Explore Workflows
View already parsed workflows here or click here to add your own
| Graph | Name | Retrieved From | View |
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kmer_cache_retrieve
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https://github.com/ncbi/pgap.git
Path: task_types/tt_kmer_cache_retrieve.cwl Branch/Commit ID: 89098668413e90519c99b35143bffec509d3599c |
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kmer_cache_store
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https://github.com/ncbi/pgap.git
Path: task_types/tt_kmer_cache_store.cwl Branch/Commit ID: be32f1363f9a9a9247d738e9593b207e9c5172c8 |
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Chipseq alignment with qc and creating homer tag directory
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https://github.com/genome/analysis-workflows.git
Path: definitions/pipelines/chipseq.cwl Branch/Commit ID: ef7f3345b352319ec22dffba26c79df033b141f9 |
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step-valuefrom3-wf_v1_0.cwl
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https://github.com/common-workflow-language/cwl-utils.git
Path: testdata/step-valuefrom3-wf_v1_0.cwl Branch/Commit ID: 124a08ce3389eb49066c34a4163cbbed210a0355 |
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Trim Galore 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 **pair-end** experiment. A corresponded input [FASTQ](http://maq.sourceforge.net/fastq.shtml) file has to be provided. Current workflow must be used with paired-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 2 (after running STAR) 5. Generate BigWig file using 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.cwl Branch/Commit ID: b4d578c2ba4713a5a22163d9f8c7105acda1f22e |
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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: 9b4dc225c537685b9c9a32d931d3892d20953dd7 |
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wgs alignment and germline variant detection
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https://github.com/genome/analysis-workflows.git
Path: definitions/pipelines/germline_wgs_gvcf.cwl Branch/Commit ID: 5be54bf09092c53e6c7797a875f64a360d511d7f |
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mut.cwl
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https://github.com/common-workflow-language/cwltool.git
Path: tests/wf/mut.cwl Branch/Commit ID: bf93dd3e6e3261e1455530984ce045f283535d17 |
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step-valuefrom2-wf.cwl
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https://github.com/common-workflow-language/cwl-v1.2.git
Path: tests/step-valuefrom2-wf.cwl Branch/Commit ID: ea9f8634e41824ac3f81c3dde698d5f0eef54f1b |
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Aligning chipseq data of mouse
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https://github.com/genome/analysis-workflows.git
Path: definitions/subworkflows/sequence_to_bqsr_mouse.cwl Branch/Commit ID: 25aa4788dd4efb1cc8ed6f609cb7803896e4d28d |
