Explore Workflows

View already parsed workflows here or click here to add your own

Graph Name Retrieved From View
workflow graph Unaligned BAM to BQSR and VCF

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

Path: definitions/subworkflows/bam_to_bqsr.cwl

Branch/Commit ID: 641083e9ed933d388f36fa04c00c20a810599e94
workflow graph rest_parallel.cwl

https://github.com/CWL-FLOps/DecentralizedFL-CWL.git

Path: CWL_Workflow/rest_parallel.cwl

Branch/Commit ID: 08e2a93bb1ec71bd02ff2c3470e39d703715fa59
workflow graph Unaligned bam to sorted, markduped bam

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

Path: definitions/subworkflows/align_sort_markdup.cwl

Branch/Commit ID: 5fda2d9eb52a363bd51011b3851c2afb86318c0c
workflow graph tt_hmmsearch_wnode.cwl

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

Path: task_types/tt_hmmsearch_wnode.cwl

Branch/Commit ID: 4ab36e0fe1b0ab18cad9d8f1c1f806ec316d7734
workflow graph Run pindel on provided region

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

Path: definitions/subworkflows/pindel_region.cwl

Branch/Commit ID: 2e298960837739717ec2928a99c5d811183012e6
workflow graph pair-workflow.cwl

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

Path: workflows/pair-workflow.cwl

Branch/Commit ID: 7c694b51d9d593439cf8ab3e5006665f0bbe2149
workflow graph sequence (bam or fastqs) to trimmed fastqs

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

Path: definitions/subworkflows/sequence_to_trimmed_fastq.cwl

Branch/Commit ID: 5fda2d9eb52a363bd51011b3851c2afb86318c0c
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: a1f6ca50fcb0881781b3ba0306dd61ebf555eaba
workflow graph workflow.cwl

https://github.com/nal-i5k/organism_onboarding.git

Path: flow_download/workflow.cwl

Branch/Commit ID: 556884e8e205295e561b1d9140d836cdd6c1d8c9
workflow graph fasta2taxa-plot

Input is a fasta file with n>1 samples, with sample id as sequence identifier prefix, and a sample id file. The workflow calls open otus and assigns taxa using greengenes. The output are taxa plots.

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

Path: CWL/Workflows/qiime/join-reads2reference2plot.cwl

Branch/Commit ID: cd7b1a7b05f0d716ad784bc4911f5850a7737a40