Explore Workflows

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

Graph Name Retrieved From View
workflow graph process VCF workflow

https://github.com/genome/cancer-genomics-workflow.git

Path: strelka/process_vcf.cwl

Branch/Commit ID: 6eb7d35ad46207f4ff49e84106b717e17331eb4b
workflow graph Trim Galore RNA-Seq pipeline single-read strand specific

Note: should be updated The original [BioWardrobe's](https://biowardrobe.com) [PubMed ID:26248465](https://www.ncbi.nlm.nih.gov/pubmed/26248465) **RNA-Seq** basic analysis for a **single-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 file 2. Use STAR to align reads from input FASTQ file according to the predefined reference indices; generate unsorted BAM file and alignment statistics file 3. Use fastx_quality_stats to analyze input FASTQ file and generate quality statistics file 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 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/trim-rnaseq-se-dutp.cwl

Branch/Commit ID: 57863b6131d8262c5ce864adaf8e4038401e71a2
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: 57863b6131d8262c5ce864adaf8e4038401e71a2
workflow graph trim-chipseq-se.cwl

Runs ChIP-Seq BioWardrobe basic analysis with single-end data file.

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

Path: workflows/trim-chipseq-se.cwl

Branch/Commit ID: a8e4c1245950715d2e07682d3ac4865ce1d73777
workflow graph l1b_workflow.cwl

https://github.com/mliukis/sounder-sips-application.git

Path: cwl/l1b_workflow.cwl

Branch/Commit ID: cb4884ad865d2ec97d7f3e98b3df697c6e3c4162
workflow graph hmmsearch_wnode and gpx_qdump combined workflow to apply scatter/gather

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

Path: task_types/tt_hmmsearch_wnode_plus_qdump.cwl

Branch/Commit ID: 369e2b6c7f4db75099d258729dec1326f55d2cc5
workflow graph count-lines7-single-source-wf_v1_0.cwl

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

Path: testdata/count-lines7-single-source-wf_v1_0.cwl

Branch/Commit ID: e949503ac0dd7e22ba9b04ac51926d13780f9cee
workflow graph Per-chromosome pindel

https://github.com/genome/cancer-genomics-workflow.git

Path: pindel/pindel_cat.cwl

Branch/Commit ID: 6eb7d35ad46207f4ff49e84106b717e17331eb4b
workflow graph kfdrc_sentieon_alignment_wf.cwl

https://github.com/kids-first/kf-alignment-workflow.git

Path: workflows/kfdrc_sentieon_alignment_wf.cwl

Branch/Commit ID: e75f0c96153a484db1f882f6ff2a9764519a3179
workflow graph original.cwl#main_pipeline

Simulation steps pipeline

 https://github.com/ILIAD-ocean-twin/application_package.git

Path: workflow_in_workflow/original.cwl

Branch/Commit ID: aab1b560c6a855c645f43635f155a15800a7ce0d

Packed ID: main_pipeline