Explore Workflows

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Graph Name Retrieved From View
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: 42dc4f70b117e78785b82865ec4c4b941ac1c259
workflow graph pindel parallel workflow

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

Path: definitions/subworkflows/pindel.cwl

Branch/Commit ID: b9e7392e72506cadd898a6ac4db330baf6535ab6
workflow graph canine_vardict_module.cwl

https://github.com/d3b-center/canine-dev.git

Path: subworkflows/canine_vardict_module.cwl

Branch/Commit ID: 462aaebbd442e84ea101b45b716df0174b88512e
workflow graph assm_assm_blastn_wnode

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

Path: task_types/tt_assm_assm_blastn_wnode.cwl

Branch/Commit ID: 8a8fffb78b1e327ba0da51840ac8acc0c218d611
workflow graph sec-wf-out.cwl

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

Path: tests/wf/sec-wf-out.cwl

Branch/Commit ID: cd1ba3df3745fba4b635f05c67ebeaf3b8a9f4ec
workflow graph rna annotation

RNAs - predict, cluster, identify, annotate

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

Path: CWL/Workflows/rna-annotation.workflow.cwl

Branch/Commit ID: 6a8727124baf77416ca797982fd4e0689c2a593a
workflow graph DiffBind - Differential Binding Analysis of ChIP-Seq or CUTß&RUN/Tag Peak Data

Differential Binding Analysis of ChIP-Seq or CUT&RUN/Tag Peak Data --------------------------------------------------- DiffBind processes ChIP-Seq or CUT&RUN/Tag data enriched for genomic loci where specific protein/DNA binding occurs, including peak sets identified by peak caller tools and aligned sequence read datasets. It is designed to work with multiple peak sets simultaneously, representing different ChIP or CUT&RUN/Tag experiments (antibodies, transcription factor and/or histone marks, experimental conditions, replicates) as well as managing the results of multiple peak callers. For more information please refer to: ------------------------------------- Ross-Innes CS, Stark R, Teschendorff AE, Holmes KA, Ali HR, Dunning MJ, Brown GD, Gojis O, Ellis IO, Green AR, Ali S, Chin S, Palmieri C, Caldas C, Carroll JS (2012). “Differential oestrogen receptor binding is associated with clinical outcome in breast cancer.” Nature, 481, -4.

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

Path: workflows/diffbind.cwl

Branch/Commit ID: 549fac35bf6b8b1c25af0f4f6c3f162c40dc130e
workflow graph diadem_workflow_test1.cwl

https://github.com/cnherrera/CWL_Workflow_DIADEM_use_case.git

Path: diadem_workflow_test1.cwl

Branch/Commit ID: b3583f47fdbc2a1252b847cdf67470da80c14302
workflow graph RNA-Seq pipeline paired-end 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 pair-end** 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 the pair-end 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-pe-dutp-mitochondrial.cwl

Branch/Commit ID: 42dc4f70b117e78785b82865ec4c4b941ac1c259
workflow graph scatter2.cwl

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

Path: tests/wf/scatter2.cwl

Branch/Commit ID: 7bfe73a708dbf31d037303bb5a8fed1a79984b0f