Explore Workflows

View already parsed workflows here or click here to add your own

Graph Name Retrieved From View
workflow graph Detect DoCM variants

https://github.com/genome/analysis-workflows.git

Path: definitions/subworkflows/docm_germline.cwl

Branch/Commit ID: d297528e53b6c1ecb69b1ab27b8e03323b4463ad
workflow graph picard_markduplicates

Mark duplicates

https://gitlab.bsc.es/lrodrig1/structuralvariants_poc.git

Path: structuralvariants/cwl/subworkflows/picard_markduplicates.cwl

Branch/Commit ID: 3f6a871f81f343cf81a345f73ff2eeac70804b8c
workflow graph workflow_input_format_expr.cwl

https://github.com/common-workflow-language/cwl-utils.git

Path: testdata/workflow_input_format_expr.cwl

Branch/Commit ID: 124a08ce3389eb49066c34a4163cbbed210a0355
workflow graph align_merge_sas

https://github.com/ncbi/pgap.git

Path: task_types/tt_align_merge_sas.cwl

Branch/Commit ID: 72c3091012f5c2dce38ad9213cda617d2c7a61ac
workflow graph step-valuefrom3-wf.cwl

https://github.com/common-workflow-language/cwltool.git

Path: cwltool/schemas/v1.0/v1.0/step-valuefrom3-wf.cwl

Branch/Commit ID: 2256a30d0c1365b30e0a7338fb883c74674fcd25
workflow graph umi duplex alignment fastq workflow

https://github.com/genome/analysis-workflows.git

Path: definitions/pipelines/alignment_umi_duplex.cwl

Branch/Commit ID: f615832615c3b41728df8e47b72ef11e37e6a9e5
workflow graph retrieve metadata from Zenodo community

For a given Zenodo community, retrieve its repository records as Zenodo JSON and (eventually) schema.org JSON-LD and DataCite v4 XML.

https://github.com/stain/ro-index-paper.git

Path: code/data-gathering/workflows/zenodo-records.cwl

Branch/Commit ID: e770ea774fc95eab29b0ca975ffa3a88919740c5
workflow graph workflow_input_sf_expr_array_v1_2.cwl

https://github.com/common-workflow-language/cwl-utils.git

Path: testdata/workflow_input_sf_expr_array_v1_2.cwl

Branch/Commit ID: 0ad6983898f0d9001fe0f416f97c4d8b940e384a
workflow graph dynresreq-workflow-inputdefault.cwl

https://github.com/common-workflow-language/cwl-v1.2.git

Path: tests/dynresreq-workflow-inputdefault.cwl

Branch/Commit ID: ea9f8634e41824ac3f81c3dde698d5f0eef54f1b
workflow graph 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