Explore Workflows

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

Graph Name Retrieved From View
workflow graph allele-vcf-alignreads-se-pe.cwl

Workflow maps FASTQ files from `fastq_files` input into reference genome `reference_star_indices_folder` and insilico generated `insilico_star_indices_folder` genome (concatenated genome for both `strain1` and `strain2` strains). For both genomes STAR is run with `outFilterMultimapNmax` parameter set to 1 to discard all of the multimapped reads. For insilico genome SAM file is generated. Then it's splitted into two SAM files based on strain names and then sorted by coordinates into the BAM format. For reference genome output BAM file from STAR slignment is also coordinate sorted.

https://github.com/Barski-lab/workflows.git

Path: subworkflows/allele-vcf-alignreads-se-pe.cwl

Branch/Commit ID: d93911fa135411fbab99513e4a672056b30490ce
workflow graph Whole genome alignment and somatic variant detection

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

Path: definitions/pipelines/somatic_wgs.cwl

Branch/Commit ID: 026bba9511561246ad65458f0f55c88cead26fbd
workflow graph RNA-Seq alignment and transcript/gene abundance workflow

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

Path: definitions/pipelines/rnaseq.cwl

Branch/Commit ID: 5c4125344b1b9125ad04d7e768ecc99901570a7a
workflow graph FASTQ to BQSR

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

Path: definitions/subworkflows/fastq_to_bqsr.cwl

Branch/Commit ID: 7b4b489474473c3d2d992a838b89632c2b97dc2c
workflow graph alignment for nonhuman with qc

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

Path: definitions/pipelines/alignment_wgs_nonhuman.cwl

Branch/Commit ID: fbeea265295ae596d5a3ba563e766be0c4fc26e8
workflow graph bacterial_kmer

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

Path: bacterial_kmer/wf_bacterial_kmer.cwl

Branch/Commit ID: 4def84df33963fc9ac9d5c5f804b911d01a0d9ad
workflow graph Create Genomic Collection for Bacterial Pipeline, ASN.1 input

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

Path: genomic_source/wf_genomic_source_asn.cwl

Branch/Commit ID: 4def84df33963fc9ac9d5c5f804b911d01a0d9ad
workflow graph varscan somatic workflow

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

Path: definitions/subworkflows/varscan.cwl

Branch/Commit ID: f7ac3eff79128831c9f7a565d5b187882f39aa58
workflow graph Apply filters to VCF file

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

Path: definitions/subworkflows/filter_vcf_mouse.cwl

Branch/Commit ID: 6949082038c1ad36d6e9848b97a2537aef2d3805
workflow graph taxonomy_check_16S

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

Path: task_types/tt_taxonomy_check_16S.cwl

Branch/Commit ID: 13b411d94a568e52797ba936732dc65f1a91bd41