Bactopia Tool - `ismapper`¶

The ismapper module uses ISMapper to search for insertion sites in your samples.

Example Usage¶

bactopia --wf ismapper \
  --bactopia /path/to/your/bactopia/results \ 
  --include includes.txt

Output Overview¶

Below is the default output structure for the ismapper tool. Where possible the file descriptions below were modified from a tools description.

<BACTOPIA_DIR>
├── <SAMPLE_NAME>
│   └── tools
│       └── ismapper
│           └── ismapper
│               ├── <INSERTION_NAME>
│               │   ├── <SAMPLE_NAME>_<FASTA_ENTRY>_{left_final,right_final}.fastq
│               │   ├── <SAMPLE_NAME>__<REFERENCE>_closest.bed
│               │   ├── <SAMPLE_NAME>__<REFERENCE>_intersect.bed
│               │   ├── <SAMPLE_NAME>__<REFERENCE>_table.txt
│               │   ├── <SAMPLE_NAME>_{left,right}_<REFERENCE>_finalcov.bed
│               │   ├── <SAMPLE_NAME>_{left,right}_<REFERENCE>_merged.sorted.bed
│               │   └── <SAMPLE_NAME>_{left,right}_<REFERENCE>_unpaired.bed
│               └── logs
│                   ├── SRR2838702.log
│                   ├── nf-ismapper.{begin,err,log,out,run,sh,trace}
│                   └── versions.yml
└── bactopia-runs
    └── ismapper-<TIMESTAMP>
        └── nf-reports
            ├── ismapper-dag.dot
            ├── ismapper-report.html
            ├── ismapper-timeline.html
            └── ismapper-trace.txt

Results¶

ISMapper¶

Below is a description of the per-sample results from ISMapper.

Extension	Description
_final.fastq	Sequences (FASTQ format) that mapped to the flanking regions of the IS query.
_closest.bed	Merged regions that are close but do not overlap.
_intersect.bed	An intersection of merged regions from the left and right flanks.
_table.txt	A detailed description of the IS query results.
_finalcov.bed	Contains information about the coverage of the IS query
_merged.sorted.bed	Merged overlapping regions that passed coverage cutoffs
_unpaired.bed	All unpaired mappings to the IS query

Audit Trail¶

Below are files that can assist you in understanding which parameters and program versions were used.

Logs¶

Each process that is executed will have a folder named logs. In this folder are helpful files for you to review if the need ever arises.

Extension	Description
.begin	An empty file used to designate the process started
.err	Contains STDERR outputs from the process
.log	Contains both STDERR and STDOUT outputs from the process
.out	Contains STDOUT outputs from the process
.run	The script Nextflow uses to stage/unstage files and queue processes based on given profile
.sh	The script executed by bash for the process
.trace	The Nextflow Trace report for the process
versions.yml	A YAML formatted file with program versions

Nextflow Reports¶

These Nextflow reports provide great a great summary of your run. These can be used to optimize resource usage and estimate expected costs if using cloud platforms.

Filename	Description
ismapper-dag.dot	The Nextflow DAG visualisation
ismapper-report.html	The Nextflow Execution Report
ismapper-timeline.html	The Nextflow Timeline Report
ismapper-trace.txt	The Nextflow Trace report

Program Versions¶

At the end of each run, each of the versions.yml files are merged into the files below.

Filename	Description
software_versions.yml	A complete list of programs and versions used by each process
software_versions_mqc.yml	A complete list of programs and versions formatted for MultiQC

Parameters¶

Required Parameters¶

Define where the pipeline should find input data and save output data.

Parameter	Description
`--bactopia`	The path to bactopia results to use as inputs Type: `string`

Filtering Parameters¶

Use these parameters to specify which samples to include or exclude.

Parameter	Description
`--include`	A text file containing sample names (one per line) to include from the analysis Type: `string`
`--exclude`	A text file containing sample names (one per line) to exclude from the analysis Type: `string`

ISMapper Parameters¶

Parameter	Description
`--reference`	Reference genome for typing against in GenBank format Type: `string`
`--insertions`	Multifasta file with insertion sequence(s) to be mapped to Type: `string`
`--min_clip`	Minimum size for softclipped region to be extracted from initial mapping Type: `integer`, Default: `10`
`--max_clip`	Maximum size for softclipped regions to be included Type: `integer`, Default: `30`
`--cutoff`	Minimum depth for mapped region to be kept in bed file Type: `integer`, Default: `6`
`--novel_gap_size`	Distance in base pairs between left and right flanks to be called a novel hit Type: `integer`, Default: `15`
`--min_range`	Minimum percent size of the gap to be called a known hit Type: `number`, Default: `0.9`
`--max_range`	Maximum percent size of the gap to be called a known hit Type: `number`, Default: `1.1`
`--merging`	Value for merging left and right hits in bed files together to simply calculation of closest and intersecting regions Type: `integer`, Default: `100`
`--ismap_all`	Switch on all alignment reporting for bwa Type: `boolean`
`--ismap_minqual`	Mapping quality score for bwa Type: `integer`, Default: `30`

Optional Parameters¶

These optional parameters can be useful in certain settings.

Parameter	Description
`--outdir`	Base directory to write results to Type: `string`, Default: `./`
`--run_name`	Name of the directory to hold results Type: `string`, Default: `bactopia`
`--skip_compression`	Ouput files will not be compressed Type: `boolean`
`--datasets`	The path to cache datasets to Type: `string`
`--keep_all_files`	Keeps all analysis files created Type: `boolean`

Max Job Request Parameters¶

Set the top limit for requested resources for any single job.

Parameter	Description
`--max_retry`	Maximum times to retry a process before allowing it to fail. Type: `integer`, Default: `3`
`--max_cpus`	Maximum number of CPUs that can be requested for any single job. Type: `integer`, Default: `4`
`--max_memory`	Maximum amount of memory (in GB) that can be requested for any single job. Type: `integer`, Default: `32`
`--max_time`	Maximum amount of time (in minutes) that can be requested for any single job. Type: `integer`, Default: `120`
`--max_downloads`	Maximum number of samples to download at a time Type: `integer`, Default: `3`

Nextflow Configuration Parameters¶

Parameters to fine-tune your Nextflow setup.

Parameter	Description
`--nfconfig`	A Nextflow compatible config file for custom profiles, loaded last and will overwrite existing variables if set. Type: `string`
`--publish_dir_mode`	Method used to save pipeline results to output directory. Type: `string`, Default: `copy`
`--infodir`	Directory to keep pipeline Nextflow logs and reports. Type: `string`, Default: `${params.outdir}/pipeline_info`
`--force`	Nextflow will overwrite existing output files. Type: `boolean`
`--cleanup_workdir`	After Bactopia is successfully executed, the `work` directory will be deleted. Type: `boolean`

Nextflow Profile Parameters¶