Explore Workflows
View already parsed workflows here or click here to add your own
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collate_unique_SSU_headers.cwl
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https://github.com/ProteinsWebTeam/ebi-metagenomics-cwl.git
Path: tools/collate_unique_SSU_headers.cwl Branch/Commit ID: c1f8b22 |
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checker-workflow-wrapping-workflow.cwl
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https://github.com/ICGC-TCGA-PanCancer/Seqware-BWA-Workflow.git
Path: checker-workflow-wrapping-workflow.cwl Branch/Commit ID: 2.6.8_1.4 |
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group-isoforms-batch.cwl
Workflow runs group-isoforms.cwl tool using scatter for isoforms_file input. genes_filename and common_tss_filename inputs are ignored. |
https://github.com/mr-c/datirium-workflows.git
Path: tools/group-isoforms-batch.cwl Branch/Commit ID: license_test |
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FragPipe: TMT Integrator and QC
This workflow step executes TMT-Integrator using the report tables generated by Philosopher. The program applies a series of statistical filters, and high-quality thresholds to filter the data. Summary report tables are created containing peptides, proteins, genes, and phosphosites (only for phospho-enriched data sets). |
https://github.com/cwl-apps/fragpipe-proteomics-pipeline-tutorial.git
Path: FragPipe-TMT-Integrator-and-QC/fragpipe-tmt-integrator-and-qc.cwl Branch/Commit ID: main |
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Trim Galore SMARTer RNA-Seq pipeline paired-end strand specific
https://chipster.csc.fi/manual/library-type-summary.html Modified original [BioWardrobe's](https://biowardrobe.com) [PubMed ID:26248465](https://www.ncbi.nlm.nih.gov/pubmed/26248465) **RNA-Seq** basic analysis for a **pair-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 single-end RNA-Seq data. It performs the following steps: 1. Trim adapters from input FASTQ files 2. Use STAR to align reads from input FASTQ files according to the predefined reference indices; generate unsorted BAM file and alignment statistics file 3. Use fastx_quality_stats to analyze input FASTQ files and generate quality statistics files 4. Use 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 files 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/trim-rnaseq-pe-smarter-dutp.cwl Branch/Commit ID: b4d578c2ba4713a5a22163d9f8c7105acda1f22e |
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pipeline-pe.cwl
STARR-seq pipeline - reads: PE |
https://github.com/alexbarrera/GGR-cwl.git
Path: v1.0/STARR-seq_pipeline/pipeline-pe.cwl Branch/Commit ID: master |
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count-lines11-null-step-wf.cwl
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https://github.com/common-workflow-language/cwl-v1.1.git
Path: tests/count-lines11-null-step-wf.cwl Branch/Commit ID: main |
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fusion_workflow.cwl
Fusion workflow, runs STARFusion and Arriba |
https://github.com/BD2KGenomics/dockstore_workflow_fusion.git
Path: fusion_workflow.cwl Branch/Commit ID: master |
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Build Bismark indices
Copy fasta_file file to the folder and run run bismark_genome_preparation script to prepare indices for Bismark Methylation Analysis. Bowtie2 aligner is used by default. The name of the output indices folder is equal to the genome input. |
https://github.com/datirium/workflows.git
Path: workflows/bismark-index.cwl Branch/Commit ID: 7eef0294395d83ff0765fce61726a59d71126422 |
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wf_get_peaks_scatter_se.cwl
The \"main\" workflow. Takes fastq files generated using the seCLIP protocol (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5991800/) and outputs candidate RBP binding regions (peaks). runs: wf_get_peaks_se.cwl through scatter across multiple samples. |
https://github.com/YeoLab/eclip.git
Path: cwl/wf_get_peaks_scatter_se.cwl Branch/Commit ID: master |
