Explore Workflows

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Graph Name Retrieved From View
workflow graph Filter Protein Alignments

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

Path: protein_alignment/wf_align_filter.cwl

Branch/Commit ID: 17bae57a1f00f5c6db8f3a82d86262f12b8153cf
workflow graph taxonomy_check_16S

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

Path: task_types/tt_taxonomy_check_16S.cwl

Branch/Commit ID: 41d14ec5e2dfa0fac7eebeefda1f26ccea14c9a0
workflow graph wf-loadContents2.cwl

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

Path: tests/wf-loadContents2.cwl

Branch/Commit ID: 0e37d46e793e72b7c16b5ec03e22cb3ce1f55ba3
workflow graph RNA-Seq pipeline paired-end stranded mitochondrial

Slightly changed original [BioWardrobe's](https://biowardrobe.com) [PubMed ID:26248465](https://www.ncbi.nlm.nih.gov/pubmed/26248465) **RNA-Seq** basic analysis for **strand specific pair-end** experiment. An additional steps were added to map data to mitochondrial chromosome only and then merge the output. Experiment files in [FASTQ](http://maq.sourceforge.net/fastq.shtml) format either compressed or not can be used. Current workflow should be used only with the pair-end strand specific RNA-Seq data. It performs the following steps: 1. `STAR` to align reads from input FASTQ file according to the predefined reference indices; generate unsorted BAM file and alignment statistics file 2. `fastx_quality_stats` to analyze input FASTQ file and generate quality statistics file 3. `samtools sort` to generate coordinate sorted BAM(+BAI) file pair from the unsorted BAM file obtained on the step 1 (after running STAR) 5. Generate BigWig file on the base of sorted BAM file 6. Map input FASTQ file to predefined rRNA reference indices using Bowtie to define the level of rRNA contamination; export resulted statistics to file 7. Calculate isoform expression level for the sorted BAM file and GTF/TAB annotation file using `GEEP` reads-counting utility; export results to file

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

Path: workflows/rnaseq-pe-dutp-mitochondrial.cwl

Branch/Commit ID: a839eb6390974089e1a558c49fc07b4c66c50767
workflow graph align_sort_sa

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

Path: task_types/tt_align_sort_sa.cwl

Branch/Commit ID: ce433f771ebf5677c9f40858e2ae91b1a7e75d30
workflow graph Align reference proteins plane complete workflow

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

Path: protein_alignment/wf_protein_alignment.cwl

Branch/Commit ID: 91181df8d9ef8eed9d8f40db707b9a4376fecaf5
workflow graph wf-loadContents3.cwl

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

Path: tests/wf-loadContents3.cwl

Branch/Commit ID: 0e37d46e793e72b7c16b5ec03e22cb3ce1f55ba3
workflow graph Run genomic CMsearch (Rfam rRNA)

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

Path: bacterial_ncrna/wf_gcmsearch.cwl

Branch/Commit ID: 91181df8d9ef8eed9d8f40db707b9a4376fecaf5
workflow graph Bacterial Annotation, pass 3, structural annotation, functional annotation: ab initio GeneMark, by WP, by HMM (second pass)

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

Path: bacterial_annot/wf_bacterial_annot_pass3.cwl

Branch/Commit ID: 91181df8d9ef8eed9d8f40db707b9a4376fecaf5
workflow graph Chipseq alignment for mouse with qc and creating homer tag directory

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

Path: definitions/pipelines/chipseq_alignment_mouse.cwl

Branch/Commit ID: 3034168d652bfa930ba09af20e473a4564a8010d