Explore Workflows
View already parsed workflows here or click here to add your own
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RNA-Seq pipeline single-read stranded mitochondrial
Slightly changed 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. An additional steps were added to map data to mitochondrial chromosome only and then merge the output. Experiment files in [FASTQ](http://maq.sourceforge.net/fastq.shtml) format either compressed or not can be used. Current workflow should be used only with single-read strand specific RNA-Seq data. It performs the following steps: 1. `STAR` to align reads from input FASTQ file according to the predefined reference indices; generate unsorted BAM file and alignment statistics file 2. `fastx_quality_stats` to analyze input FASTQ file and generate quality statistics file 3. `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/rnaseq-se-dutp-mitochondrial.cwl Branch/Commit ID: 2caa50434966ebdf4b33e5ca689c2e4df32f9058 |
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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: 0c4855bf23622828413ecb09dd30754691c28014 |
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tt_univec_wnode.cwl
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https://github.com/ncbi/pgap.git
Path: task_types/tt_univec_wnode.cwl Branch/Commit ID: ca75d68eb74c93b35b404ec7908dc5b260e16466 |
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workflow_input_sf_expr.cwl
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https://github.com/common-workflow-language/cwl-utils.git
Path: testdata/workflow_input_sf_expr.cwl Branch/Commit ID: c1875d54dedc41b1d2fa08634dcf1caa8f1bc631 |
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Pipeline for evaluating differential expression of genes across datasets
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https://github.com/hubmapconsortium/rna-data-products.git
Path: pipeline.cwl Branch/Commit ID: 9f5ba2e7b2001400c879f2dfabfaeeaec2a106dc |
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Nested workflow example
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https://github.com/common-workflow-language/cwltool.git
Path: tests/wf/double-nested.cwl Branch/Commit ID: f94719e862f86cc88600caf3628faba6c0d05042 |
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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: a68821bf3a9ceadc3b2ffbb535d601d9a645b377 |
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Bacterial Annotation, structural annotation, functional annotation: ab initio GeneMark, by WP, by HMM (second pass)
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https://github.com/ncbi/pgap.git
Path: bacterial_annot/wf_bacterial_annot_2nd_pass.cwl Branch/Commit ID: 8ea3637b0f11eac1ea5599c41d74e00d85fb778d |
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taxcheck.cwl
Perform taxonomic identification tasks on an input genome |
https://github.com/ncbi/pgap.git
Path: taxcheck.cwl Branch/Commit ID: 2afb5ebafd1353ba063cc74ee9a7eaf347afce5c |
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delay-calibration.cwl
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https://git.astron.nl/RD/VLBI-cwl.git
Path: workflows/delay-calibration.cwl Branch/Commit ID: 0e6eea3d7afbcc7cc1ee46f6b91bc37f73c32ce4 |
