Explore Workflows
View already parsed workflows here or click here to add your own
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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. |
https://github.com/datirium/workflows.git
Path: workflows/rgt-thor.cwl Branch/Commit ID: 4f48ee6f8665a34cdf96e89c012ee807f80c7a3d |
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scatter-wf1.cwl
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https://github.com/common-workflow-language/cwl-v1.2.git
Path: tests/scatter-wf1.cwl Branch/Commit ID: c7c97715b400ff2194aa29fc211d3401cea3a9bf |
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RNA-Seq pipeline paired-end
The original [BioWardrobe's](https://biowardrobe.com) [PubMed ID:26248465](https://www.ncbi.nlm.nih.gov/pubmed/26248465) **RNA-Seq** basic analysis for a **paired-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 paired-end RNA-Seq data. It performs the following steps: 1. Use STAR to align reads from input FASTQ files according to the predefined reference indices; generate unsorted BAM file and alignment statistics file 2. Use fastx_quality_stats to analyze input FASTQ files and generate quality statistics files 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) 4. Generate BigWig file on the base of sorted BAM file 5. Map input FASTQ files to predefined rRNA reference indices using Bowtie to define the level of rRNA contamination; export resulted statistics to file 6. 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-pe.cwl Branch/Commit ID: 7eef0294395d83ff0765fce61726a59d71126422 |
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Detect DoCM variants
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https://github.com/genome/analysis-workflows.git
Path: definitions/subworkflows/docm_germline.cwl Branch/Commit ID: 24e5290aec441665c6976ee3ee8ae3574c49c6b5 |
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count-lines5-wf.cwl
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https://github.com/common-workflow-language/cwltool.git
Path: cwltool/schemas/v1.0/v1.0/count-lines5-wf.cwl Branch/Commit ID: ae401a813472ca453a99ad067a5e6fc3bd71112b |
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mutect panel-of-normals workflow
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https://github.com/genome/analysis-workflows.git
Path: definitions/pipelines/panel_of_normals.cwl Branch/Commit ID: a670f323e77e02d9b77be9a13d73d5276dd3676c |
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group-isoforms-batch.cwl
Workflow runs group-isoforms.cwl tool using scatter for isoforms_file input. genes_filename and common_tss_filename inputs are ignored. |
https://github.com/datirium/workflows.git
Path: tools/group-isoforms-batch.cwl Branch/Commit ID: 7eef0294395d83ff0765fce61726a59d71126422 |
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Subworkflow to allow calling different SV callers which require bam files as inputs
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https://github.com/genome/analysis-workflows.git
Path: definitions/subworkflows/single_sample_sv_callers.cwl Branch/Commit ID: 9c0b1497c467393e1a54735575043dced73e95c4 |
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Exome QC workflow
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https://github.com/apaul7/cancer-genomics-workflow.git
Path: definitions/subworkflows/qc_exome.cwl Branch/Commit ID: low-vaf |
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Detect Docm variants
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https://github.com/genome/analysis-workflows.git
Path: definitions/subworkflows/docm_cle.cwl Branch/Commit ID: 0a9a4ce83b49ed4e7eee5bcc09d83725136a36b0 |
