Explore Workflows

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

Graph Name Retrieved From View
workflow graph bam to trimmed fastqs and biscuit alignments

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

Path: definitions/subworkflows/bam_to_trimmed_fastq_and_biscuit_alignments.cwl

Branch/Commit ID: 22fce2dbdada0c4135b6f0677f78535cf980cb07
workflow graph Apply filters to VCF file

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

Path: definitions/subworkflows/germline_filter_vcf.cwl

Branch/Commit ID: 6d03a918639a69ddf6a7b93fe9f72128ef37edc3
workflow graph scatter GATK HaplotypeCaller over intervals

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

Path: definitions/subworkflows/gatk_haplotypecaller_iterator.cwl

Branch/Commit ID: 6d03a918639a69ddf6a7b93fe9f72128ef37edc3
workflow graph bgzip and index VCF

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

Path: definitions/subworkflows/bgzip_and_index.cwl

Branch/Commit ID: da335d9963418f7bedd84cb2791a0df1b3165ffe
workflow graph foldseek easy-search workflow

\"foldseek easy-search sub-workflow for plant2human workflow Step 1: listing files Step 2: foldseek easy-search process\"

https://github.com/yonesora56/plant2human.git

Path: Workflow/10_foldseek_easy_search_wf.cwl

Branch/Commit ID: 11b46d8d8c0db462edbd2657fc62cf31bc93ecee
workflow graph record-output-wf_v1_1.cwl

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

Path: testdata/record-output-wf_v1_1.cwl

Branch/Commit ID: 7af75226f084349e401b1114f25bdcdee060e127
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: 664de58d95728edbf7d369d894f9037ebe2475fa
workflow graph sum-wf.cwl

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

Path: tests/sum-wf.cwl

Branch/Commit ID: 664835e83eb5e57eee18a04ce7b05fb9d70d77b7
workflow graph Deprecated. RNA-Seq pipeline paired-end strand specific

The original [BioWardrobe's](https://biowardrobe.com) [PubMed ID:26248465](https://www.ncbi.nlm.nih.gov/pubmed/26248465) **RNA-Seq** basic analysis for a **paired-end** experiment. A corresponded input [FASTQ](http://maq.sourceforge.net/fastq.shtml) file has to be provided. Current workflow should be used only with the paired-end RNA-Seq data. It performs the following steps: 1. Use STAR to align reads from input FASTQ files according to the predefined reference indices; generate unsorted BAM file and alignment statistics file 2. Use fastx_quality_stats to analyze input FASTQ files and generate quality statistics files 3. Use samtools sort to generate coordinate sorted BAM(+BAI) file pair from the unsorted BAM file obtained on the step 1 (after running STAR) 4. Generate BigWig file on the base of sorted BAM file 5. Map input FASTQ files to predefined rRNA reference indices using Bowtie to define the level of rRNA contamination; export resulted statistics to file 6. 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.cwl

Branch/Commit ID: 7030da528559c7106d156284e50ff0ecedab0c4e
workflow graph count-lines7-wf_v1_0.cwl

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

Path: testdata/count-lines7-wf_v1_0.cwl

Branch/Commit ID: 7af75226f084349e401b1114f25bdcdee060e127