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/datirium/workflows.git

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

Branch/Commit ID: 62323c137c0ce9b3f843df0dfbda28dafa7c90cf
workflow graph step-valuefrom2-wf.cwl

https://github.com/common-workflow-language/cwl-v1.1.git

Path: tests/step-valuefrom2-wf.cwl

Branch/Commit ID: 0e37d46e793e72b7c16b5ec03e22cb3ce1f55ba3
workflow graph align_sort_sa

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

Path: task_types/tt_align_sort_sa.cwl

Branch/Commit ID: 16d1198871195e2229fd44dd0ad94a4ed6a87caf
workflow graph taxonomy_check_16S

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

Path: task_types/tt_taxonomy_check_16S.cwl

Branch/Commit ID: 9abcceb95c8dcb74b98d7eeda265d8f3a9a4329e
workflow graph cache_asnb_entries

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

Path: task_types/tt_cache_asnb_entries.cwl

Branch/Commit ID: 686b570a9fa46f3ace3f8e9935490b75df86a1fc
workflow graph step-valuefrom2-wf.cwl

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

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

Branch/Commit ID: d7b1bf353dcc43c707c49a018f2870584821d389
workflow graph chksum_for_a_corrupted_xam_file.cwl

https://github.com/cancerit/workflow-seq-import.git

Path: cwls/chksum_for_a_corrupted_xam_file.cwl

Branch/Commit ID: 0b1274e5c3a0a70dc989ac6463f7a6db5cf563c1
workflow graph align_merge_sas

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

Path: task_types/tt_align_merge_sas.cwl

Branch/Commit ID: 9abcceb95c8dcb74b98d7eeda265d8f3a9a4329e
workflow graph wgs alignment with qc

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

Path: definitions/pipelines/alignment_wgs.cwl

Branch/Commit ID: 789267ce0e3fed674ea5212a562315218fcf1bfc
workflow graph step-valuefrom-wf.cwl

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

Path: cwltool/schemas/v1.0/v1.0/step-valuefrom-wf.cwl

Branch/Commit ID: d7b1bf353dcc43c707c49a018f2870584821d389