Explore Workflows

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Graph Name Retrieved From View
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: bf80c9339d81a78aefb8de661bff998ed86e836e
workflow graph tt_blastn_wnode

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

Path: task_types/tt_blastn_wnode.cwl

Branch/Commit ID: 205f4ceb47ba7537a6923d2dfb03668317c2fd89
workflow graph cluster_blastp_wnode and gpx_qdump combined

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

Path: task_types/tt_cluster_and_qdump.cwl

Branch/Commit ID: e4d6182d5f7a6a880e5f2b21273cf40d25e187df
workflow graph consensus_maf.cwl

Workflow to merge a large number of maf files into a single consensus maf file for use with GetBaseCountsMultiSample

https://github.com/mskcc/pluto-cwl.git

Path: cwl/consensus_maf.cwl

Branch/Commit ID: d8a8af9fdb69c0a4003680c1d3b96f35d5e48f0e
workflow graph extract_gencoll_ids

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

Path: task_types/tt_extract_gencoll_ids.cwl

Branch/Commit ID: 55b6ee46b0c9fb1c9949cd0888b388c6f11b73b1
workflow graph umi molecular alignment fastq workflow

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

Path: definitions/pipelines/alignment_umi_molecular.cwl

Branch/Commit ID: f615832615c3b41728df8e47b72ef11e37e6a9e5
workflow graph completeWorkflow.cwl

https://github.com/h3abionet/h3abionet16S.git

Path: workflows-cwl/completeWorkflow.cwl

Branch/Commit ID: cacddec9c7a14a22365d9b251e584c7f96f7b4bf
workflow graph count-lines8-wf.cwl

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

Path: tests/count-lines8-wf.cwl

Branch/Commit ID: a5073143db4155e05df8d2e7eb59d9e62acd65a5
workflow graph indexing_bed

https://gitlab.bsc.es/lrodrig1/structuralvariants_poc.git

Path: structuralvariants/subworkflows/indexing_bed.cwl

Branch/Commit ID: d07f44fc5c253dc4044d86ea79ac6f9e03c01bfa
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: dc2c019c1aa24cc01b451a0f048cf94a35f163c4