Explore Workflows

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

Graph Name Retrieved From View
workflow graph Hello World

Outputs a message using echo

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

Path: tests/wf/hello-workflow.cwl

Branch/Commit ID: 7bfe73a708dbf31d037303bb5a8fed1a79984b0f
workflow graph canine_snpeff_module.cwl

https://github.com/d3b-center/canine-dev.git

Path: subworkflows/canine_snpeff_module.cwl

Branch/Commit ID: 462aaebbd442e84ea101b45b716df0174b88512e
workflow graph PCA - Principal Component Analysis

Principal Component Analysis --------------- Principal component analysis (PCA) is a statistical procedure that uses an orthogonal transformation to convert a set of observations of possibly correlated variables (entities each of which takes on various numerical values) into a set of values of linearly uncorrelated variables called principal components. The calculation is done by a singular value decomposition of the (centered and possibly scaled) data matrix, not by using eigen on the covariance matrix. This is generally the preferred method for numerical accuracy.

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

Path: workflows/pca.cwl

Branch/Commit ID: bf80c9339d81a78aefb8de661bff998ed86e836e
workflow graph Run tRNAScan

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

Path: bacterial_trna/wf_trnascan.cwl

Branch/Commit ID: 9f45453202aedb6c91ecd6a0e8c91730cca646de
workflow graph count-lines2-wf.cwl

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

Path: cwltool/schemas/v1.0/v1.0/count-lines2-wf.cwl

Branch/Commit ID: bfe56f3138e9e6fc0b9b8c06447553d4cea03d59
workflow graph WGS QC workflow

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

Path: definitions/subworkflows/qc_wgs.cwl

Branch/Commit ID: 258bd4353ad1ca7790b3ae626bf42ab8194e7561
workflow graph umi per-lane alignment subworkflow

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

Path: definitions/subworkflows/umi_alignment.cwl

Branch/Commit ID: 31a179d7a2f2ac86bfd7fcc4dc79832c3739ae76
workflow graph Bisulfite QC tools

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

Path: definitions/subworkflows/bisulfite_qc.cwl

Branch/Commit ID: aba52e94b6d7470132d3c092c26d67e29d615300
workflow graph RNA-Seq pipeline paired-end stranded mitochondrial

Slightly changed original [BioWardrobe's](https://biowardrobe.com) [PubMed ID:26248465](https://www.ncbi.nlm.nih.gov/pubmed/26248465) **RNA-Seq** basic analysis for **strand specific pair-end** experiment. An additional steps were added to map data to mitochondrial chromosome only and then merge the output. Experiment files in [FASTQ](http://maq.sourceforge.net/fastq.shtml) format either compressed or not can be used. Current workflow should be used only with the pair-end strand specific RNA-Seq data. It performs the following steps: 1. `STAR` to align reads from input FASTQ file according to the predefined reference indices; generate unsorted BAM file and alignment statistics file 2. `fastx_quality_stats` to analyze input FASTQ file and generate quality statistics file 3. `samtools sort` to generate coordinate sorted BAM(+BAI) file pair from the unsorted BAM file obtained on the step 1 (after running STAR) 5. Generate BigWig file on the base of sorted BAM file 6. Map input FASTQ file to predefined rRNA reference indices using Bowtie to define the level of rRNA contamination; export resulted statistics to file 7. Calculate isoform expression level for the sorted BAM file and GTF/TAB annotation file using `GEEP` reads-counting utility; export results to file

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

Path: workflows/rnaseq-pe-dutp-mitochondrial.cwl

Branch/Commit ID: bf80c9339d81a78aefb8de661bff998ed86e836e
workflow graph tt_blastn_wnode

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

Path: task_types/tt_blastn_wnode.cwl

Branch/Commit ID: 205f4ceb47ba7537a6923d2dfb03668317c2fd89