Explore Workflows

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Graph Name Retrieved From View
workflow graph RNA-Seq pipeline single-read

The original [BioWardrobe's](https://biowardrobe.com) [PubMed ID:26248465](https://www.ncbi.nlm.nih.gov/pubmed/26248465) **RNA-Seq** basic analysis for a **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.cwl

Branch/Commit ID: 4ab9399a4777610a579ea2c259b9356f27641dcc
workflow graph Merge, annotate, and generate a TSV for SVs

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

Path: definitions/subworkflows/merge_svs.cwl

Branch/Commit ID: ffd73951157c61c1581d346628d75b61cdd04141
workflow graph fail-unconnected.cwl

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

Path: tests/fail-unconnected.cwl

Branch/Commit ID: a5073143db4155e05df8d2e7eb59d9e62acd65a5
workflow graph qc_workflow.cwl

https://github.com/andurill/ACCESS-Pipeline.git

Path: workflows/QC/qc_workflow.cwl

Branch/Commit ID: e7754fb4d3cd14068eef0c498cc5c6fcf53dc31f
workflow graph mut3.cwl

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

Path: tests/wf/mut3.cwl

Branch/Commit ID: 65aedc5e7e1f3ccace7f9022f8a54b3f0d5c9a8c
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: 4ab9399a4777610a579ea2c259b9356f27641dcc
workflow graph js-expr-req-wf.cwl#wf

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

Path: tests/js-expr-req-wf.cwl

Branch/Commit ID: a5073143db4155e05df8d2e7eb59d9e62acd65a5

Packed ID: wf
workflow graph kmer_seq_entry_extract_wnode

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

Path: task_types/tt_kmer_seq_entry_extract_wnode.cwl

Branch/Commit ID: 803f6367d1b279a7b6dc1a4e8ae43f1bbec9f760
workflow graph Subworkflow to allow calling different SV callers which require bam files as inputs

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

Path: definitions/subworkflows/single_sample_sv_callers.cwl

Branch/Commit ID: ae75b938e6e8ae777a55686bbacad824b3c6788c
workflow graph bird_workflow.cwl

https://github.com/ReddyLab/bird-workflow.git

Path: bird_workflow.cwl

Branch/Commit ID: 5e08b9b8a0323a1f4740a65bdb356e9b75074093