Explore Workflows

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

Graph Name Retrieved From View
workflow graph RNA-Seq alignment and transcript/gene abundance workflow

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

Path: definitions/pipelines/rnaseq.cwl

Branch/Commit ID: 789267ce0e3fed674ea5212a562315218fcf1bfc
workflow graph gathered exome alignment and somatic variant detection

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

Path: definitions/pipelines/gathered_somatic_exome.cwl

Branch/Commit ID: ddb49a0951d9ad537269d7db3fe8f904495a8bf4
workflow graph wgs alignment and germline variant detection

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

Path: definitions/pipelines/germline_wgs.cwl

Branch/Commit ID: a59a803e1809a8fbfabca6b8962a8ad66dd01f1d
workflow graph scatter-wf4.cwl#main

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

Path: tests/wf/scatter-wf4.cwl

Branch/Commit ID: 2a8af96d334e6979cb00af4569581d192d43ce41

Packed ID: main
workflow graph umi duplex alignment fastq workflow

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

Path: definitions/pipelines/alignment_umi_duplex.cwl

Branch/Commit ID: 0d2f354af9192a56af258a7d2426c7c160f4ec1a
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: b5e16e359007150647b14dc6e038f4eb8dccda79
workflow graph scatter-wf4.cwl#main

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

Path: tests/wf/scatter-wf4.cwl

Branch/Commit ID: 047e69bb169e79fad6a7285ee798c4ecec3b218b

Packed ID: main
workflow graph AltAnalyze Prepare Genome

Devel version of AltAnalyze Prepare Genome ========================================== hg38 is not supported. Use hardcoded EnsMart72 until AltAnalyze starts support more recent Ensembl releases.

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

Path: workflows/altanalyze-prepare-genome.cwl

Branch/Commit ID: 5561f7ee11dd74848680351411a19aa87b13d27b
workflow graph extract_gencoll_ids

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

Path: task_types/tt_extract_gencoll_ids.cwl

Branch/Commit ID: 72804b6506c9f54ec75627f82aafe6a28d7a49fa
workflow graph samples_fillout_index_batch_workflow.cwl

Wrapper to run bam indexing on all bams before submitting for samples fillout Also includes steps to pre-filter some maf input files NOTE: each sample in a sample_group must have a .bam file, and there must be a minumum of 1 .maf file amoungst samples in the same sample_group this means that for each sample in the sample_group, a .bam is required but a .maf is optional as long as one sample in the group has a .maf this also means that singleton sample groups, or a sample group with only one sample, MUST include a .maf file; singletons cannot lack a .maf NOTE: all .maf files must be valid, at a minimum they must have a header and at least one variant if a sample has no variants in its .maf file, or has an empty .maf file, then it should NOT have a maf_file entry associated with it

https://github.com/mskcc/pluto-cwl.git

Path: cwl/samples_fillout_index_batch_workflow.cwl

Branch/Commit ID: 462f6015c9268a4205b6e81de018a470b8a4a153