Explore Workflows

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

Path: definitions/pipelines/tumor_only_exome.cwl

Branch/Commit ID: 22fce2dbdada0c4135b6f0677f78535cf980cb07

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

Path: tests/count-lines11-wf.cwl

Branch/Commit ID: 664835e83eb5e57eee18a04ce7b05fb9d70d77b7

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

Path: tests/wf/count-lines1-wf.cwl

Branch/Commit ID: 1b5633876aabd4cb57ef3f1fe91c853f3ee82e46

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

Path: task_types/tt_extract_gencoll_ids.cwl

Branch/Commit ID: c64599f5db2437f9323d41cc3d8d9efb20a2667e

https://github.com/mskcc/argos-cwl.git

Path: workflows/sample-workflow.cwl

Branch/Commit ID: 0b9721d7d512352c7f80b27f42b3192a585ed5f6

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

Path: definitions/pipelines/alignment_umi_molecular.cwl

Branch/Commit ID: 22fce2dbdada0c4135b6f0677f78535cf980cb07

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

Path: tests/count-lines8-wf-noET.cwl

Branch/Commit ID: 664835e83eb5e57eee18a04ce7b05fb9d70d77b7

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: 69643d8c15f5357a320aa7e2f6adb2e71302fd20

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

Path: testdata/count-lines7-single-source-wf_v1_2.cwl

Branch/Commit ID: 5759b4275906e6cfe13912c8426de2a2237cb4b0

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

Path: testdata/step-valuefrom3-wf_v1_0.cwl

Branch/Commit ID: 5759b4275906e6cfe13912c8426de2a2237cb4b0