Explore Workflows

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Graph Name Retrieved From View
workflow graph Complete Mapping and Quality Control pipeline for Paired-end data

A workflow which: i) Runs Hisat2 on each fastq pair while generating the fastq files containing unmapped reads ii) Runs Bowtie2 using the --very-sensitive-local option, on the unmapped reads iii) A subworkflow is employed to prepare BAM files, corresponding to the unmapped-remaped reads, to be merged with the mapped reads form Hisat2 iv) After the merged BAMs are created, they are sorted and assigned a user defined name (according to samle identifier) v) Corresponding index file for each sample is generated. vi) At the same time it performs quality control over the FASTQ using fastqc and assembles the MultiQC report

https://github.com/mr-c/elixir-gr-project.git

Path: CWL/workflows/mapping-pe-qc.cwl

Branch/Commit ID: 6a1a6b9d5a152e783fe3f794ccce35387d02fd0d
workflow graph trim-rnaseq-se-dutp.cwl

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

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

Path: workflows/trim-rnaseq-se-dutp.cwl

Branch/Commit ID: 812b0ff40dda18ab7a9a872ff13a577be8531ba6
workflow graph count-lines15-wf.cwl

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

Path: tests/count-lines15-wf.cwl

Branch/Commit ID: 0e37d46e793e72b7c16b5ec03e22cb3ce1f55ba3
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: 875b928ce50a3202f5954843b79ea86683c160fa

Packed ID: main
workflow graph Bacterial Annotation, pass 2, blastp-based functional annotation (first pass)

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

Path: bacterial_annot/wf_bacterial_annot_pass2.cwl

Branch/Commit ID: 609aead9804a8f31fa9b3dbc7e52105aec487f31
workflow graph gcaccess_from_list

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

Path: task_types/tt_gcaccess_from_list.cwl

Branch/Commit ID: a7fced3ed8c839272c8f3a8db9da7bc8cd50271f
workflow graph kmer_seq_entry_extract_wnode

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

Path: task_types/tt_kmer_seq_entry_extract_wnode.cwl

Branch/Commit ID: e71779665f42fcf34601b0f65e030bb0dd47fa79
workflow graph align_sort_sa

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

Path: task_types/tt_align_sort_sa.cwl

Branch/Commit ID: 0bc1c33a2293e054ad00974971edc79c13252cc7
workflow graph annotate.cwl

https://github.com/hubmapconsortium/hra-workflows.git

Path: steps/annotate.cwl

Branch/Commit ID: 4f75e87eb56925d456e78d9e06cf543c2fb0dada
workflow graph download_gtf.cwl

https://github.com/yyoshiaki/VIRTUS.git

Path: workflow/download_gtf.cwl

Branch/Commit ID: 43982758be93a31a0c079f448b377cae9fb9f3c7