Explore Workflows

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

Path: cwltool/schemas/v1.0/v1.0/js-expr-req-wf.cwl

Branch/Commit ID: 09323506da219ba3ddb5313bd83022b52cac9adc

Packed ID: wf

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

Path: definitions/subworkflows/pvacseq.cwl

Branch/Commit ID: 4bc0a4577d626b65a4b44683e5a1ab2f7d7faf4c

Filters differentially expressed genes from DESeq for Tag Density Profile Analyses ================================================================================== Tool filters output from DESeq pipeline run for genes to create a file with regions of interest for Tag Density Profile Analyses.

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

Path: workflows/filter-deseq-for-heatmap.cwl

Branch/Commit ID: 93b844a80f4008cc973ea9b5efedaff32a343895

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

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

Path: workflows/rnaseq-se-dutp.cwl

Branch/Commit ID: bc75349ad3a7bdce82b4cd8584501f4d0280bb8d

Remove reads from fasta files based on sequence stats. Return fasta files with reads passed and reads removed.

https://github.com/MG-RAST/pipeline.git

Path: CWL/Workflows/preprocess-fasta.workflow.cwl

Branch/Commit ID: f906212e2c9a88280ae36545e5422f25752aa8f4

Sequence reads are first cleaned from adapters and transformed into fully bisulfite-converted forward (C->T) and reverse read (G->A conversion of the forward strand) versions, before they are aligned to similarly converted versions of the genome (also C->T and G->A converted). Sequence reads that produce a unique best alignment from the four alignment processes against the bisulfite genomes (which are running in parallel) are then compared to the normal genomic sequence and the methylation state of all cytosine positions in the read is inferred. A read is considered to align uniquely if an alignment has a unique best alignment score (as reported by the AS:i field). If a read produces several alignments with the same number of mismatches or with the same alignment score (AS:i field), a read (or a read-pair) is discarded altogether. On the next step we extract the methylation call for every single C analysed. The position of every single C will be written out to a new output file, depending on its context (CpG, CHG or CHH), whereby methylated Cs will be labelled as forward reads (+), non-methylated Cs as reverse reads (-). The output of the methylation extractor is then transformed into a bedGraph and coverage file. The bedGraph counts output is then used to generate a genome-wide cytosine report which reports the number on every single CpG (optionally every single cytosine) in the genome, irrespective of whether it was covered by any reads or not. As this type of report is informative for cytosines on both strands the output may be fairly large (~46mn CpG positions or >1.2bn total cytosine positions in the human genome).

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

Path: workflows/bismark-methylation-se.cwl

Branch/Commit ID: 93b844a80f4008cc973ea9b5efedaff32a343895

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

Path: definitions/subworkflows/pindel_region.cwl

Branch/Commit ID: 60edaf6f57eaaf02cda1a3d8cb9a825aa64a43e2

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

Path: task_types/tt_taxonomy_check_16S.cwl

Branch/Commit ID: 093b60e546237c06cfe7820d6ac8d66467e66725

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

Path: testdata/workflow_input_sf_expr_array_v1_2.cwl

Branch/Commit ID: b76b039edb62dea76c43f173848cdc57e4b4aab7

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

Path: testdata/step_valuefrom5_wf_with_id_v1_1.cwl

Branch/Commit ID: b76b039edb62dea76c43f173848cdc57e4b4aab7