Explore Workflows

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

Graph Name Retrieved From View
workflow graph strelka workflow

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

Path: definitions/subworkflows/strelka_and_post_processing.cwl

Branch/Commit ID: a7838a5ca72b25db5c2af20a15f34303a839980e
workflow graph RNA-Seq pipeline paired-end

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.cwl

Branch/Commit ID: b957a4f681bf0ca8ebba4e0d0ec3936bf79620c5
workflow graph kmer_ref_compare_wnode

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

Path: task_types/tt_kmer_ref_compare_wnode.cwl

Branch/Commit ID: f5c11df465aaadf712c38ba4933679fe1cbe03ca
workflow graph mpi_simple_wf.cwl

Simple 2 step workflow to check that workflow steps are independently picking up on the number of processes. First run the parallel get PIDs step (on the input num procs) then run (on a single proc) the line count. This should equal the input.

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

Path: tests/wf/mpi_simple_wf.cwl

Branch/Commit ID: 981c03099f79b5aad74555787d406f695dd0b320
workflow graph tt_kmer_top_n.cwl

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

Path: task_types/tt_kmer_top_n.cwl

Branch/Commit ID: bba6c580ab88e077f6aa2c2ee7c73159f3f9156e
workflow graph Long-covid.cwl

https://github.com/cwlviewer-test/Long-covid---aedea650-7a21-11ed-b9d2-e51f21933d80-1.git

Path: Long-covid---aede7f40-7a21-11ed-b9d2-e51f21933d80/Long-covid.cwl

Branch/Commit ID: read-potential-cases-disc
workflow graph count-lines11-wf.cwl

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

Path: cwltool/schemas/v1.0/v1.0/count-lines11-wf.cwl

Branch/Commit ID: 3e9bca4e006eae7e9febd76eb9b8292702eba2cb
workflow graph bam to trimmed fastqs and HISAT alignments

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

Path: definitions/subworkflows/bam_to_trimmed_fastq_and_hisat_alignments.cwl

Branch/Commit ID: 441b85003fdc10cf4cbf333d89acb4d23b0fef32
workflow graph Generate ATDP heatmap using Homer

Generate ATDP heatmap centered on TSS from an array of input BAM files and genelist TSV file. Returns array of heatmap JSON files with the names that have the same basenames as input BAM files, but with .json extension

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

Path: workflows/heatmap.cwl

Branch/Commit ID: 12c29f88855329192bfff977f046990031f04931
workflow graph ani_top_n

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

Path: task_types/tt_ani_top_n.cwl

Branch/Commit ID: 146df33e2e44afa2a608ac72c036e6b6b871af93