: 31ec48a8d81ef7c1b2c5e9c0a19e7623efe4a1e2
workflow graph steplevel-resreq.cwl

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

Path: cwltool/schemas/v1.0/v1.0/steplevel-resreq.cwl

Branch/Commit ID: b82ce7ae901a54c7a062fd5eefd8d5ceb5a4d684
workflow graph main.cwl

https://github.com/CLAIRE-COVID/AI-Covid19-pipelines.git

Path: offline/streamflow/cwl/main.cwl

Branch/Commit ID: e2c8ee3c187cb951066909296ead46b784cd2dee
workflow graph Single-Cell Preprocessing Cell Ranger Pipeline

Devel version of Single-Cell Preprocessing Cell Ranger Pipeline ===============================================================

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

Path: workflows/single-cell-preprocess-cellranger.cwl

Branch/Commit ID: 564156a9e1cc7c3679a926c479ba3ae133b1bfd4
workflow graph ani_top_n

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

Path: task_types/tt_ani_top_n.cwl

Branch/Commit ID: 708e141d99f6e5f30d9402d9f890562606a0d97e
workflow graph RNA-Seq pipeline single-read

The original [BioWardrobe's](https://biowardrobe.com) [PubMed ID:26248465](https://www.ncbi.nlm.nih.gov/pubmed/26248465) **RNA-Seq** basic analysis for a **single-read** 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-read RNA-Seq data. It performs the following steps: 1. Use STAR to align reads from input FASTQ file according to the predefined reference indices; generate unsorted BAM file and alignment statistics file 2. Use fastx_quality_stats to analyze input FASTQ file and generate quality statistics file 3. 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 file 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/rnaseq-se.cwl

Branch/Commit ID: a68821bf3a9ceadc3b2ffbb535d601d9a645b377
workflow graph count-lines10-wf.cwl

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

Path: cwltool/schemas/v1.0/v1.0/count-lines10-wf.cwl

Branch/Commit ID: b82ce7ae901a54c7a062fd5eefd8d5ceb5a4d684
workflow graph schemadef-wf.cwl

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

Path: tests/schemadef-wf.cwl

Branch/Commit ID: ea9f8634e41824ac3f81c3dde698d5f0eef54f1b
workflow graph js-expr-req-wf.cwl#wf

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

Path: tests/js-expr-req-wf.cwl

Branch/Commit ID: ea9f8634e41824ac3f81c3dde698d5f0eef54f1b

Packed ID: wf