Explore Workflows
View already parsed workflows here or click here to add your own
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WGS QC workflow mouse
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Path: definitions/subworkflows/qc_wgs_mouse.cwl Branch/Commit ID: c6bbd4cdd612b3b5cc6e9000df4800c21e192bf5 |
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THOR - differential peak calling of ChIP-seq signals with replicates
What is THOR? -------------- THOR is an HMM-based approach to detect and analyze differential peaks in two sets of ChIP-seq data from distinct biological conditions with replicates. THOR performs genomic signal processing, peak calling and p-value calculation in an integrated framework. For more information please refer to: ------------------------------------- Allhoff, M., Sere K., Freitas, J., Zenke, M., Costa, I.G. (2016), Differential Peak Calling of ChIP-seq Signals with Replicates with THOR, Nucleic Acids Research, epub gkw680. |
Path: workflows/rgt-thor.cwl Branch/Commit ID: fa4f172486288a1a9d23864f1d6962d85a453e16 |
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Genelists heatmap - RNA-seq expression data visualized
# Genelists heatmap - RNA-seq expression data visualized This visualization workflow takes as input 1 or more genelists derived from the DESeq and/or diffbind workflows along with user-selected samples and visualizes RNA-Seq expression data in a single morpheus heatmap. ### __References__ - Morpheus, https://software.broadinstitute.org/morpheus |
Path: workflows/genelists-deseq-only.cwl Branch/Commit ID: fa4f172486288a1a9d23864f1d6962d85a453e16 |
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Single-Cell ATAC-Seq Dimensionality Reduction Analysis
Single-Cell ATAC-Seq Dimensionality Reduction Analysis Removes noise and confounding sources of variation by reducing dimensionality of chromatin accessibility data from the outputs of “Single-Cell Multiome ATAC and RNA-Seq Filtering Analysis” pipelines. The results of this workflow are primarily used in “Single-Cell ATAC-Seq Cluster Analysis” or “Single-Cell WNN Cluster Analysis” pipelines. |
Path: workflows/sc-atac-reduce.cwl Branch/Commit ID: b4d578c2ba4713a5a22163d9f8c7105acda1f22e |
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WGS and MT analysis for fastq files
rna / protein - qc, preprocess, filter, annotation, index, abundance |
Path: CWL/Workflows/wgs-fastq.workflow.cwl Branch/Commit ID: f906212e2c9a88280ae36545e5422f25752aa8f4 |
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RNA-Seq pipeline single-read strand specific
Note: should be updated The original [BioWardrobe's](https://biowardrobe.com) [PubMed ID:26248465](https://www.ncbi.nlm.nih.gov/pubmed/26248465) **RNA-Seq** basic analysis for **strand specific 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 |
Path: workflows/rnaseq-se-dutp.cwl Branch/Commit ID: 4dcc405133f22c63478b6091fb5f591b6be8950f |
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count-lines5-wf.cwl
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Path: cwltool/schemas/v1.0/v1.0/count-lines5-wf.cwl Branch/Commit ID: 48bd6c751aceef30614d9e43d91865980035781f |
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count-lines1-wf-noET.cwl
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Path: tests/count-lines1-wf-noET.cwl Branch/Commit ID: a0f2d38e37ff51721fdeaf993bb2ab474b17246b |
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tt_blastn_wnode
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Path: task_types/tt_blastn_wnode.cwl Branch/Commit ID: a2d6cd4c53bf3501f6bd79edebb7ca30bba8456f |
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env-wf3.cwl
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Path: cwltool/schemas/v1.0/v1.0/env-wf3.cwl Branch/Commit ID: a3d565bf8e630101d25d31804cfbceb0a0ba28de |
