ORSON: workflow for proteome and transcriptome functional annotation

public public 1yr ago Version: Version 1 0 bookmarks
View Workflow
Report
orson-workflow-for-proteome-and-transcriptome-func
orson-workflow-for-proteome-and-transcriptome-func
orson-workflow-for-proteome-and-transcriptome-func
View Workflow

ORSON combine state-of-the-art tools for annotation processes within a Nextflow pipeline: sequence similarity search (PLAST, BLAST or Diamond), functional annotation retrieval (BeeDeeM) and functional prediction (InterProScan). When required, BUSCO completness evaluation and eggNOG Orthogroup annotation can be activated. While ORSON results can be analyzed through the command-line, it also offers the possibility to be compatible with BlastViewer or Blast2GO graphical tools.

Code Snippets

14
15
16
"""
beedeem_annotation.sh ${params.db_dir} ${params.steps_data} ${xml} beedeem_annotation.zml ${params.annot_type} beedeem_annotation.cmd >& beedeem_annotation.log 2>&1
"""
NextFlow BeeDeeM From line 14 of modules/beedeem_annotation.nf 
14
15
16
"""
extract_species_taxids.sh ${params.restricted_tax_id} txids.cmd >& txids.log 2>&1
"""
NextFlow From line 14 of modules/blast.nf 
35
36
37
"""
blast.sh ${task.cpus} ${params.query_type} ${sequences} ${params.blast_db} blast_hits.xml ${params.restricted_search} ${taxids} blast.cmd >& blast.log 2>&1
"""
NextFlow BLAST From line 35 of modules/blast.nf 
50
51
52
"""
BlastXMLmerge.py merged_blast.xml ${blastXML} >& merged_blast_xml.log 2>&1
"""
NextFlow From line 50 of modules/blast.nf 
66
67
68
"""
blastxml_to_tabular.py ${blastXML} > merged_blast.tab >& merged_blast_tab.log 2>&1
"""
NextFlow From line 66 of modules/blast.nf 
18
19
20
"""
busco.sh ${task.cpus} ${transcriptome} busco_results ${lineageList} ${params.query_type} ${params.busco_db} busco.cmd >& busco.log 2>&1
"""
NextFlow BUSCO From line 18 of modules/busco.nf 
16
17
18
"""
diamond.sh ${task.cpus} ${params.query_type} ${chunks} ${params.blast_db} ${params.sensitivity} diamond_hits.xml diamond.cmd >& diamond.log 2>&1
"""
NextFlow Diamond From line 16 of modules/diamond.nf 
31
32
33
"""
BlastXMLmerge.py merged_diamond.xml ${diamondXML} >& merged_diamond_xml.log 2>&1
"""
NextFlow From line 31 of modules/diamond.nf 
47
48
49
	"""
 	blastxml_to_tabular.py ${diamondXML} > merged_diamond.tab 2>&1
 	"""
NextFlow From line 47 of modules/diamond.nf 
14
15
16
"""
downloadDB.sh ${params.db_dir} ${workflow.workDir}/databases ${params.bank_list} database_present downloadDB.cmd >& downloadDB.log 2>&1
"""
NextFlow From line 14 of modules/downloadDB.nf 
15
16
17
"""
eggnogmapper.sh ${task.cpus} ${params.query_type} ${query} result eggnog-mapper.cmd >& eggnog-mapper.log 2>&1
"""
NextFlow From line 15 of modules/eggnogmapper.nf 
 8
 9
10
"""
get_singularity_images.sh ${baseDir} singularity_images_ok >& get_singularity_images.log 2>&1
"""
NextFlow From line 8 of modules/get_singularity_images.nf 
 8
 9
10
"""
get_test_data.sh ${baseDir} query.fasta >& get_test_data.log 2>&1
"""
NextFlow From line 8 of modules/get_test_data.nf 
16
17
18
"""
interpro.sh ${task.cpus} ${query} ${params.query_type} iprscan.cmd >& iprscan.log 2>&1
"""
NextFlow InterPro From line 16 of modules/interpro.nf 
31
32
33
"""
IPRScanXMLmerge.sh merged_iprscan.xml ${params.query_type} >& merged_iprscan_xml.log 2>&1
"""
NextFlow From line 31 of modules/interpro.nf 
46
47
48
"""
IPRScanTSVmerge.sh merged_iprscan.tsv >& merged_iprscan_tsv.log 2>&1
"""
NextFlow From line 46 of modules/interpro.nf 
16
17
18
"""
beedeem-plast.sh ${params.db_dir} log ${task.cpus} ${params.query_type} ${seq} ${params.plast_db} plast_hits.xml plast.cmd >& plast.log 2>&1
"""
NextFlow PLAST From line 16 of modules/plast.nf 
31
32
33
"""
BlastXMLmerge.py merged_plast.xml ${plastXML} >& merged_plast_xml.log 2>&1
"""
NextFlow From line 31 of modules/plast.nf
ShowHide 12 more snippets with no or duplicated tags.

