Explore Workflows

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Graph Name Retrieved From View
workflow graph chipseq-se.cwl

Runs ChIP-Seq BioWardrobe basic analysis with single-end data file.

https://github.com/Barski-lab/workflows.git

Path: workflows/chipseq-se.cwl

Branch/Commit ID: 80d64741638b14de5cf58236b6d6d99713c62086
workflow graph bam_readcount workflow

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

Path: definitions/subworkflows/bam_readcount.cwl

Branch/Commit ID: 0805e8e0d358136468e0a9f49e06005e41965adc
workflow graph Replace legacy AML Trio Assay

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

Path: definitions/pipelines/aml_trio_cle.cwl

Branch/Commit ID: 3bebaf9b70331de9f4845e2223c55082f5a812fb
workflow graph Varscan Workflow

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

Path: definitions/subworkflows/varscan_pre_and_post_processing.cwl

Branch/Commit ID: 641083e9ed933d388f36fa04c00c20a810599e94
workflow graph paramref_arguments_self.cwl

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

Path: tests/wf/paramref_arguments_self.cwl

Branch/Commit ID: 898fddf9167620645177eb94c8ea68ede0667f96
workflow graph RNA-Seq pipeline single-read 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 single-read** 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 single-read 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-se-dutp-mitochondrial.cwl

Branch/Commit ID: 4dcc405133f22c63478b6091fb5f591b6be8950f
workflow graph CLE gold vcf evaluation workflow

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

Path: definitions/subworkflows/vcf_eval_cle_gold.cwl

Branch/Commit ID: 049f4aeff4c4a1b8421cac9b1c1c1f0da5848315
workflow graph wf-loadContents.cwl

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

Path: tests/wf-loadContents.cwl

Branch/Commit ID: 31ec48a8d81ef7c1b2c5e9c0a19e7623efe4a1e2
workflow graph mutect parallel workflow

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

Path: definitions/subworkflows/mutect.cwl

Branch/Commit ID: 4aba7c6591c2f1ebd827a36d325a58738c429bea
workflow graph count-lines9-wf.cwl

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

Path: cwltool/schemas/v1.0/v1.0/count-lines9-wf.cwl

Branch/Commit ID: 6003cbb94f16103241b562f2133e7c4acac6c621