Explore Workflows
View already parsed workflows here or click here to add your own
Graph | Name | Retrieved From | View |
---|---|---|---|
|
exome alignment and germline variant detection
|
![]() Path: definitions/subworkflows/germline_detect_variants.cwl Branch/Commit ID: 6949082038c1ad36d6e9848b97a2537aef2d3805 |
|
|
heatmap-prepare.cwl
Workflow runs homer-make-tag-directory.cwl tool using scatter for the following inputs - bam_file - fragment_size - total_reads `dotproduct` is used as a `scatterMethod`, so one element will be taken from each array to construct each job: 1) bam_file[0] fragment_size[0] total_reads[0] 2) bam_file[1] fragment_size[1] total_reads[1] ... N) bam_file[N] fragment_size[N] total_reads[N] `bam_file`, `fragment_size` and `total_reads` arrays should have the identical order. |
![]() Path: subworkflows/heatmap-prepare.cwl Branch/Commit ID: e9a24699d8b5ffe64412b1ba0af8448c281b223a |
|
|
taxonomy_check_16S
|
![]() Path: task_types/tt_taxonomy_check_16S.cwl Branch/Commit ID: 909f26beaf96c2cdfe208f87ecd1e9c3de20b81c |
|
|
kmer_cache_store
|
![]() Path: task_types/tt_kmer_cache_store.cwl Branch/Commit ID: 609aead9804a8f31fa9b3dbc7e52105aec487f31 |
|
|
Kallisto index pipeline
This workflow indexes the input reference FASTA with kallisto, and generates a kallisto index file (.kdx). This index sample can then be used as input into the kallisto transcript-level quantification workflow (kallisto-quant-pe.cwl), or others that may include this workflow as an upstream source. ### __Inputs__ - FASTA file of the reference genome that will be indexed - number of threads to use for multithreading processes ### __Outputs__ - kallisto index file (.kdx). - stdout log file (output in Overview tab as well) - stderr log file ### __Data Analysis Steps__ 1. cwl calls dockercontainer robertplayer/scidap-kallisto to index reference FASTA with `kallisto index`, generating a kallisto index file. ### __References__ - Bray, N. L., Pimentel, H., Melsted, P. & Pachter, L. Near-optimal probabilistic RNA-seq quantification, Nature Biotechnology 34, 525-527(2016), doi:10.1038/nbt.3519 |
![]() Path: workflows/kallisto-index.cwl Branch/Commit ID: 261c0232a7a40880f2480b811ed2d7e89c463869 |
|
|
xenbase-chipseq-pe.cwl
XenBase workflow for analysing ChIP-Seq paired-end data |
![]() Path: workflows/xenbase-chipseq-pe.cwl Branch/Commit ID: 9a2c389364674221fab3f0f6afdda799e6aa3247 |
|
|
RNA-Seq pipeline paired-end strand specific
The original [BioWardrobe's](https://biowardrobe.com) [PubMed ID:26248465](https://www.ncbi.nlm.nih.gov/pubmed/26248465) **RNA-Seq** basic analysis for a **paired-end** experiment. A corresponded input [FASTQ](http://maq.sourceforge.net/fastq.shtml) file has to be provided. Current workflow should be used only with the paired-end RNA-Seq data. It performs the following steps: 1. Use STAR to align reads from input FASTQ files according to the predefined reference indices; generate unsorted BAM file and alignment statistics file 2. Use fastx_quality_stats to analyze input FASTQ files and generate quality statistics files 3. Use samtools sort to generate coordinate sorted BAM(+BAI) file pair from the unsorted BAM file obtained on the step 1 (after running STAR) 4. Generate BigWig file on the base of sorted BAM file 5. Map input FASTQ files to predefined rRNA reference indices using Bowtie to define the level of rRNA contamination; export resulted statistics to file 6. Calculate isoform expression level for the sorted BAM file and GTF/TAB annotation file using GEEP reads-counting utility; export results to file |
![]() Path: workflows/rnaseq-pe-dutp.cwl Branch/Commit ID: a1f6ca50fcb0881781b3ba0306dd61ebf555eaba |
|
|
protein annotation
Proteins - predict, cluster, identify, annotate |
![]() Path: CWL/Workflows/protein-annotation.workflow.cwl Branch/Commit ID: d9cf22cd615542c94f7974e8bce4cf29b24d985f |
|
|
bam-bedgraph-bigwig.cwl
Workflow converts input BAM file into bigWig and bedGraph files. Input BAM file should be sorted by coordinates (required by `bam_to_bedgraph` step). If `split` input is not provided use true by default. Default logic is implemented in `valueFrom` field of `split` input inside `bam_to_bedgraph` step to avoid possible bug in cwltool with setting default values for workflow inputs. `scale` has higher priority over the `mapped_reads_number`. The last one is used to calculate `-scale` parameter for `bedtools genomecov` (step `bam_to_bedgraph`) only in a case when input `scale` is not provided. All logic is implemented inside `bedtools-genomecov.cwl`. `bigwig_filename` defines the output name only for generated bigWig file. `bedgraph_filename` defines the output name for generated bedGraph file and can influence on generated bigWig filename in case when `bigwig_filename` is not provided. All workflow inputs and outputs don't have `format` field to avoid format incompatibility errors when workflow is used as subworkflow. |
![]() Path: tools/bam-bedgraph-bigwig.cwl Branch/Commit ID: cf678db8304ffaa20c1d6c854364db5ed41803c2 |
|
|
exome alignment and somatic variant detection
|
![]() Path: definitions/pipelines/somatic_exome_mouse.cwl Branch/Commit ID: 27dcb1ae121be6a23057b74332b8c752ea425735 |