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Fix typo in UnifiedGenotyper IndelRealigner command #707

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merged 5 commits into from
Mar 20, 2021
Merged

Fix typo in UnifiedGenotyper IndelRealigner command #707

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b5a8f0f
Merge pull request #703 from nf-core/dev
jfy133 Mar 16, 2021
1591207
Fix typo in UnifiedGenotyper IndelRealigner command
IdoBar Mar 20, 2021
a810c45
Update CHANGELOG.md
IdoBar Mar 20, 2021
14615f5
Update CHANGELOG.md
IdoBar Mar 20, 2021
1a2f3ca
Merge branch 'dev' into patch-5
jfy133 Mar 20, 2021
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12 changes: 12 additions & 0 deletions CHANGELOG.md
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Expand Up @@ -3,6 +3,18 @@
The format is based on [Keep a Changelog](http://keepachangelog.com/en/1.0.0/)
and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.html).

## [2.3.3]

### `Added`

### `Fixed`

- [#707](https://github.com/nf-core/eager/pull/707) - Fix typo in UnifiedGenotyper IndelRealigner command

### `Dependencies`

### `Deprecated`

## [2.3.2] - 2021-03-16

### `Added`
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2 changes: 1 addition & 1 deletion main.nf
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Expand Up @@ -2334,7 +2334,7 @@ process genotyping_ug {
"""
samtools index ${bam}
gatk3 -T RealignerTargetCreator -R ${fasta} -I ${bam} -nt ${task.cpus} -o ${samplename}.intervals ${defaultbasequalities}
gatk3 -T IndelRealigner -R ${fasta} -I ${bam} -targetIntervals ${samplenane}.intervals -o ${samplename}.realign.bam ${defaultbasequalities}
gatk3 -T IndelRealigner -R ${fasta} -I ${bam} -targetIntervals ${samplename}.intervals -o ${samplename}.realign.bam ${defaultbasequalities}
gatk3 -T UnifiedGenotyper -R ${fasta} -I ${samplename}.realign.bam -o ${samplename}.unifiedgenotyper.vcf -nt ${task.cpus} --dbsnp ${params.gatk_dbsnp} --genotype_likelihoods_model ${params.gatk_ug_genotype_model} -stand_call_conf ${params.gatk_call_conf} --sample_ploidy ${params.gatk_ploidy} -dcov ${params.gatk_downsample} --output_mode ${params.gatk_ug_out_mode} ${defaultbasequalities}

$keep_realign
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