Explore Workflows

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

Graph Name Retrieved From View
workflow graph tindaisy-hotspot.cwl

https://github.com/ding-lab/TinDaisy.git

Path: cwl/workflows/tindaisy-hotspot.cwl

Branch/Commit ID: e60b00da50d6479bf0a943c258d11dbf01203265
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: 00ced0fc44ceeb3495e891232e1000235e56ee6b
workflow graph step-valuefrom2-wf.cwl

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

Path: cwltool/schemas/v1.0/v1.0/step-valuefrom2-wf.cwl

Branch/Commit ID: f997d13af87216e9b5048c732a511053c7ba714c
workflow graph count-lines11-null-step-wf-noET.cwl

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

Path: tests/count-lines11-null-step-wf-noET.cwl

Branch/Commit ID: 50251ef931d108c09bed2d330d3d4fe9c562b1c3
workflow graph xenbase-sra-to-fastq-pe.cwl

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

Path: subworkflows/xenbase-sra-to-fastq-pe.cwl

Branch/Commit ID: 00ced0fc44ceeb3495e891232e1000235e56ee6b
workflow graph indexing_bed

https://gitlab.bsc.es/lrodrig1/structuralvariants_poc.git

Path: structuralvariants/cwl/subworkflows/indexing_bed.cwl

Branch/Commit ID: b62c7bfcf5eb7ac3c1ed06879200fdf5db947e4b
workflow graph Hello World

Outputs a message using echo

 https://github.com/common-workflow-library/legacy.git

Path: workflows/hello/hello.cwl

Branch/Commit ID: 767d700e602805112a4c953d166e570cddfa2605
workflow graph scatter-wf2.cwl

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

Path: tests/scatter-wf2.cwl

Branch/Commit ID: 5f27e234b4ca88ed1280dedf9e3391a01de12912
workflow graph RNA-Seq pipeline single-read strand specific

Note: should be updated The original [BioWardrobe's](https://biowardrobe.com) [PubMed ID:26248465](https://www.ncbi.nlm.nih.gov/pubmed/26248465) **RNA-Seq** basic analysis for **strand specific single-read** experiment. A corresponded input [FASTQ](http://maq.sourceforge.net/fastq.shtml) file has to be provided. Current workflow should be used only with the single-read RNA-Seq data. It performs the following steps: 1. Use STAR to align reads from input FASTQ file according to the predefined reference indices; generate unsorted BAM file and alignment statistics file 2. Use fastx_quality_stats to analyze input FASTQ file and generate quality statistics file 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) 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-se-dutp.cwl

Branch/Commit ID: 91bb63948c0a264334b9007ef85f936768d90d11
workflow graph count-lines11-extra-step-wf-noET.cwl

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

Path: tests/count-lines11-extra-step-wf-noET.cwl

Branch/Commit ID: 50251ef931d108c09bed2d330d3d4fe9c562b1c3