Explore Workflows

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

Graph Name Retrieved From View
workflow graph umi duplex alignment fastq workflow

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

Path: definitions/pipelines/umi_duplex_alignment.cwl

Branch/Commit ID: 8cee1920920ed73384fb3ab74272da9c92a20cf2
workflow graph exome alignment and somatic variant detection for cle purpose

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

Path: definitions/pipelines/cle_somatic_exome.cwl

Branch/Commit ID: 1249b5d4e23d57ca5e3b8ad6d8e5f10ddb019f68
workflow graph exome alignment with qc

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

Path: definitions/pipelines/alignment_exome.cwl

Branch/Commit ID: 0d2f354af9192a56af258a7d2426c7c160f4ec1a
workflow graph EMG pipeline v3.0 (single end version)

https://github.com/ProteinsWebTeam/ebi-metagenomics-cwl.git

Path: workflows/emg-pipeline-v3.cwl

Branch/Commit ID: 56dafa4dab5892c5afa35713563dddc78ec5a00d
workflow graph extract_gencoll_ids

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

Path: task_types/tt_extract_gencoll_ids.cwl

Branch/Commit ID: 9abcceb95c8dcb74b98d7eeda265d8f3a9a4329e
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: 4106b7dc96e968db291b7a61ecd1641aa3b3dd6d
workflow graph taxonomy_check_16S

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

Path: task_types/tt_taxonomy_check_16S.cwl

Branch/Commit ID: 22ffe27d9d4a899def7592d75d5871c1856adbdb
workflow graph xbrain_unets_train.cwl

https://github.com/elenimath/saber.git

Path: saber/xbrain/workflows/xbrain_unets_train.cwl

Branch/Commit ID: master
workflow graph count-lines10-wf.cwl

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

Path: tests/count-lines10-wf.cwl

Branch/Commit ID: 0e37d46e793e72b7c16b5ec03e22cb3ce1f55ba3
workflow graph RNA-seq (VCF) alelle specific pipeline for paired-end data

Allele specific RNA-Seq (using vcf) paired-end workflow

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

Path: workflows/allele-vcf-rnaseq-pe.cwl

Branch/Commit ID: 4106b7dc96e968db291b7a61ecd1641aa3b3dd6d