Explore Workflows

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Graph Name Retrieved From View
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: 10ce6e113f749c7bd725e426445220c3bdc5ddf1
workflow graph WGS QC workflow

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

Path: definitions/subworkflows/qc_wgs.cwl

Branch/Commit ID: 1750cd5cc653f058f521b6195e3bec1e7df1a086
workflow graph align_sort_sa

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

Path: task_types/tt_align_sort_sa.cwl

Branch/Commit ID: a34f47d1e37af51e387ecdfa5c3047f106c1146b
workflow graph Genomic regions intersection and visualization

Genomic regions intersection and visualization ============================================== 1. Merges intervals within each of the filtered peaks files from ChIP/ATAC experiments 2. Overlaps merged intervals and assigns the nearest genes to them

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

Path: workflows/intervene.cwl

Branch/Commit ID: 581156366f91861bd4dbb5bcb59f67d468b32af3
workflow graph EMG pipeline v4.0 (single end version)

https://github.com/EBI-Metagenomics/ebi-metagenomics-cwl.git

Path: workflows/emg-pipeline-v4-single.cwl

Branch/Commit ID: cac44f2cf14110fde9951161c663c4525772f616
workflow graph Subworkflow that runs cnvkit in single sample mode and returns a vcf file

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

Path: definitions/subworkflows/cnvkit_single_sample.cwl

Branch/Commit ID: a7838a5ca72b25db5c2af20a15f34303a839980e
workflow graph Get Proteins

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

Path: wf_bacterial_prot_src.cwl

Branch/Commit ID: 22ffe27d9d4a899def7592d75d5871c1856adbdb
workflow graph format_rrnas_from_seq_entry

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

Path: task_types/tt_format_rrnas_from_seq_entry.cwl

Branch/Commit ID: 7319ccfd2108929588bdc266d9df198629dfaa65
workflow graph harmonization_novoalign_multi_readgroup.cwl

https://github.com/uc-cdis/genomel_pipelines.git

Path: genomel/cwl/workflows/harmonization/harmonization_novoalign_multi_readgroup.cwl

Branch/Commit ID: 3c62f1ddf8a54601da3cfc16c37d0cb0d6a2ea28
workflow graph conflict-wf.cwl#collision

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

Path: cwltool/schemas/v1.0/v1.0/conflict-wf.cwl

Branch/Commit ID: 9e7c68c0834645ba53a7e2b5f70d53df9d051c92

Packed ID: collision