Login to post a comment if you would like to share your experience with this workflow.

Do you know this workflow well? If so, you can request seller status , and start supporting this workflow.

Free

Created: 1yr ago
Updated: 1yr ago
Maitainers: public
URL: https://gitlab.ifremer.fr/bioinfo/orson
Name: orson-workflow-for-proteome-and-transcriptome-func
Version: Version 1
Badge:
workflow icon

Insert copied code into your website to add a link to this workflow.

Downloaded: 0
Copyright: Public Domain
License: None
  • Future updates

Related Workflows

psychip_snakemake
Show Details View Workflow
ENCODE pipeline for histone marks developed for the psychENCODE project
public

public

psychip pipeline is an improved version of the ENCODE pipeline for histone marks developed for the psychENCODE project. The o...
raw sequence reads Alignment Sequence alignment report macs2 ucsc-bedclip bedGraphToBigWig BEDTools BWA Picard SAMtools Snakemake
Free
74
ncov_2
Show Details View Workflow
Near-real time tracking of SARS-CoV-2 in Connecticut
public

public

Repository containing scripts to perform near-real time tracking of SARS-CoV-2 in Connecticut using genomic data. This pipeli...
JSON nextclade Augur Biopython FOCUS Pandas Snakemake bs4 epiweeks geopy matplotlib numpy pycountry pycountry-convert uszipcode
Free
28
cellranger-snakemake-gke
Show Details View Workflow
snakemake workflow to run cellranger on a given bucket using gke.
public

public

A Snakemake workflow for running cellranger on a given bucket using Google Kubernetes Engine. The usage of this workflow ...
macs2 ucsc-bedclip bedGraphToBigWig BEDTools BWA Picard SAMtools Snakemake
Free
74
atlas
Show Details View Workflow
ATLAS - Three commands to start analyzing your metagenome data
public

public

Metagenome-atlas is a easy-to-use metagenomic pipeline based on snakemake. It handles all steps from QC, Assembly, Binning, t...
raw sequence reads Genome assembly Annotation track checkm2 gunc prodigal snakemake-wrapper-utils MEGAHIT Atlas BBMap Biopython BioRuby Bwa-mem2 cd-hit CheckM DAS Diamond eggNOG-mapper v2 MetaBAT 2 Minimap2 MMseqs MultiQC Pandas Picard pyfastx SAMtools SemiBin Snakemake SPAdes SqueezeMeta TADpole VAMB CONCOCT ete3 gtdbtk h5py networkx numpy plotly psutil utils metagenomics
Free
175
rna-seq-star-deseq2
Show Details View Workflow
RNA-seq workflow using STAR and DESeq2
public

public

This workflow performs a differential gene expression analysis with STAR and Deseq2. The usage of this workflow is described ...
raw sequence reads Gene expression profiling ID list snakemake-wrapper-utils biomaRt PCAtools BiocParallel BWA Cutadapt DESeq2 GFFutils MultiQC Pandas SAMtools Snakemake STAR cli stringr tidyverse RNA-Seq
Free
41
dna-seq-gatk-variant-calling
Show Details View Workflow
This Snakemake pipeline implements the GATK best-practices workflow
public

public

This Snakemake pipeline implements the GATK best-practices workflow for calling small germline variants. The usage of thi...
VCF raw sequence reads Variant calling genetic variants gatk rust-bio-tools snakemake-wrapper-utils tabix BCFtools BWA FastQC MultiQC Pandas Picard SAMtools Snakemake Trimmomatic Variant Effect Predictor (VEP) common matplotlib numpy seaborn DNA
Free
57