Explore Workflows

https://github.com/kmooog/amplicon-pipeline.git

Path: script/1-preproccess/amplicon_preprocess_workflow.cwl

Branch/Commit ID: eccef9b8e80e1a8729e7bd54f06f895a847b024d

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

Path: definitions/subworkflows/filter_vcf.cwl

Branch/Commit ID: ece70ac30cd87100a70f7dc64d08fa72724e9416

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

Path: definitions/pipelines/somatic_exome_gathered.cwl

Branch/Commit ID: 43c790e2ee6a0f3f42e40fb4d9a9005eb8de747a

Workflow converts input BAM file into bigWig and bedGraph files. Input BAM file should be sorted by coordinates (required by `bam_to_bedgraph` step). If `split` input is not provided use true by default. Default logic is implemented in `valueFrom` field of `split` input inside `bam_to_bedgraph` step to avoid possible bug in cwltool with setting default values for workflow inputs. `scale` has higher priority over the `mapped_reads_number`. The last one is used to calculate `-scale` parameter for `bedtools genomecov` (step `bam_to_bedgraph`) only in a case when input `scale` is not provided. All logic is implemented inside `bedtools-genomecov.cwl`. `bigwig_filename` defines the output name only for generated bigWig file. `bedgraph_filename` defines the output name for generated bedGraph file and can influence on generated bigWig filename in case when `bigwig_filename` is not provided. All workflow inputs and outputs don't have `format` field to avoid format incompatibility errors when workflow is used as subworkflow.

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

Path: tools/bam-bedgraph-bigwig.cwl

Branch/Commit ID: 8049a781ac4aae579fbd3036fa0bf654532f15be

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

Path: task_types/tt_kmer_build_tree.cwl

Branch/Commit ID: a539d600357a48a558daf43fc41a89aae79f9e86

GSEAPY: Gene Set Enrichment Analysis in Python ============================================== Gene Set Enrichment Analysis is a computational method that determines whether an a priori defined set of genes shows statistically significant, concordant differences between two biological states (e.g. phenotypes). GSEA requires as input an expression dataset, which contains expression profiles for multiple samples. While the software supports multiple input file formats for these datasets, the tab-delimited GCT format is the most common. The first column of the GCT file contains feature identifiers (gene ids or symbols in the case of data derived from RNA-Seq experiments). The second column contains a description of the feature; this column is ignored by GSEA and may be filled with “NA”s. Subsequent columns contain the expression values for each feature, with one sample's expression value per column. It is important to note that there are no hard and fast rules regarding how a GCT file's expression values are derived. The important point is that they are comparable to one another across features within a sample and comparable to one another across samples. Tools such as DESeq2 can be made to produce properly normalized data (normalized counts) which are compatible with GSEA.

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

Path: workflows/gseapy.cwl

Branch/Commit ID: 8049a781ac4aae579fbd3036fa0bf654532f15be

Cellranger Reanalyze ====================

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

Path: workflows/cellranger-reanalyze.cwl

Branch/Commit ID: 8049a781ac4aae579fbd3036fa0bf654532f15be

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

Path: definitions/subworkflows/molecular_alignment.cwl

Branch/Commit ID: 7638b3075863ae8172f4adaec82fb2eb8e80d3d5

AltAnalyze ICGS ===============

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

Path: workflows/altanalyze-icgs.cwl

Branch/Commit ID: 8049a781ac4aae579fbd3036fa0bf654532f15be

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

Path: definitions/pipelines/bisulfite.cwl

Branch/Commit ID: 7638b3075863ae8172f4adaec82fb2eb8e80d3d5