Explore Workflows

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Graph Name Retrieved From View
workflow graph Build STAR indices

Workflow runs [STAR](https://github.com/alexdobin/STAR) v2.5.3a (03/17/2017) PMID: [23104886](https://www.ncbi.nlm.nih.gov/pubmed/23104886) to build indices for reference genome provided in a single FASTA file as fasta_file input and GTF annotation file from annotation_gtf_file input. Generated indices are saved in a folder with the name that corresponds to the input genome.

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

Path: workflows/star-index.cwl

Branch/Commit ID: bf80c9339d81a78aefb8de661bff998ed86e836e
workflow graph AcceptParameterFailure

validation or review of parameter updates failed. Action required and feedback to be provided.

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

Path: workflows/AcceptParameterFailure.cwl

Branch/Commit ID: 789752af87eb190387ff2acb4c95c7a5cdb961e7
workflow graph trim-rnaseq-pe.cwl

Runs RNA-Seq BioWardrobe basic analysis with pair-end data file.

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

Path: workflows/trim-rnaseq-pe.cwl

Branch/Commit ID: 812b0ff40dda18ab7a9a872ff13a577be8531ba6
workflow graph Quality assessment, amplicon classification and functional prediction

Workflow for quality assessment of paired reads and classification using NGTax 2.0 and functional annotation using picrust2. In addition files are exported to their respective subfolders for easier data management in a later stage. Steps: - FastQC (read quality control) - NGTax 2.0 - Picrust 2 - Export module for ngtax

https://git.wur.nl/unlock/cwl.git

Path: cwl/workflows/workflow_ngtax_picrust2.cwl

Branch/Commit ID: 2242521957bb07fc589d6bb07046f6a166bc975a
workflow graph animal-genome-assembly.with_canu.cwl

Animal Genome Assembly pipeline by Kazuharu Arakawa (@gaou_ak), CWLized by Tazro Ohta (@inutano). This workflow contains assembly step by canu which may take a few weeks to complete. Be careful to run!

 https://github.com/pitagora-network/DAT2-cwl.git

Path: workflow/animal-genome-assembly/animal-genome-assembly.with_canu.cwl

Branch/Commit ID: b63171820f546def8c26f558182912a71af88b48
workflow graph exomeseq-01-preprocessing.cwl

https://github.com/Duke-GCB/bespin-cwl.git

Path: subworkflows/exomeseq-01-preprocessing.cwl

Branch/Commit ID: 727ad5dbd15ef6aaa9cd5a3f7b23e74ff74663ea
workflow graph bam-bedgraph-bigwig.cwl

Workflow converts input BAM file into bigWig and bedGraph files. Input BAM file should be sorted by coordinates (required by `bam_to_bedgraph` step). If `split` input is not provided use true by default. Default logic is implemented in `valueFrom` field of `split` input inside `bam_to_bedgraph` step to avoid possible bug in cwltool with setting default values for workflow inputs. `scale` has higher priority over the `mapped_reads_number`. The last one is used to calculate `-scale` parameter for `bedtools genomecov` (step `bam_to_bedgraph`) only in a case when input `scale` is not provided. All logic is implemented inside `bedtools-genomecov.cwl`. `bigwig_filename` defines the output name only for generated bigWig file. `bedgraph_filename` defines the output name for generated bedGraph file and can influence on generated bigWig filename in case when `bigwig_filename` is not provided. All workflow inputs and outputs don't have `format` field to avoid format incompatibility errors when workflow is used as subworkflow.

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

Path: tools/bam-bedgraph-bigwig.cwl

Branch/Commit ID: 94c6ea7bf4b64599746d778568efbd8e10f0d5ba
workflow graph bam_readcount workflow

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

Path: definitions/subworkflows/bam_readcount.cwl

Branch/Commit ID: 5cb188131f786ed33156e2f0e3dd63ab9c04245d
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: 5cb188131f786ed33156e2f0e3dd63ab9c04245d
workflow graph Running cellranger count and lineage inference

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

Path: definitions/subworkflows/single_cell_rnaseq.cwl

Branch/Commit ID: bcc6adaf15035f5ce6fc851e27b1173b0fd20c1c