Explore Workflows

View already parsed workflows here or click here to add your own

Graph Name Retrieved From View
workflow graph scatter-wf3.cwl#main

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

Path: cwltool/schemas/v1.0/v1.0/scatter-wf3.cwl

Branch/Commit ID: 9a8e654a91ea5d26e8452dd1cecf3faf22b7a12e

Packed ID: main
workflow graph kmer_cache_retrieve

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

Path: task_types/tt_kmer_cache_retrieve.cwl

Branch/Commit ID: 5463361069e263ad6455858e054c1337b1d9e752
workflow graph umi duplex alignment workflow

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

Path: definitions/subworkflows/duplex_alignment.cwl

Branch/Commit ID: 00df82a529a58d362158110581e1daa28b4d7ecb
workflow graph align_merge_sas

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

Path: task_types/tt_align_merge_sas.cwl

Branch/Commit ID: 001e133e0eedaf0dd8447e3f8b3cc898ec6e3e1d
workflow graph Merge, annotate, and generate a TSV for SVs

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

Path: definitions/subworkflows/merge_svs.cwl

Branch/Commit ID: 00df82a529a58d362158110581e1daa28b4d7ecb
workflow graph Unaligned BAM to BQSR and VCF

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

Path: definitions/subworkflows/bam_to_bqsr_no_dup_marking.cwl

Branch/Commit ID: 04d21c33a5f2950e86db285fa0a32a6659198d8a
workflow graph cram_to_bam workflow

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

Path: definitions/subworkflows/cram_to_bam_and_index.cwl

Branch/Commit ID: 844c10a4466ab39c02e5bfa7a210c195b8efa77a
workflow graph Bismark Methylation - pipeline for BS-Seq data analysis

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: 2f0db4b3c515f91c5cfda19c78cf90d339390986
workflow graph samtools_mpileup_subpipeline.cwl

https://github.com/PMCC-BioinformaticsCore/janis-pipelines.git

Path: janis_pipelines/wgs_somatic/cwl/tools/samtools_mpileup_subpipeline.cwl

Branch/Commit ID: 1d45492ae0085824a7ac532d0dfa6621c1cbe415
workflow graph Vcf concordance evaluation workflow

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

Path: definitions/subworkflows/vcf_eval_concordance.cwl

Branch/Commit ID: bed420556091b7b8b45cf20a95e5947e1de9a416