Explore Workflows

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

Graph Name Retrieved From View
workflow graph Functional analyis of sequences that match the 16S SSU

https://github.com/EBI-Metagenomics/ebi-metagenomics-cwl.git

Path: workflows/16S_taxonomic_analysis.cwl

Branch/Commit ID: f993cada89d2c6f7480a0d56baa7836a361b1f3a
workflow graph protein_extract

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

Path: progs/protein_extract.cwl

Branch/Commit ID: 656113dcac0de7cef6cff6c688f61441ee05872a
workflow graph bacterial_orthology_cond

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

Path: bacterial_orthology/wf_bacterial_orthology_conditional.cwl

Branch/Commit ID: 22ffe27d9d4a899def7592d75d5871c1856adbdb
workflow graph align_merge_sas

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

Path: task_types/tt_align_merge_sas.cwl

Branch/Commit ID: 0d0ba0c3410e8aee55c82f077cee31d8ee929b5a
workflow graph workflow.cwl

https://github.com/nal-i5k/organism_onboarding.git

Path: flow_dispatch/2blat/workflow.cwl

Branch/Commit ID: f7894707dd30a0edd199d3b67c4c8678f64c90b3
workflow graph abra_workflow.cwl

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

Path: workflows/ABRA/abra_workflow.cwl

Branch/Commit ID: 09ddd9711fb550f56d52f1806cdefd4a8cd943b0
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: 104059e07a2964673e21d371763e33c0afeb2d03
workflow graph retrieve metadata from Zenodo community

For a given Zenodo community, retrieve its repository records as Zenodo JSON and (eventually) schema.org JSON-LD and DataCite v4 XML.

https://github.com/stain/ro-index-paper.git

Path: code/data-gathering/workflows/zenodo-records.cwl

Branch/Commit ID: 322f215ffb58ca5f735f8f4f6a0cdc96cbd0e0aa
workflow graph blastp_wnode_naming

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

Path: task_types/tt_blastp_wnode_naming.cwl

Branch/Commit ID: 22ffe27d9d4a899def7592d75d5871c1856adbdb
workflow graph nestedworkflows.cwl

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

Path: cwltool/schemas/v1.0/examples/nestedworkflows.cwl

Branch/Commit ID: 445f6b3a214f0c48317b25f7af278ae919ce5403