Explore Workflows
View already parsed workflows here or click here to add your own
| Graph | Name | Retrieved From | View |
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timelimit2-wf.cwl
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https://github.com/common-workflow-language/cwl-v1.2.git
Path: tests/timelimit2-wf.cwl Branch/Commit ID: ea9f8634e41824ac3f81c3dde698d5f0eef54f1b |
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Trim Galore 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 a **single-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 single-end RNA-Seq data. It performs the following steps: 1. Trim adapters from input FASTQ file 2. Use STAR to align reads from input FASTQ file according to the predefined reference indices; generate unsorted BAM file and alignment statistics file 3. Use fastx_quality_stats to analyze input FASTQ file and generate quality statistics file 4. 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/trim-rnaseq-se-dutp.cwl Branch/Commit ID: ce058d892d330125cd03d0a0d5fb3b321cda0be3 |
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Build STAR indices
Workflow runs [STAR](https://github.com/alexdobin/STAR) v2.5.3a (03/17/2017) PMID: [23104886](https://www.ncbi.nlm.nih.gov/pubmed/23104886) to build indices for reference genome provided in a single FASTA file as fasta_file input and GTF annotation file from annotation_gtf_file input. Generated indices are saved in a folder with the name that corresponds to the input genome. |
https://github.com/datirium/workflows.git
Path: workflows/star-index.cwl Branch/Commit ID: a68821bf3a9ceadc3b2ffbb535d601d9a645b377 |
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Varscan Workflow
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https://github.com/genome/analysis-workflows.git
Path: definitions/subworkflows/varscan_pre_and_post_processing.cwl Branch/Commit ID: e0b3c76e38630fb6234414b5adebfb6a4fb23117 |
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count-lines9-wf.cwl
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https://github.com/common-workflow-language/cwltool.git
Path: cwltool/schemas/v1.0/v1.0/count-lines9-wf.cwl Branch/Commit ID: e9c83739a93fa0b18f8dea2f98b632a9e32725c9 |
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chipseq-se.cwl
Runs ChIP-Seq BioWardrobe basic analysis with single-end data file. |
https://github.com/Barski-lab/workflows.git
Path: workflows/chipseq-se.cwl Branch/Commit ID: b4b7b2e7e508be5eac639f9e323d141daf714c0d |
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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: 49cd284a8fc7884de763573075d3e1d6a4c1ffdd |
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trim-rnaseq-pe-dutp.cwl
Runs RNA-Seq BioWardrobe basic analysis with strand specific pair-end data file. |
https://github.com/datirium/workflows.git
Path: workflows/trim-rnaseq-pe-dutp.cwl Branch/Commit ID: 4b8bb1a1ec39056253ca8eee976078e51f4a954e |
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workflow_input_format_expr_v1_2.cwl
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https://github.com/common-workflow-language/cwl-utils.git
Path: testdata/workflow_input_format_expr_v1_2.cwl Branch/Commit ID: 0ab1d42d10f7311bb4032956c4a6f3d2730d9507 |
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pass-unconnected.cwl
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https://github.com/common-workflow-language/cwl-v1.2.git
Path: tests/pass-unconnected.cwl Branch/Commit ID: 57baec040c99d7edef8242ef51b5470b1c82d733 |
