Explore Workflows

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Graph Name Retrieved From View
workflow graph allele-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/datirium/workflows.git

Path: workflows/allele-alignreads-se-pe.cwl

Branch/Commit ID: 4b8bb1a1ec39056253ca8eee976078e51f4a954e
workflow graph bam_readcount workflow

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

Path: definitions/subworkflows/bam_readcount.cwl

Branch/Commit ID: 040a3d1a719736d7fce6db83702d3fb7f9d69eac
workflow graph cache_test_workflow.cwl

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

Path: tests/wf/cache_test_workflow.cwl

Branch/Commit ID: 31aa094dce60cbb176229d6b918bfd5ae09c0390
workflow graph Add snv and indel bam-readcount files to a vcf

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

Path: definitions/subworkflows/vcf_readcount_annotator.cwl

Branch/Commit ID: 040a3d1a719736d7fce6db83702d3fb7f9d69eac
workflow graph step-valuefrom2-wf.cwl

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

Path: v1.0/v1.0/step-valuefrom2-wf.cwl

Branch/Commit ID: 17695244222b0301b37cb749fe4a8d89622cd1ad
workflow graph umi molecular alignment workflow

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

Path: definitions/subworkflows/molecular_qc.cwl

Branch/Commit ID: 25aa4788dd4efb1cc8ed6f609cb7803896e4d28d
workflow graph exome alignment and germline variant detection

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

Path: definitions/pipelines/germline_exome.cwl

Branch/Commit ID: 457e101e3fb87e7fd792357afce00ed8ccbfbcdb
workflow graph downsample unaligned BAM and align

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

Path: definitions/subworkflows/downsampled_alignment.cwl

Branch/Commit ID: adcae308fdccaa1190083616118dfadb4df65dca
workflow graph picard_markduplicates

Mark duplicates

https://gitlab.bsc.es/lrodrig1/structuralvariants_poc.git

Path: structuralvariants/cwl/abstract_operations/subworkflows/picard_markduplicates.cwl

Branch/Commit ID: de9cb009f8fe0c8d5a94db5c882cf21ddf372452
workflow graph gatk4W.cwl

Author: AMBARISH KUMAR er.ambarish@gmail.com & ambari73_sit@jnu.ac.in This is a proposed standard operating procedure for genomic variant detection using GATK4. It is hoped to be effective and useful for getting SARS-CoV-2 genome variants. It uses Illumina RNASEQ reads and genome sequence.

https://github.com/ambarishK/bio-cwl-tools.git

Path: gatk4W.cwl

Branch/Commit ID: f2dab2d4e626a2a840fa840d7b190a82d4200b21