Explore Workflows

https://github.com/reanahub/reana-demo-worldpopulation.git

Path: workflow/cwl/worldpopulation-slurmcern.cwl

Branch/Commit ID: 7d08708a8deff739a2b9bc0a7b2d4e50105f21d8

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: d6ec0dee61ef65a110e10141bde1a79332a64ab0

https://github.com/NCI-GDC/gdc-dnaseq-cwl.git

Path: subworkflows/main/gdc_dnaseq_main_workflow.cwl

Branch/Commit ID: e0f19eb6da82b643ce891f81a8a127dee48ba97a

https://github.com/FAIR-tools/workflow-description.git

Path: cwl/workflow.cwl

Branch/Commit ID: f701312fc2a6066aab39c516a0a37ff95cd1ec4b

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

Path: definitions/pipelines/aml_trio_cle.cwl

Branch/Commit ID: 2e298960837739717ec2928a99c5d811183012e6

https://github.com/common-workflow-language/cwl-v1.1.git

Path: tests/wf-loadContents3.cwl

Branch/Commit ID: 368b562a1449e8cd39ae8b7f05926b2bfb9b22df

GATK4.1.2 Alignment artifacts filtration workflow

https://github.com/nci-gdc/gatk4_mutect2_cwl.git

Path: subworkflows/filter_alignment_artifacts.cwl

Branch/Commit ID: 138d484362084dfc97d9fb7d839855b4bc2c5599

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

Path: spurious_annot/wf_spurious_annot_pass1.cwl

Branch/Commit ID: 4ab36e0fe1b0ab18cad9d8f1c1f806ec316d7734

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

Path: v1.0/v1.0/scatter-valuefrom-wf3.cwl

Branch/Commit ID: 22490926651174c6cbe01c76c2ded3c9e8d0ee6f

Packed ID: main

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

Path: tests/wf/1st-workflow.cwl

Branch/Commit ID: 691dea280b40ac177b4a38b33375139ca0ce7e81