Explore Workflows

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

Graph Name Retrieved From View
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: e71779665f42fcf34601b0f65e030bb0dd47fa79
workflow graph align_sort_sa

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

Path: task_types/tt_align_sort_sa.cwl

Branch/Commit ID: 0bc1c33a2293e054ad00974971edc79c13252cc7
workflow graph annotate.cwl

https://github.com/hubmapconsortium/hra-workflows.git

Path: steps/annotate.cwl

Branch/Commit ID: 4f75e87eb56925d456e78d9e06cf543c2fb0dada
workflow graph download_gtf.cwl

https://github.com/yyoshiaki/VIRTUS.git

Path: workflow/download_gtf.cwl

Branch/Commit ID: 43982758be93a31a0c079f448b377cae9fb9f3c7
workflow graph exome alignment and somatic variant detection for cle purpose

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

Path: definitions/pipelines/somatic_exome_cle.cwl

Branch/Commit ID: 8dc462a7d9ba1479f764682af99c69d8574cb3dc
workflow graph Chipseq alignment with qc and creating homer tag directory

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

Path: definitions/pipelines/chipseq.cwl

Branch/Commit ID: 97572e3a088d79f6a4166385f79e79ea77b11470
workflow graph scatter2.cwl

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

Path: tests/wf/scatter2.cwl

Branch/Commit ID: 2dce710246e091f0189fab41b589ee062ee94500
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: 807fe40bca1fbd18ede6250851b9f71de98da69b
workflow graph 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 **strand specific 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-dutp.cwl

Branch/Commit ID: 2b8146f76595f0c4d8bf692de78b21280162b1d0
workflow graph step-valuefrom-wf.cwl

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

Path: cwltool/schemas/v1.0/v1.0/step-valuefrom-wf.cwl

Branch/Commit ID: 7dec97bb8f0bc2d9e9eb710faf41f2e98cc7cdda