Explore Workflows

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

Graph Name Retrieved From View
workflow graph count-lines7-wf_v1_1.cwl

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

Path: testdata/count-lines7-wf_v1_1.cwl

Branch/Commit ID: e78db9870cb744fe36674f43b3223c688e9989e1
workflow graph umi molecular alignment workflow

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

Path: definitions/subworkflows/molecular_qc.cwl

Branch/Commit ID: e59c77629936fad069007ba642cad49fef7ad29f
workflow graph Bacterial Annotation, pass 1, genemark training, by HMMs (first pass)

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

Path: bacterial_annot/wf_orf_hmms.cwl

Branch/Commit ID: 2afb5ebafd1353ba063cc74ee9a7eaf347afce5c
workflow graph AltAnalyze cell-level matching and comparison of single-cell transcriptomes

Devel version of AltAnalyze CellHarmony ======================================= cellHarmony is a cell-matching algorithm designed to identify a cell's most similar analogue in a distinct single-cell RNA-Seq (scRNA-Seq) dataset and find differentially expressed genes in each cell population.

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

Path: workflows/altanalyze-cellharmony.cwl

Branch/Commit ID: 7ced5a5259dbd8b3fc64456beaeffd44f4a24081
workflow graph SoupX (workflow) - an R package for the estimation and removal of cell free mRNA contamination

Wrapped in a workflow SoupX tool for easy access to Cell Ranger pipeline compressed outputs.

https://github.com/Barski-lab/workflows.git

Path: tools/soupx-subworkflow.cwl

Branch/Commit ID: a84cefded73e7c864ee2b6c7ab0604a0397462ec
workflow graph cond-wf-003.1.cwl

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

Path: testdata/cond-wf-003.1.cwl

Branch/Commit ID: 0ab1d42d10f7311bb4032956c4a6f3d2730d9507
workflow graph kmer_cache_store

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

Path: task_types/tt_kmer_cache_store.cwl

Branch/Commit ID: ca75d68eb74c93b35b404ec7908dc5b260e16466
workflow graph Trim Galore SMARTer RNA-Seq pipeline paired-end strand specific

https://chipster.csc.fi/manual/library-type-summary.html Modified original [BioWardrobe's](https://biowardrobe.com) [PubMed ID:26248465](https://www.ncbi.nlm.nih.gov/pubmed/26248465) **RNA-Seq** basic analysis for a **pair-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 files 2. Use STAR to align reads from input FASTQ files according to the predefined reference indices; generate unsorted BAM file and alignment statistics file 3. Use fastx_quality_stats to analyze input FASTQ files and generate quality statistics files 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 files 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-pe-smarter-dutp.cwl

Branch/Commit ID: 7ced5a5259dbd8b3fc64456beaeffd44f4a24081
workflow graph conflict-wf.cwl#collision

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

Path: tests/conflict-wf.cwl

Branch/Commit ID: e62f99dd79d6cb9c157cceb458f74200da84f6e9

Packed ID: collision
workflow graph Single-Cell RNA-Seq Trajectory Analysis

Single-Cell RNA-Seq Trajectory Analysis Infers developmental trajectories and pseudotime from cells clustered by similarity of gene expression data.

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

Path: workflows/sc-rna-trajectory.cwl

Branch/Commit ID: 46d3d403ddb240d5a8f4f31ab992b6d6a2686745