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Update tasmanian-mismatch to 2.0.5 #75

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Update tasmanian-mismatch to 2.0.5 #75

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12 changes: 8 additions & 4 deletions modules/tasmanian.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -2,7 +2,7 @@ process tasmanian {
label 'medium_cpu'
tag { library }
publishDir "${params.outputDir}/stats/tasmanian"
conda "bioconda::samtools=1.22 bioconda::tasmanian-mismatch=1.0.9"
conda "bioconda::tasmanian-mismatch=2.0.5"

errorStrategy { task.attempt <= 1 ? 'retry' : 'terminate' }
maxRetries 1
Expand All @@ -15,14 +15,18 @@ process tasmanian {

output:
tuple val(library), path("${library}.tasmanian.csv"), emit: for_agg
tuple val("${task.process}"), val('samtools'), eval('samtools --version | head -n 1 | sed \'s/^samtools //\''), topic: versions
tuple val("${task.process}"), val('tasmanian'), val('*should be* 1.0.9'), topic: versions
tuple val("${task.process}"), val('tasmanian-mismatch'), val('*should be* 2.0.5'), topic: versions

script:
"""
set +e
set +o pipefail
Comment on lines 22 to 23
samtools view -q 30 -F 3840 ${bam} | head -n 2000000 | run_tasmanian -r ${genome_fa} > ${library}.tasmanian.csv
tasmanian-mismatch ${bam} ${genome_fa} \
--position-mode read \
--min-base-quality 20 \
--min-map-quality 30 \
-F 3840 \
Comment on lines +24 to +28
-o ${library}.tasmanian.csv
"""

}
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