Explore Workflows

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

Graph Name Retrieved From View
workflow graph step-valuefrom5-wf.cwl

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

Path: tests/step-valuefrom5-wf.cwl

Branch/Commit ID: 31ec48a8d81ef7c1b2c5e9c0a19e7623efe4a1e2
workflow graph align_sort_sa

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

Path: task_types/tt_align_sort_sa.cwl

Branch/Commit ID: 0d0ba0c3410e8aee55c82f077cee31d8ee929b5a
workflow graph extract_gencoll_ids

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

Path: task_types/tt_extract_gencoll_ids.cwl

Branch/Commit ID: 6d8d29a2156b93a75f1d1c6952738bd63f6bd98e
workflow graph Identifies non-coding RNAs using Rfams covariance models

https://github.com/EBI-Metagenomics/pipeline-v5.git

Path: workflows/subworkflows/cmsearch-condition.cwl

Branch/Commit ID: 6ec8d032feb120eb0eebf9a0c01d48deabf42eea
workflow graph RNA-Seq pipeline paired-end strand specific

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-dutp.cwl

Branch/Commit ID: ee66d03be8a7fd61367db40c37a973ff55ece4da
workflow graph Single-cell RNA-Seq Dimensionality Reduction Analysis

Single-cell RNA-Seq Dimensionality Reduction Analysis Integrates multiple single-cell RNA-Seq datasets, reduces dimensionality using PCA.

 https://github.com/datirium/workflows.git

Path: workflows/sc-rna-reduce.cwl

Branch/Commit ID: 36fd18f11e939d3908b1eca8d2939402f7a99b0f
workflow graph align_sort_sa

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

Path: task_types/tt_align_sort_sa.cwl

Branch/Commit ID: 7f9cfcbda5998b164bd1d8f1f6006aefda0f47f3
workflow graph scatter-valuefrom-wf6.cwl

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

Path: cwltool/schemas/v1.0/v1.0/scatter-valuefrom-wf6.cwl

Branch/Commit ID: 26870e38cec81af880cd3e4789ae6cee8fc27020
workflow graph gathered exome alignment and somatic variant detection

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

Path: definitions/pipelines/somatic_exome_gathered.cwl

Branch/Commit ID: f615832615c3b41728df8e47b72ef11e37e6a9e5
workflow graph kallisto_scatter_synapse_paired_end_workflow.cwl

https://github.com/CRI-iAtlas/iatlas-workflows.git

Path: Kallisto/workflow/kallisto_scatter_synapse_paired_end_workflow.cwl

Branch/Commit ID: c7fa0fa9ef94c657b664f680462dbc3f5b7a32e8