Explore Workflows

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Graph Name Retrieved From View
workflow graph metabarcode (gene amplicon) analysis for fastq files

protein - qc, preprocess, annotation, index, abundance

 https://github.com/MG-RAST/pipeline.git

Path: CWL/Workflows/metabarcode-fasta.workflow.cwl

Branch/Commit ID: d9cf22cd615542c94f7974e8bce4cf29b24d985f
workflow graph conflict-wf.cwl#collision

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

Path: tests/conflict-wf.cwl

Branch/Commit ID: 1f3ef888d9ef2306c828065c460c1800604f0de4

Packed ID: collision
workflow graph Detect DoCM variants

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

Path: definitions/subworkflows/docm_germline.cwl

Branch/Commit ID: e59c77629936fad069007ba642cad49fef7ad29f
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: a68821bf3a9ceadc3b2ffbb535d601d9a645b377
workflow graph ani.cwl

Perform taxonomic identification tasks on an input genome

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

Path: ani.cwl

Branch/Commit ID: bba6c580ab88e077f6aa2c2ee7c73159f3f9156e
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: c5bae2ca862c764911b83d1f15ff6af4e2a0db28
workflow graph kmer_top_n_extract

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

Path: task_types/tt_kmer_top_n_extract.cwl

Branch/Commit ID: 9e43bc5cff985574e1f8135d4c50b5a347517c9e
workflow graph umi duplex alignment workflow

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

Path: definitions/subworkflows/duplex_alignment.cwl

Branch/Commit ID: c711498c04d6b8ddf92ddceb6219f074765f7993
workflow graph parallel_no_threshold.cwl

https://github.com/yuandou168/FL_workflows.git

Path: workflows/parallel_no_threshold.cwl

Branch/Commit ID: 0f9e76d981ca7b100fb9e170519b427926e590a0
workflow graph rnaseq-se.cwl

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

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

Path: workflows/rnaseq-se.cwl

Branch/Commit ID: ea2a2ab57710fcf067f67305f3dd6ad29094da1a