Explore Workflows

Workflow runs group-isoforms.cwl tool using scatter for isoforms_file input. genes_filename and common_tss_filename inputs are ignored.

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

Path: tools/group-isoforms-batch.cwl

Branch/Commit ID: 2ffe30af333aead4f2a7e181ab151587e825b384

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

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

Branch/Commit ID: 09323506da219ba3ddb5313bd83022b52cac9adc

Packed ID: main

Workflow runs [STAR](https://github.com/alexdobin/STAR) v2.5.3a (03/17/2017) PMID: [23104886](https://www.ncbi.nlm.nih.gov/pubmed/23104886) to build indices for reference genome provided in a single FASTA file as fasta_file input and GTF annotation file from annotation_gtf_file input. Generated indices are saved in a folder with the name that corresponds to the input genome.

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

Path: workflows/star-index.cwl

Branch/Commit ID: 46a077b51619c6a14f85e0aa5260ae8a04426fab

Runs DESeq2 using LRT (Likelihood Ratio Test) ============================================= The LRT examines two models for the counts, a full model with a certain number of terms and a reduced model, in which some of the terms of the full model are removed. The test determines if the increased likelihood of the data using the extra terms in the full model is more than expected if those extra terms are truly zero. The LRT is therefore useful for testing multiple terms at once, for example testing 3 or more levels of a factor at once, or all interactions between two variables. The LRT for count data is conceptually similar to an analysis of variance (ANOVA) calculation in linear regression, except that in the case of the Negative Binomial GLM, we use an analysis of deviance (ANODEV), where the deviance captures the difference in likelihood between a full and a reduced model. When one performs a likelihood ratio test, the p values and the test statistic (the stat column) are values for the test that removes all of the variables which are present in the full design and not in the reduced design. This tests the null hypothesis that all the coefficients from these variables and levels of these factors are equal to zero. The likelihood ratio test p values therefore represent a test of all the variables and all the levels of factors which are among these variables. However, the results table only has space for one column of log fold change, so a single variable and a single comparison is shown (among the potentially multiple log fold changes which were tested in the likelihood ratio test). This indicates that the p value is for the likelihood ratio test of all the variables and all the levels, while the log fold change is a single comparison from among those variables and levels. **Technical notes** 1. At least two biological replicates are required for every compared category 2. Metadata file describes relations between compared experiments, for example ``` ,time,condition DH1,day5,WT DH2,day5,KO DH3,day7,WT DH4,day7,KO DH5,day7,KO ``` where `time, condition, day5, day7, WT, KO` should be a single words (without spaces) and `DH1, DH2, DH3, DH4, DH5` correspond to the experiment aliases set in **RNA-Seq experiments** input. 3. Design and reduced formulas should start with **~** and include categories or, optionally, their interactions from the metadata file header. See details in DESeq2 manual [here](https://bioconductor.org/packages/release/bioc/vignettes/DESeq2/inst/doc/DESeq2.html#interactions) and [here](https://bioconductor.org/packages/release/bioc/vignettes/DESeq2/inst/doc/DESeq2.html#likelihood-ratio-test) 4. Contrast should be set based on your metadata file header and available categories in a form of `Factor Numerator Denominator`, where `Factor` - column name from metadata file, `Numerator` - category from metadata file to be used as numerator in fold change calculation, `Denominator` - category from metadata file to be used as denominator in fold change calculation. For example `condition WT KO`.

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

Path: workflows/deseq-lrt.cwl

Branch/Commit ID: f3e44d3b0f198cf5245c49011124dc3b6c2b06fd

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

Path: task_types/tt_cluster_and_qdump.cwl

Branch/Commit ID: 76a9637a06e2102645eae29aff10b6f7185892a5

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

Path: definitions/subworkflows/bam_to_bqsr.cwl

Branch/Commit ID: 31602b94b34ff55876147c7299e1bec47e8d1a31

Pairwise genomic regions intersection ============================================= Overlaps peaks from two ChIP/ATAC experiments

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

Path: workflows/peak-intersect.cwl

Branch/Commit ID: bf80c9339d81a78aefb8de661bff998ed86e836e

Runs RNA-Seq BioWardrobe basic analysis with single-end data file.

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

Path: workflows/trim-rnaseq-se.cwl

Branch/Commit ID: 801f7b363e0599b9a28ecda696dfdb1c0e40ce71

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

Path: definitions/subworkflows/vcf_eval_concordance.cwl

Branch/Commit ID: 2f65fc96207a71b1cda4e246f808bed056608cd0

Inspect provided directory and return filenames. Generate a new directory and return it (including content).

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

Path: tests/wf/directory.cwl

Branch/Commit ID: ec2cf2da6c31ffedf827a0fb213b5204e172f510