Explore Workflows
View already parsed workflows here or click here to add your own
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RNA-Seq pipeline paired-end 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 pair-end** 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 the pair-end 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-pe-dutp-mitochondrial.cwl Branch/Commit ID: a68821bf3a9ceadc3b2ffbb535d601d9a645b377 |
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Cut-n-Run pipeline paired-end
Experimental pipeline for Cut-n-Run analysis. Uses mapping results from the following experiment types: - `chipseq-pe.cwl` - `trim-chipseq-pe.cwl` - `trim-atacseq-pe.cwl` Note, the upstream analyses should not have duplicates removed |
https://github.com/datirium/workflows.git
Path: workflows/trim-chipseq-pe-cut-n-run.cwl Branch/Commit ID: 4f48ee6f8665a34cdf96e89c012ee807f80c7a3d |
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step-valuefrom3-wf.cwl
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https://github.com/common-workflow-language/cwltool.git
Path: cwltool/schemas/v1.0/v1.0/step-valuefrom3-wf.cwl Branch/Commit ID: e9c83739a93fa0b18f8dea2f98b632a9e32725c9 |
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cache_asnb_entries
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https://github.com/ncbi/pgap.git
Path: task_types/tt_cache_asnb_entries.cwl Branch/Commit ID: 49732e54e2fe2eafd2f82df3c482c73e642f6d64 |
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Bacterial Annotation, pass 4, blastp-based functional annotation (second pass)
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https://github.com/ncbi/pgap.git
Path: bacterial_annot/wf_bacterial_annot_pass4.cwl Branch/Commit ID: 2afb5ebafd1353ba063cc74ee9a7eaf347afce5c |
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Single-Cell ATAC-Seq Differential Accessibility Analysis
Single-Cell ATAC-Seq Differential Accessibility Analysis Identifies differentially accessible regions between any two groups of cells, optionally aggregating chromatin accessibility data from single-cell to pseudobulk form. |
https://github.com/datirium/workflows.git
Path: workflows/sc-atac-dbinding.cwl Branch/Commit ID: 93b844a80f4008cc973ea9b5efedaff32a343895 |
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step-valuefrom-wf.cwl
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https://github.com/common-workflow-language/cwltool.git
Path: cwltool/schemas/v1.0/v1.0/step-valuefrom-wf.cwl Branch/Commit ID: 4a31f2a1c1163492ae37bbc748a299e8318c462c |
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step-valuefrom2-wf_v1_2.cwl
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https://github.com/common-workflow-language/cwl-utils.git
Path: testdata/step-valuefrom2-wf_v1_2.cwl Branch/Commit ID: 0ab1d42d10f7311bb4032956c4a6f3d2730d9507 |
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steplevel-resreq.cwl
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https://github.com/common-workflow-language/cwltool.git
Path: cwltool/schemas/v1.0/v1.0/steplevel-resreq.cwl Branch/Commit ID: 2256a30d0c1365b30e0a7338fb883c74674fcd25 |
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indices-header.cwl
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https://github.com/datirium/workflows.git
Path: metadata/indices-header.cwl Branch/Commit ID: 60854b5d299df91e135e05d02f4be61f6a310fbc |
