Explore Workflows
View already parsed workflows here or click here to add your own
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Per-region pindel
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https://github.com/genome/analysis-workflows.git
Path: definitions/subworkflows/pindel_cat.cwl Branch/Commit ID: 28d1065759cbd389594ee33b41fd1103ced5436d |
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DiffBind - Differential Binding Analysis of ChIP-Seq Peak Data
Differential Binding Analysis of ChIP-Seq Peak Data --------------------------------------------------- DiffBind processes ChIP-Seq data enriched for genomic loci where specific protein/DNA binding occurs, including peak sets identified by ChIP-Seq peak callers and aligned sequence read datasets. It is designed to work with multiple peak sets simultaneously, representing different ChIP experiments (antibodies, transcription factor and/or histone marks, experimental conditions, replicates) as well as managing the results of multiple peak callers. For more information please refer to: ------------------------------------- Ross-Innes CS, Stark R, Teschendorff AE, Holmes KA, Ali HR, Dunning MJ, Brown GD, Gojis O, Ellis IO, Green AR, Ali S, Chin S, Palmieri C, Caldas C, Carroll JS (2012). “Differential oestrogen receptor binding is associated with clinical outcome in breast cancer.” Nature, 481, -4. |
https://github.com/datirium/workflows.git
Path: workflows/diffbind.cwl Branch/Commit ID: c6bfa0de917efb536dd385624fc7702e6748e61d |
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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: c6bfa0de917efb536dd385624fc7702e6748e61d |
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varscan somatic workflow
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https://github.com/genome/analysis-workflows.git
Path: definitions/subworkflows/varscan.cwl Branch/Commit ID: b7d9ace34664d3cedb16f2512c8a6dc6debfc8ca |
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Per-region pindel
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https://github.com/genome/analysis-workflows.git
Path: definitions/subworkflows/pindel_cat.cwl Branch/Commit ID: da335d9963418f7bedd84cb2791a0df1b3165ffe |
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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: 252e7214ac64cb1128881e76743013e61bc7ec38 |
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1st-workflow.cwl
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https://github.com/common-workflow-language/cwltool.git
Path: tests/wf/1st-workflow.cwl Branch/Commit ID: dbc4c4c2ad30ed31367b4fbcc3bb4084fdcabaa2 |
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Exome QC workflow
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https://github.com/genome/analysis-workflows.git
Path: definitions/subworkflows/qc_exome.cwl Branch/Commit ID: da335d9963418f7bedd84cb2791a0df1b3165ffe |
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Per-region pindel
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https://github.com/genome/analysis-workflows.git
Path: definitions/subworkflows/pindel_cat.cwl Branch/Commit ID: 258bd4353ad1ca7790b3ae626bf42ab8194e7561 |
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umi molecular alignment workflow
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https://github.com/genome/analysis-workflows.git
Path: definitions/subworkflows/molecular_alignment.cwl Branch/Commit ID: da335d9963418f7bedd84cb2791a0df1b3165ffe |
