Explore Workflows

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

Graph Name Retrieved From View
workflow graph env-wf3.cwl

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

Path: v1.0/v1.0/env-wf3.cwl

Branch/Commit ID: 4fd45edb9531a03223c18a586e32d0baf0d5acb2
workflow graph workflow-blast-ebeye-pdbe.cwl

https://github.com/ebi-wp/webservice-cwl.git

Path: workflows/workflow-blast-ebeye-pdbe.cwl

Branch/Commit ID: 7c2c01c23d7a68a4f0c608881280576d65a01325
workflow graph mpi_simple_wf.cwl

Simple 2 step workflow to check that workflow steps are independently picking up on the number of processes. First run the parallel get PIDs step (on the input num procs) then run (on a single proc) the line count. This should equal the input.

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

Path: tests/wf/mpi_simple_wf.cwl

Branch/Commit ID: d5f7fa162611243f0c66dd3e933c16a4964a09ca
workflow graph kmer_seq_entry_extract_wnode

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

Path: task_types/tt_kmer_seq_entry_extract_wnode.cwl

Branch/Commit ID: a7fced3ed8c839272c8f3a8db9da7bc8cd50271f
workflow graph Bacterial Annotation, pass 1, genemark training, by HMMs (first pass)

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

Path: bacterial_annot/wf_ab_initio_training.cwl

Branch/Commit ID: 8af4e2aabf43d5e3c7162efae4ad4649df5601e2
workflow graph mut.cwl

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

Path: tests/wf/mut.cwl

Branch/Commit ID: 63f539ba60e91f0cb3ce7cda2c5da5c65525c375
workflow graph align_merge_sas

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

Path: task_types/tt_align_merge_sas.cwl

Branch/Commit ID: e6fd7898b71a89b667d2eb38f412999920be5902
workflow graph split_bam_subpipeline.cwl

https://github.com/PMCC-BioinformaticsCore/janis-pipelines.git

Path: janis_pipelines/wgs_somatic/cwl/tools/split_bam_subpipeline.cwl

Branch/Commit ID: c1aeec7b68acdd1eab3f1d1bd75d768e31abd6d2
workflow graph Get Proteins

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

Path: wf_bacterial_prot_src.cwl

Branch/Commit ID: 8af4e2aabf43d5e3c7162efae4ad4649df5601e2
workflow graph Deprecated. RNA-Seq pipeline single-read

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-read** 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-read RNA-Seq data. It performs the following steps: 1. Use STAR to align reads from input FASTQ file according to the predefined reference indices; generate unsorted BAM file and alignment statistics file 2. Use fastx_quality_stats to analyze input FASTQ file and generate quality statistics file 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) 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-se.cwl

Branch/Commit ID: 7030da528559c7106d156284e50ff0ecedab0c4e