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Add Bt2 --maxins #732

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Merged
apeltzer merged 2 commits into from
Apr 26, 2021
Merged

Add Bt2 --maxins #732

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6c495df
Added --maxins for bt2
jfy133 Apr 25, 2021
1687722
Update CHANGELOG.md
jfy133 Apr 25, 2021
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2 changes: 2 additions & 0 deletions CHANGELOG.md
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Expand Up @@ -7,6 +7,8 @@ and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.

### `Added`

- [#729](https://github.com/nf-core/eager/issues/729) Added Bowtie2 flag `--maxins` for PE mapping modern DNA mapping contexts

### `Fixed`

- Corrected explanation of the "--min_adap_overlap" parameter for AdapterRemoval in the docs
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2 changes: 1 addition & 1 deletion main.nf
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Expand Up @@ -1357,7 +1357,7 @@ process bowtie2 {
//PE data without merging, PE data without any AR applied
if ( seqtype == 'PE' && ( params.skip_collapse || params.skip_adapterremoval ) ){
"""
bowtie2 -x ${fasta} -1 ${r1} -2 ${r2} -p ${task.cpus} ${sensitivity} ${bt2n} ${bt2l} ${trim5} ${trim3} --rg-id ILLUMINA-${libraryid} --rg SM:${libraryid} --rg PL:illumina --rg PU:ILLUMINA-${libraryid}-${seqtype} 2> "${libraryid}"_bt2.log | samtools sort -@ ${task.cpus} -O bam > "${libraryid}"_"${seqtype}".mapped.bam
bowtie2 -x ${fasta} -1 ${r1} -2 ${r2} -p ${task.cpus} ${sensitivity} ${bt2n} ${bt2l} ${trim5} ${trim3} --maxins ${bt2_maxins} --rg-id ILLUMINA-${libraryid} --rg SM:${libraryid} --rg PL:illumina --rg PU:ILLUMINA-${libraryid}-${seqtype} 2> "${libraryid}"_bt2.log | samtools sort -@ ${task.cpus} -O bam > "${libraryid}"_"${seqtype}".mapped.bam
samtools index "${libraryid}"_"${seqtype}".mapped.bam ${size}
"""
} else {
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1 change: 1 addition & 0 deletions nextflow.config
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Expand Up @@ -89,6 +89,7 @@ params {
bt2l = 0
bt2_trim5 = 0
bt2_trim3 = 0
bt2_maxins = 500

//Mapped read removal from input FASTQ
hostremoval_input_fastq = false
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9 changes: 8 additions & 1 deletion nextflow_schema.json
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Expand Up @@ -634,6 +634,13 @@
"description": "Specify number of bases to trim off from 3' (right) end of read before alignment.",
"fa_icon": "fas fa-cut",
"help_text": "Number of bases to trim at the 3' (right) end of read prior alignment. Maybe useful when left-over sequencing artefacts of in-line barcodes present Default: 0.\n\n> Modifies Bowtie2 parameters: `-bt2_trim3`"
},
"bt2_maxins": {
"type": "integer",
"default": 500,
"fa_icon": "fas fa-exchange-alt",
"description": "Specify the maximum fragment length for Bowtie2 paired-end mapping mode only.",
"help_text": "The maximum fragment for valid paired-end alignments. Only for paired-end mapping (i.e. unmerged), and therefore typically only useful for modern data.\n\n See [Bowtie2 documentation](http://bowtie-bio.sourceforge.net/bowtie2/manual.shtml) for more information.\n\n> Modifies Bowtie2 parameters: `--maxins`"
}
},
"fa_icon": "fas fa-layer-group",
Expand Down Expand Up @@ -1642,4 +1649,4 @@
"$ref": "#/definitions/metagenomic_authentication"
}
]
}
}