Explore Workflows

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

Graph Name Retrieved From View
workflow graph FastQC parallel

This CWL scatters FastQC quality control over multiple processors, one for each file. version: 0.11.9

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

Path: CWL/workflows/fastqc-wf.cwl

Branch/Commit ID: 6a1a6b9d5a152e783fe3f794ccce35387d02fd0d
workflow graph Samtools process for unmapped reads aligned by Bowtie2

This CWL converts aligned SAM files to BAM using samtools-view. Samtools-reheader is used as Bowtie2 returns different header than Hisat2. Finally, satools-sort is used to acquire the final unmapped - remapped BAM. version: 0.01

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

Path: CWL/workflows/unmapped.cwl

Branch/Commit ID: 6a1a6b9d5a152e783fe3f794ccce35387d02fd0d
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: 4bc0a4577d626b65a4b44683e5a1ab2f7d7faf4c
workflow graph process VCF workflow

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

Path: definitions/subworkflows/strelka_process_vcf.cwl

Branch/Commit ID: ad65dc1dfff9afa5077f498b85e699716c47f6cb
workflow graph process VCF workflow

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

Path: definitions/subworkflows/strelka_process_vcf.cwl

Branch/Commit ID: 9a657bc8c462542dc7f57fba9e04dc1669f966ba
workflow graph Complete Mapping and Quality Control pipeline for Single-end data

A workflow which: i) Runs Hisat2 on each fastq while generating a fastq file 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 (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-se-qc.cwl

Branch/Commit ID: 6a1a6b9d5a152e783fe3f794ccce35387d02fd0d
workflow graph strelka workflow

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

Path: definitions/subworkflows/strelka_and_post_processing.cwl

Branch/Commit ID: ddd748516b25256a461ea9277303406fa2759b00
workflow graph pindel parallel workflow

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

Path: definitions/subworkflows/pindel.cwl

Branch/Commit ID: ddd748516b25256a461ea9277303406fa2759b00
workflow graph Varscan Workflow

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

Path: definitions/subworkflows/varscan_pre_and_post_processing.cwl

Branch/Commit ID: ddd748516b25256a461ea9277303406fa2759b00
workflow graph Filter Protein Seeds I; Find ProSplign Alignments I

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

Path: protein_alignment/wf_compart_filter_prosplign.cwl

Branch/Commit ID: b12ec8c8e832151033b9e6c0a76a3c3df18d45da