Explore Workflows

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

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

Branch/Commit ID: e284e3f6dff25037b209895c52f2abd37a1ce1bf
workflow graph allele-process-strain.cwl

https://github.com/datirium/workflows.git

Path: subworkflows/allele-process-strain.cwl

Branch/Commit ID: e9a24699d8b5ffe64412b1ba0af8448c281b223a
workflow graph Workflow to run pVACseq from detect_variants and rnaseq pipeline outputs

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

Path: definitions/subworkflows/pvacseq.cwl

Branch/Commit ID: 6949082038c1ad36d6e9848b97a2537aef2d3805
workflow graph cond-wf-001.cwl

https://github.com/common-workflow-language/cwl-v1.2.git

Path: tests/conditionals/cond-wf-001.cwl

Branch/Commit ID: 707ebcd2173889604459c5f4ffb55173c508abb3
workflow graph Nested workflow example

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

Path: tests/wf/nested.cwl

Branch/Commit ID: d6000d32f6c8fbd26421a2d30d79b28901d58fb0
workflow graph Per-chromosome pindel

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

Path: definitions/subworkflows/pindel_cat.cwl

Branch/Commit ID: a670f323e77e02d9b77be9a13d73d5276dd3676c
workflow graph heatmap-prepare.cwl

Workflow runs homer-make-tag-directory.cwl tool using scatter for the following inputs - bam_file - fragment_size - total_reads `dotproduct` is used as a `scatterMethod`, so one element will be taken from each array to construct each job: 1) bam_file[0] fragment_size[0] total_reads[0] 2) bam_file[1] fragment_size[1] total_reads[1] ... N) bam_file[N] fragment_size[N] total_reads[N] `bam_file`, `fragment_size` and `total_reads` arrays should have the identical order.

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

Path: tools/heatmap-prepare.cwl

Branch/Commit ID: b8e28a017f7b1a2900ec0fd3b3549f123f0c91b4
workflow graph gathered exome alignment and somatic variant detection for cle purpose

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

Path: definitions/pipelines/somatic_exome_cle_gathered.cwl

Branch/Commit ID: 27dcb1ae121be6a23057b74332b8c752ea425735
workflow graph rnaseq-se-dutp.cwl

RNA-Seq basic analysis workflow for strand specific single-read experiment.

https://github.com/datirium/workflows.git

Path: workflows/rnaseq-se-dutp.cwl

Branch/Commit ID: a9551ece898f619167db58e4b74a6cae2d7f7d13
workflow graph Build Bismark indices

Copy fasta_file file to the folder and run run bismark_genome_preparation script to prepare indices for Bismark Methylation Analysis. Bowtie2 aligner is used by default. The name of the output indices folder is equal to the genome input.

 https://github.com/datirium/workflows.git

Path: workflows/bismark-index.cwl

Branch/Commit ID: cbefc215d8286447620664fb47076ba5d81aa47f