Explore Workflows

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Graph Name Retrieved From View
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: 664de58d95728edbf7d369d894f9037ebe2475fa
workflow graph Create target and anti-target files for CNA analysis

https://github.com/ChrisMaherLab/PACT.git

Path: subworkflows/cnvkit_prep_regions.cwl

Branch/Commit ID: 656d9ae18f164f983c5672bcf51037cd73309f4f
workflow graph Process cnvkit outputs

https://github.com/ChrisMaherLab/PACT.git

Path: subworkflows/process_cnvkit_results.cwl

Branch/Commit ID: 656d9ae18f164f983c5672bcf51037cd73309f4f
workflow graph Calculate reference coverage

https://github.com/ChrisMaherLab/PACT.git

Path: subworkflows/cna_reference_coverage.cwl

Branch/Commit ID: 656d9ae18f164f983c5672bcf51037cd73309f4f
workflow graph BwaAligner_1_0_0.cwl

https://github.com/PMCC-BioinformaticsCore/janis-pipelines.git

Path: janis_pipelines/wgs_somatic/cwl/tools/BwaAligner_1_0_0.cwl

Branch/Commit ID: d1bcf010d5c39d5fc01b8862db4f258df7d4f65d
workflow graph exome alignment and germline variant detection, with optitype for HLA typing

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

Path: definitions/pipelines/germline_exome_hla_typing.cwl

Branch/Commit ID: 8da2b1cd6fa379b2c22baf9dad762d39630e6f46
workflow graph Seed Protein Alignments

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

Path: protein_alignment/wf_seed_1.cwl

Branch/Commit ID: 96dbb414d287f4382e2d477fb1851aeaa5f14f2b
workflow graph Seed Search Compartments

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

Path: protein_alignment/wf_seed.cwl

Branch/Commit ID: 96dbb414d287f4382e2d477fb1851aeaa5f14f2b
workflow graph func_summaries.cwl

https://github.com/EBI-Metagenomics/pipeline-v5.git

Path: workflows/subworkflows/func_summaries.cwl

Branch/Commit ID: a83ee883bb3c7480010fa952939fac771491ddf4
workflow graph Per-region pindel

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

Path: definitions/subworkflows/pindel_cat.cwl

Branch/Commit ID: 8da2b1cd6fa379b2c22baf9dad762d39630e6f46