Explore Workflows

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

Graph Name Retrieved From View
workflow graph Deprecated. RNA-Seq pipeline paired-end

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.cwl

Branch/Commit ID: cc6fa135d04737fdde3b4414d6e214cf8c812f6e
workflow graph workflow.cwl

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

Path: flow_dispatch/2blat/workflow.cwl

Branch/Commit ID: 556884e8e205295e561b1d9140d836cdd6c1d8c9
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: c009eeba7379efbbd37b8d5013a83f161f06939b
workflow graph wgs alignment and tumor-only variant detection

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

Path: definitions/pipelines/tumor_only_wgs.cwl

Branch/Commit ID: 8da2b1cd6fa379b2c22baf9dad762d39630e6f46
workflow graph umi duplex alignment workflow

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

Path: definitions/subworkflows/duplex_alignment.cwl

Branch/Commit ID: 8da2b1cd6fa379b2c22baf9dad762d39630e6f46
workflow graph workflow.cwl

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

Path: flow_md5checksums/workflow.cwl

Branch/Commit ID: 556884e8e205295e561b1d9140d836cdd6c1d8c9
workflow graph spurious_annot

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

Path: spurious_annot/wf_spurious_annot_pass1.cwl

Branch/Commit ID: c7c674b873b9925b28ffbd602974eec4bfe78cf9
workflow graph cellpose.cwl

https://github.com/hubmapconsortium/spatial-transcriptomics-pipeline.git

Path: steps/cellpose.cwl

Branch/Commit ID: 2e31b8ddd4d509c7bbcb983ad41e401687623ddb
workflow graph revsort_step_bad_schema.cwl

Reverse the lines in a document, then sort those lines.

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

Path: tests/wf/revsort_step_bad_schema.cwl

Branch/Commit ID: 1397d96ad97fe8abfd1184675d728a8a04699d67
workflow graph workflow-pepinfo-backtranseq-cpgplot.cwl

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

Path: workflows/workflow-pepinfo-backtranseq-cpgplot.cwl

Branch/Commit ID: 88b9948c4977ca90ab5ceb391b2235043135480d