MoMofy: Module for integrative Mobilome prediction

public public 1yr ago Version: Version 1 0 bookmarks
View Workflow
Report
momofy-module-for-integrative-mobilome-prediction
momofy-module-for-integrative-mobilome-prediction
momofy-module-for-integrative-mobilome-prediction
momofy-module-for-integrative-mobilome-prediction
momofy-module-for-integrative-mobilome-prediction
View Workflow

Module for integrative Mobilome prediction

Bacteria can acquire genetic material through horizontal gene transfer, allowing them to rapidly adapt to changing environmental conditions. These mobile genetic elements can be classified into three main categories: plasmids, phages, and integrons. Autonomous elements are those capable of excising themselves from the chromosome, reintegrating elsewhere, and potentially modifying the host's physiology. Small integrative elements like insertion sequences usually contain one or two genes and are frequently present in multiple copies in the genome, whereas large elements like integrative conjugative elements, often carry multiple cargo genes. The acquisition of large mobile genetic elements may provide genes for defence against other mobile genetic elements or impart new metabolic capabilities to the host.

MoMofy is a wraper that integrates the ouptput of different tools designed for the prediction of autonomous integrative mobile genetic elements in prokaryotic genomes and metagenomes.

Code Snippets

21
22
23
24
25
26
27
28
29
30
31
"""
diamond blastp -q proteins.faa \
--db ${diamond_db} \
--outfmt 6 stitle qtitle pident bitscore slen evalue qlen sstart send qstart qend \
-k 15 \
-o blastp_out.tsv \
-e 1e-20 \
--query-cover 90 \
--id 90 \
--threads ${task.cpus}
"""
NextFlow Diamond From line 21 of modules/diamond.nf 
33
34
35
36
        """
	echo 'No input files for diamond... generating dummy files'
        touch blastp_out.tsv
        """
NextFlow From line 33 of modules/diamond.nf 
26
27
28
29
30
31
32
33
34
35
36
        """    
        gbk_splitter.pl contigs.gbk

	if -s input.list
	then
	    echo 'The file is not empty'
	else
            echo 'No contigs of size > 5kb ... generating dummy files'
            touch dummy.gbk
        fi
        """
NextFlow From line 26 of modules/gbk_splitter.nf 
38
39
40
41
42
"""
echo 'ICEfinder dir empty due to empty input... generating dummy files'
touch input.list
touch dummy.gbk
"""
NextFlow From line 38 of modules/gbk_splitter.nf 
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
        """
        cd /install/ICEfinder_linux/ && perl ./ICEfinder_local.pl input.list

        if ls -ld result/contig* 2>/dev/null | grep -q .
        then
	    cat result/*/DNA_*.fas > result/icf_concat.fasta 
            cat result/*/*summary.txt > result/icf_concat.summary
            grep 'DR:' result/*/ICE* > result/icf_dr.txt
        else
            echo 'ICEfinder found 0 ICE/IME in assembly... generating dummy files'
	    touch result/icf_concat.summary
	    touch result/icf_concat.fasta
            touch result/icf_dr.txt
        fi
        """
NextFlow From line 31 of modules/icefinder.nf 
47
48
49
50
51
52
        """
        echo 'No input files for ICEfinder... generating dummy files'
	touch result/icf_concat.summary
	touch result/icf_concat.fasta
        touch result/icf_dr.txt
        """
NextFlow From line 47 of modules/icefinder.nf 
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
    	"""    
    	mge_integrator.py --user 'T' \
    	--cds_gff ${cds_gff} \
    	--map ${mapping_file} \
    	--iss_fa ${iss_fasta} \
    	--iss_tsv ${iss_table} \
    	--pal_fa ${pal_fasta} \
    	--pal_tsv ${pal_table} \
    	--inf_tsv ${inf_table} \
    	--inf_gbks ${inf_list.join(' ')} \
    	--icf_tsv ${icf_table} \
    	--icf_fa ${icf_fasta} \
    	--icf_lim ${icf_dr} \
    	--mog_tsv ${mog_table}
	"""
NextFlow From line 34 of modules/integrator.nf 
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
	"""
	mge_integrator.py --user 'F' \
        --cds_gff ${cds_gff} \
        --map ${mapping_file} \
        --iss_fa ${iss_fasta} \
        --iss_tsv ${iss_table} \
        --pal_fa ${pal_fasta} \
        --pal_tsv ${pal_table} \
        --inf_tsv ${inf_table} \
        --inf_gbks ${inf_list.join(' ')} \
        --icf_tsv ${icf_table} \
        --icf_fa ${icf_fasta} \
        --icf_lim ${icf_dr} \
        --mog_tsv ${mog_table}
	"""
NextFlow From line 50 of modules/integrator.nf 
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
        """
        integron_finder --union-integrases \
        --mute \
        --local-max \
        --cpu ${task.cpus} \
        --func-annot \
        --gbk \
        contigs.fasta

	if ls -l Results_Integron_Finder_contigs/contig_*.gbk 2>/dev/null | grep -q .
        then
	    echo 'IntegronFinder outputs complete'
        else
            echo 'IntegronFinder found 0 integrons in assembly... generating dummy files'
            touch Results_Integron_Finder_contigs/contig_dummy.gbk
        fi
        """
NextFlow Integron Finder From line 23 of modules/integronfinder.nf 
41
42
43
44
45
46
"""
echo 'IntegronFinder dir empty due to empty input... generating dummy files'
mkdir Results_Integron_Finder_contigs
touch Results_Integron_Finder_contigs/contigs.summary
touch Results_Integron_Finder_contigs/contig_dummy.gbk
"""
NextFlow From line 41 of modules/integronfinder.nf 
23
24
25
26
27
28
29
30
31
32
33
34
35
36
        """
        isescan.py --seqfile contigs.fasta \
        --output isescan_results \
        --nthread ${task.cpus}

        if ls -l isescan_results/contigs.fasta.tsv 2>/dev/null | grep -q .
        then
            echo 'ISEScan results exists'
        else
	    echo 'ISEScan found 0 insertion sequences in input file... generating dummy files'
            touch isescan_results/contigs.fasta.is.fna
            touch isescan_results/contigs.fasta.tsv
        fi
        """
NextFlow isescan From line 23 of modules/isescan.nf 
38
39
40
41
42
43
        """
	echo 'ISEScan is not running due to empty input... generating dummy files'
        mkdir isescan_results
	touch isescan_results/contigs.fasta.is.fna
        touch isescan_results/contigs.fasta.tsv
        """
NextFlow From line 38 of modules/isescan.nf 
24
25
26
27
28
29
30
"""
prokka --outdir prokka_out \
--prefix contigs \
--cpus ${task.cpus} \
--metagenome \
contigs.fasta
"""
NextFlow metaprokka From line 24 of modules/prokka.nf 
32
33
34
35
36
"""
echo 'PROKKA dir empty due to empty input... generating dummy files'
mkdir prokka_out
touch prokka_out/contigs.gbk
"""
NextFlow From line 32 of modules/prokka.nf 
20
21
22
"""    
assembly_filter_rename.py --assembly contigs.fasta
"""
NextFlow From line 20 of modules/rename_contigs.nf 
15
16
17
        """
	gt gff3validator momofy_predictions.gff
        """
NextFlow From line 15 of modules/validator.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://github.com/EBI-Metagenomics/momofy.git
Name: momofy-module-for-integrative-mobilome-prediction
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: Boost Software License 1.0
  • 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