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Graph Name Retrieved From View
workflow graph contig LCA

create LCA consistant across input contigs contigs order of precedence - rRNA, single copy gene, LCA of genes

https://github.com/MG-RAST/pipeline.git

Path: CWL/Workflows/contig-lca.workflow.cwl

Branch/Commit ID: 6a8727124baf77416ca797982fd4e0689c2a593a
workflow graph Run pindel on provided region

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

Path: definitions/subworkflows/pindel_region.cwl

Branch/Commit ID: 4bc0a4577d626b65a4b44683e5a1ab2f7d7faf4c
workflow graph assm_assm_blastn_wnode

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

Path: task_types/tt_assm_assm_blastn_wnode.cwl

Branch/Commit ID: 205f4ceb47ba7537a6923d2dfb03668317c2fd89
workflow graph kmer_build_tree

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

Path: task_types/tt_kmer_build_tree.cwl

Branch/Commit ID: 205f4ceb47ba7537a6923d2dfb03668317c2fd89
workflow graph tt_univec_wnode.cwl

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

Path: task_types/tt_univec_wnode.cwl

Branch/Commit ID: 8a8fffb78b1e327ba0da51840ac8acc0c218d611
workflow graph align_sort_sa

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

Path: task_types/tt_align_sort_sa.cwl

Branch/Commit ID: e4d6182d5f7a6a880e5f2b21273cf40d25e187df
workflow graph exome_metrics.cwl

https://github.com/NCI-GDC/gdc-dnaseq-cwl.git

Path: workflows/bamfastq_align/exome_metrics.cwl

Branch/Commit ID: 14558b578bad217685ae3c4807ead2a4392d0319
workflow graph 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: bf80c9339d81a78aefb8de661bff998ed86e836e
workflow graph scatter-valuefrom-wf1.cwl

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

Path: cwltool/schemas/v1.0/v1.0/scatter-valuefrom-wf1.cwl

Branch/Commit ID: 7bfd77118cdc80dd7150115dd7a1a7ee6046f6fe
workflow graph exome alignment and germline variant detection

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

Path: definitions/subworkflows/germline_detect_variants.cwl

Branch/Commit ID: 4bc0a4577d626b65a4b44683e5a1ab2f7d7faf4c