Explore Workflows

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

Path: task_types/tt_kmer_cache_retrieve.cwl

Branch/Commit ID: c64599f5db2437f9323d41cc3d8d9efb20a2667e

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

Path: testdata/count-lines7-wf_v1_1.cwl

Branch/Commit ID: e949503ac0dd7e22ba9b04ac51926d13780f9cee

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: 3a311af320e65271f3efb4f27a6ed10aa5d50a0e

A CWL workflow for discovering known or novel miRNAs from deep sequencing data using the miRDeep2 tool. The ExoCarta exosome database is also used for identifying exosome-related miRNAs, and TargetScan's organism-specific databases are used for identifying miRNA gene targets. ## __Outputs__ #### Primary Output files: - mirs_known.tsv, detected known mature miRNAs, \"Known miRNAs\" tab - mirs_novel.tsv, detected novel mature miRNAs, \"Novel miRNAs\" tab #### Secondary Output files: - mirs_known_exocarta_deepmirs.tsv, list of detected miRNA also in ExoCarta's exosome database, \"Detected Exosome miRNAs\" tab - mirs_known_gene_targets.tsv, pre-computed gene targets of known mature mirs, downloadable - known_mirs_mature.fa, known mature mir sequences, downloadable - known_mirs_precursor.fa, known precursor mir sequences, downloadable - novel_mirs_mature.fa, novel mature mir sequences, downloadable - novel_mirs_precursor.fa, novel precursor mir sequences, downloadable #### Reports: - overview.md (input list, alignment & mir metrics), \"Overview\" tab - mirdeep2_result.html, summary of mirdeep2 results, \"miRDeep2 Results\" tab ## __Inputs__ #### General Info - Sample short name/Alias: unique name for sample - Experimental condition: condition, variable, etc name (e.g. \"control\" or \"20C 60min\") - Cells: name of cells used for the sample - Catalog No.: vender catalog number if available - Bowtie2 index: Bowtie2 index directory of the reference genome. - Reference Genome FASTA: Reference genome FASTA file to be used for alignment. - Genome short name: Name used for setting organism name, genus, species, and tax ID. - Input FASTQ file: FASTQ file from a single-end miRNA sequencing run. #### Advanced - Adapter: Adapter sequence to be trimmed from miRNA sequence reads. (Default: TCGTAT) - Threads: Number of threads to use for steps that support multithreading (Default: 4). ## Hints & Tips: #### For the identification of novel miRNA candidates, the following may be used as a filtering guideline: 1. miRDeep score > 4 (some authors use 1) 2. not present a match with rfam 3. should present a significant RNAfold (\"yes\") 4. a number of mature reads > 10 5. if applicable, novel mir must be expressed in multiple samples #### For filtering mirbase by organism. | genome | organism | division | name | tree | NCBI-taxid | | ---- | --- | --- | ----------- | ----------- | ----------- | | hg19 | hsa | HSA | Homo sapiens | Metazoa;Bilateria;Deuterostoma;Chordata;Vertebrata;Mammalia;Primates;Hominidae | 9606 | | hg38 | hsa | HSA | Homo sapiens | Metazoa;Bilateria;Deuterostoma;Chordata;Vertebrata;Mammalia;Primates;Hominidae | 9606 | | mm10 | mmu | MMU | Mus musculus | Metazoa;Bilateria;Deuterostoma;Chordata;Vertebrata;Mammalia;Rodentia | 10090 | | rn7 | rno | RNO | Rattus norvegicus | Metazoa;Bilateria;Deuterostoma;Chordata;Vertebrata;Mammalia;Rodentia | 10116 | | dm3 | dme | DME | Drosophila melanogaster | Metazoa;Bilateria;Ecdysozoa;Arthropoda;Hexapoda | 7227 | ## __Data Analysis Steps__ 1. The miRDeep2 Mapper module processes Illumina FASTQ output and maps it to the reference genome. 2. The miRDeep2 miRDeep2 module identifies known and novel (mature and precursor) miRNAs. 3. The ExoCarta database of miRNA found in exosomes is then used to find overlap between mirs_known.tsv and exosome associated miRNAs. 4. Finally, TargetScan organism-specific miRNA gene target database is used to find overlap between mirs_known.tsv and gene targets. ## __References__ 1. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3245920 2. https://github.com/rajewsky-lab/mirdeep2 3. https://biocontainers.pro/tools/mirdeep2 4. https://www.mirbase.org/ 5. http://exocarta.org/index.html 6. https://www.targetscan.org/vert_80/

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

Path: workflows/mirna-mirdeep2-se.cwl

Branch/Commit ID: 3a311af320e65271f3efb4f27a6ed10aa5d50a0e

Cell Ranger Aggregate (ATAC) Combines outputs from multiple runs of “Cell Ranger Count (ATAC)” pipeline.

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

Path: workflows/cellranger-atac-aggr.cwl

Branch/Commit ID: 3a311af320e65271f3efb4f27a6ed10aa5d50a0e

https://github.com/hubmapconsortium/sc-atac-seq-pipeline.git

Path: steps/bulk_analysis.cwl

Branch/Commit ID: 44dbe381f68878ab607b167b62267c4ea97f3322

Resize sentinel2ard collection

https://github.com/EO-DataHub/eodh-training.git

Path: cwl/resize-sentinel2ard.cwl

Branch/Commit ID: 9047f151da2db909a091ca9fd27e62b6bfe54ea0

Packed ID: resize-sentinel2ard

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

Path: definitions/subworkflows/sequence_to_bqsr_mouse.cwl

Branch/Commit ID: a59a803e1809a8fbfabca6b8962a8ad66dd01f1d

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

Path: testdata/step-valuefrom3-wf_v1_0.cwl

Branch/Commit ID: e949503ac0dd7e22ba9b04ac51926d13780f9cee

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

Path: testdata/step_valuefrom5_wf_with_id_v1_0.cwl

Branch/Commit ID: e949503ac0dd7e22ba9b04ac51926d13780f9cee