Explore Workflows

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Graph Name Retrieved From View
workflow graph ValidateArrayElementCoordinates

Plot and compare array element coordinates. Validate coordinate transformation from those used in observatory database to simulation systems.

 https://github.com/gammasim/workflows.git

Path: workflows/ValidateArrayElementCoordinates.cwl

Branch/Commit ID: 789752af87eb190387ff2acb4c95c7a5cdb961e7
workflow graph Build STAR indices

Workflow runs [STAR](https://github.com/alexdobin/STAR) v2.5.3a (03/17/2017) PMID: [23104886](https://www.ncbi.nlm.nih.gov/pubmed/23104886) to build indices for reference genome provided in a single FASTA file as fasta_file input and GTF annotation file from annotation_gtf_file input. Generated indices are saved in a folder with the name that corresponds to the input genome.

https://github.com/datirium/workflows.git

Path: workflows/star-index.cwl

Branch/Commit ID: d76110e0bfc40c874f82e37cef6451d74df4f908
workflow graph exome alignment and germline variant detection

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

Path: definitions/pipelines/germline_exome.cwl

Branch/Commit ID: 5fda2d9eb52a363bd51011b3851c2afb86318c0c
workflow graph star_align_workflow.cwl

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

Path: rnaseq-star-align/subworkflows/rnaseq_processing/star_align_workflow.cwl

Branch/Commit ID: 88fb720c62a3c2b00ca475d412fba088c4a08f92
workflow graph SetEffectiveFocalLength

Calculate effective focal length for the given telescope optics.

 https://github.com/gammasim/workflows.git

Path: workflows/SetEffectiveFocalLength.cwl

Branch/Commit ID: 789752af87eb190387ff2acb4c95c7a5cdb961e7
workflow graph scatter-wf3.cwl#main

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

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

Branch/Commit ID: 9a23706ec061c5d2c02ff60238d218aadf0b5db9

Packed ID: main
workflow graph ValidateAtmosphericModel

Validate model of atmosphere

 https://github.com/gammasim/workflows.git

Path: workflows/ValidateAtmosphericModel.cwl

Branch/Commit ID: 789752af87eb190387ff2acb4c95c7a5cdb961e7
workflow graph Apply filters to VCF file

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

Path: definitions/subworkflows/filter_vcf_nonhuman.cwl

Branch/Commit ID: 5fda2d9eb52a363bd51011b3851c2afb86318c0c
workflow graph Per-region pindel

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

Path: definitions/subworkflows/pindel_cat.cwl

Branch/Commit ID: 5fda2d9eb52a363bd51011b3851c2afb86318c0c
workflow graph Trim Galore 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 **pair-end** experiment. A corresponded input [FASTQ](http://maq.sourceforge.net/fastq.shtml) file has to be provided. Current workflow must be used with paired-end RNA-Seq data. It performs the following steps: 1. Trim adapters from input FASTQ files 2. Use STAR to align reads from input FASTQ files according to the predefined reference indices; generate unsorted BAM file and alignment statistics file 3. Use fastx_quality_stats to analyze input FASTQ files and generate quality statistics files 4. Use samtools sort to generate coordinate sorted BAM(+BAI) file pair from the unsorted BAM file obtained on the step 2 (after running STAR) 5. Generate BigWig file using sorted BAM file 6. Map input FASTQ files 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/trim-rnaseq-pe.cwl

Branch/Commit ID: d76110e0bfc40c874f82e37cef6451d74df4f908