Explore Workflows

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

Graph Name Retrieved From View
workflow graph PerformanceSummaryGenome_v0_1_0.cwl

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

Path: janis_pipelines/wgs_somatic/cwl/tools/PerformanceSummaryGenome_v0_1_0.cwl

Branch/Commit ID: d3ae7483f860339a12c5f404de9db0f026571f77
workflow graph checkm_wnode

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

Path: task_types/tt_checkm_wnode.cwl

Branch/Commit ID: 91181df8d9ef8eed9d8f40db707b9a4376fecaf5
workflow graph allele-process-strain.cwl

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

Path: subworkflows/allele-process-strain.cwl

Branch/Commit ID: 915ea871cc28f7b666a4d7b476fdaa7b454ce7c3
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: 915ea871cc28f7b666a4d7b476fdaa7b454ce7c3
workflow graph tt_kmer_top_n.cwl

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

Path: task_types/tt_kmer_top_n.cwl

Branch/Commit ID: 4533a5e930305c674057bc4cf5dda4f39d39b5df
workflow graph count-lines9-wf.cwl

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

Path: cwltool/schemas/v1.0/v1.0/count-lines9-wf.cwl

Branch/Commit ID: d7b1bf353dcc43c707c49a018f2870584821d389
workflow graph xenbase-fastq-bowtie-bigwig-se-pe.cwl

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

Path: subworkflows/xenbase-fastq-bowtie-bigwig-se-pe.cwl

Branch/Commit ID: 915ea871cc28f7b666a4d7b476fdaa7b454ce7c3
workflow graph spurious_annot

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

Path: spurious_annot/wf_spurious_annot_pass1.cwl

Branch/Commit ID: 91181df8d9ef8eed9d8f40db707b9a4376fecaf5
workflow graph Bacterial Annotation, pass 4, blastp-based functional annotation (second pass)

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

Path: bacterial_annot/wf_bacterial_annot_pass4.cwl

Branch/Commit ID: 91181df8d9ef8eed9d8f40db707b9a4376fecaf5
workflow graph process VCF workflow

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

Path: definitions/subworkflows/strelka_process_vcf.cwl

Branch/Commit ID: 0d2f354af9192a56af258a7d2426c7c160f4ec1a