Explore Workflows

Wrapped in a workflow SoupX tool for easy access to Cell Ranger pipeline compressed outputs.

https://github.com/Barski-lab/workflows.git

Path: tools/soupx-subworkflow.cwl

Branch/Commit ID: 80d64741638b14de5cf58236b6d6d99713c62086

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

Path: tests/wf/secret_wf.cwl

Branch/Commit ID: ead263db0e167db39ddbdc79b04d343943d129b6

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

Path: cwltool/schemas/v1.0/v1.0/scatter-valuefrom-wf4.cwl

Branch/Commit ID: 7ec307b01442936fad9b1149f4500496557505ff

Packed ID: main

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

Path: tests/count-lines9-wf-noET.cwl

Branch/Commit ID: 664835e83eb5e57eee18a04ce7b05fb9d70d77b7

What is THOR? -------------- THOR is an HMM-based approach to detect and analyze differential peaks in two sets of ChIP-seq data from distinct biological conditions with replicates. THOR performs genomic signal processing, peak calling and p-value calculation in an integrated framework. For more information please refer to: ------------------------------------- Allhoff, M., Sere K., Freitas, J., Zenke, M., Costa, I.G. (2016), Differential Peak Calling of ChIP-seq Signals with Replicates with THOR, Nucleic Acids Research, epub gkw680.

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

Path: workflows/rgt-thor.cwl

Branch/Commit ID: 664de58d95728edbf7d369d894f9037ebe2475fa

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

Path: tests/wf/mut3.cwl

Branch/Commit ID: 55ccde7c2fe3e7899136ce8606a341e292d7050a

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: 5561f7ee11dd74848680351411a19aa87b13d27b

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

Path: progs/gp_makeblastdb.cwl

Branch/Commit ID: 62210a247eb03af7503210fe40102fa00cfb9f9b

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

Path: metadata/indices-header.cwl

Branch/Commit ID: 44214a9d02e6d85b03eb708552ed812ae3d4a733

Interval overlapping alignments counts ====================================== Reports the count of alignments from multiple samples that overlap specific intervals.

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

Path: workflows/bedtools-multicov.cwl

Branch/Commit ID: 7030da528559c7106d156284e50ff0ecedab0c4e