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Snippy_Variants: Calculate % reads aligned #616

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merged 8 commits into from
Oct 3, 2024
Merged

Snippy_Variants: Calculate % reads aligned #616

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2119e0b
Snippy_Variants: Calculate % reads aligned snippy
fraser-combe Sep 4, 2024
ea9861d
add output snippy percent aligned
fraser-combe Sep 6, 2024
948c669
amended TOTAL_READS_ALIGNED to correct samtools
fraser-combe Sep 6, 2024
f421b8e
update snippy percent reads name
fraser-combe Sep 24, 2024
041cc40
add percent reads aligned to snippy variant and streamline
fraser-combe Sep 26, 2024
0f5763d
Merge branch 'main' into fc-snippyvariantscalculatepercentreadsaligne…
fraser-combe Sep 26, 2024
f634814
Merge branch 'main' into fc-snippyvariantscalculatepercentreadsaligne…
fraser-combe Oct 2, 2024
6e8202b
update docs for snippy streamline and variants output
fraser-combe Oct 2, 2024
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14 changes: 12 additions & 2 deletions tasks/gene_typing/variant_detection/task_snippy_variants.wdl
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Original file line number Diff line number Diff line change
Expand Up @@ -61,8 +61,8 @@ task snippy_variants {
# Compress output dir
tar -cvzf "./~{samplename}_snippy_variants_outdir.tar" "./~{samplename}"

# compute number of reads aligned to reference
samtools view -c "~{samplename}/~{samplename}.bam" > READS_ALIGNED_TO_REFERENCE
# compute number of reads aligned to reference (excluding unmapped reads)
samtools view -c -F 4 "~{samplename}/~{samplename}.bam" > READS_ALIGNED_TO_REFERENCE

# create coverage stats file
samtools coverage "~{samplename}/~{samplename}.bam" -o "~{samplename}/~{samplename}_coverage.tsv"
Expand Down Expand Up @@ -93,6 +93,15 @@ task snippy_variants {
echo $reference_length_passed_depth $reference_length | awk '{ print ($1/$2)*100 }' > PERCENT_REF_COVERAGE
fi

# Compute percentage of reads aligned
reads_aligned=$(cat READS_ALIGNED_TO_REFERENCE)
total_reads=$(samtools view -c "~{samplename}/~{samplename}.bam")
if [ "$total_reads" -eq 0 ]; then
echo "Could not compute percent reads aligned: total reads is 0" > PERCENT_READS_ALIGNED
else
echo $reads_aligned $total_reads | awk '{ print ($1/$2)*100 }' > PERCENT_READS_ALIGNED
fi

>>>
output {
String snippy_variants_version = read_string("VERSION")
Expand All @@ -111,6 +120,7 @@ task snippy_variants {
String snippy_variants_ref_length = read_string("REFERENCE_LENGTH")
String snippy_variants_ref_length_passed_depth = read_string("REFERENCE_LENGTH_PASSED_DEPTH")
String snippy_variants_percent_ref_coverage = read_string("PERCENT_REF_COVERAGE")
String snippy_variants_percent_read_aligned = read_string("PERCENT_READS_ALIGNED")
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}
runtime {
docker: "~{docker}"
Expand Down