Explore Workflows

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

Graph Name Retrieved From View
workflow graph waltz_workflow_all_bams.cwl

https://github.com/andurill/ACCESS-Pipeline.git

Path: workflows/waltz/waltz_workflow_all_bams.cwl

Branch/Commit ID: 3441040dfaecba58150c13a95a6a93657b00778a
workflow graph record-output-wf_v1_2.cwl

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

Path: testdata/record-output-wf_v1_2.cwl

Branch/Commit ID: e78db9870cb744fe36674f43b3223c688e9989e1
workflow graph download_quality_control.cwl

https://github.com/ncbi/cwl-ngs-workflows-cbb.git

Path: workflows/sra/download_quality_control.cwl

Branch/Commit ID: 1b1cb5bbbe53a2dd5d7de7cdbff19c1bdbe23a49
workflow graph SetPhotonDelay

Derive additional delay of photon arrival times at the photodetectors.

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

Path: workflows/SetPhotonDelay.cwl

Branch/Commit ID: 789752af87eb190387ff2acb4c95c7a5cdb961e7
workflow graph tt_fscr_calls_pass1

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

Path: task_types/tt_fscr_calls_pass1.cwl

Branch/Commit ID: c009eeba7379efbbd37b8d5013a83f161f06939b
workflow graph workflow-htcondorcern.cwl

https://github.com/reanahub/reana-demo-root6-roofit.git

Path: workflow/cwl/workflow-htcondorcern.cwl

Branch/Commit ID: 2cbb3ae1500417c12fd5403908ab1299a889172f
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: cc6fa135d04737fdde3b4414d6e214cf8c812f6e
workflow graph worldpopulation.cwl

https://github.com/reanahub/reana-demo-worldpopulation.git

Path: workflow/cwl/worldpopulation.cwl

Branch/Commit ID: 7d08708a8deff739a2b9bc0a7b2d4e50105f21d8
workflow graph workflow_same_level.cwl#second_pipeline

Simulation of 2 workflows

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

Path: workflow_in_workflow/workflow_same_level.cwl

Branch/Commit ID: 7e4399c3dd48a929d202b0e0a24bdbf520640e89

Packed ID: second_pipeline
workflow graph accessioning-prediction_subwf.cwl

https://github.com/kinow/pipeline-v5.git

Path: workflows/subworkflows/assembly/accessioning-prediction_subwf.cwl

Branch/Commit ID: 337033417c49dcf4ab394aba1ec517b97637da13