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Merge pull request #324 from RoanKanninga/master
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fixing issue where Darwin tool cannot handle decimals
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@pneerincx
pneerincx authored Aug 31, 2023
2 parents 2c94e89 + 967e2d9 commit f340d04
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Showing 4 changed files with 102 additions and 102 deletions.
2 changes: 1 addition & 1 deletion protocols/CoverageCalculations_gvcf.sh
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Expand Up @@ -125,7 +125,7 @@ then

grep -v "NC_001422.1" "${intermediateDir}/${externalSampleID}.${perBase}.coveragePerBase.txt" > "${intermediateDir}/${externalSampleID}.${perBase}.coveragePerBase.txt.tmp"
echo "phiX is removed for ${externalSampleID}.${perBase} perBase"
mv -v "${intermediateDir}/${externalSampleID}.${perBase}.coveragePerBase.txt.tmp" "${projectResultsDir}/coverage/CoveragePerBase/${Gender,,}/${externalSampleID}.${perBase}.coveragePerBase.txt"
awk '{if (NR>1){printf "%s\t%s\t%s\t%s\t%.0f\t%s\t%s\n",$1,$2,$3,$4,$5,$6,$7}else {print $0}}' "${intermediateDir}/${externalSampleID}.${perBase}.coveragePerBase.txt.tmp" > "${projectResultsDir}/coverage/CoveragePerBase/${Gender,,}/${externalSampleID}.${perBase}.coveragePerBase.txt"

echo "coveragePerTarget file can be found here: ${projectResultsDir}/coverage/CoveragePerBase/${Gender,,}/${externalSampleID}.${perBase}.coveragePerBase.txt"

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0 protocols/processDragenTrendanalysis.sh → protocols/ProcessDragenTrendAnalysis.sh
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File renamed without changes.
198 changes: 99 additions & 99 deletions test/results/PlatinumSample_NA12878.NGS_DNA_Test_v1.coveragePerBase.selection_True.txt
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Original file line number Diff line number Diff line change
@@ -1,100 +1,100 @@
Index Chr Chr Position Start Description Min Counts CDS Contig
1 2 197550 AC079779.7 33.0 CDS 1
2 2 197551 AC079779.7 33.0 CDS 1
3 2 197552 AC079779.7 33.0 CDS 1
4 2 197553 AC079779.7 33.0 CDS 1
5 2 197554 AC079779.7 33.0 CDS 1
6 2 197555 AC079779.7 33.0 CDS 1
7 2 197556 AC079779.7 33.0 CDS 1
8 2 197557 AC079779.7 33.0 CDS 1
9 2 197558 AC079779.7 33.0 CDS 1
10 2 197559 AC079779.7 33.0 CDS 1
11 2 197560 AC079779.7 33.0 CDS 1
12 2 197561 AC079779.7 33.0 CDS 1
13 2 197562 AC079779.7 33.0 CDS 1
14 2 197563 AC079779.7 33.0 CDS 1
15 2 197564 AC079779.7 36.0 CDS 1
16 2 197565 AC079779.7 36.0 CDS 1
17 2 197566 AC079779.7 36.0 CDS 1
18 2 197567 AC079779.7 36.0 CDS 1
19 2 197568 AC079779.7 31.0 CDS 1
20 2 197569 AC079779.7 31.0 CDS 1
21 2 197570 AC079779.7 31.0 CDS 1
22 2 197571 AC079779.7 31.0 CDS 1
23 2 197572 AC079779.7 31.0 CDS 1
24 2 197573 AC079779.7 31.0 CDS 1
25 2 197574 AC079779.7 31.0 CDS 1
26 2 197575 AC079779.7 31.0 CDS 1
27 2 197576 AC079779.7 31.0 CDS 1
28 2 197577 AC079779.7 31.0 CDS 1
29 2 197578 AC079779.7 31.0 CDS 1
30 2 197579 AC079779.7 31.0 CDS 1
31 2 197580 AC079779.7 31.0 CDS 1
32 2 197581 AC079779.7 31.0 CDS 1
33 2 197582 AC079779.7 31.0 CDS 1
34 2 197583 AC079779.7 31.0 CDS 1
35 2 197584 AC079779.7 28.0 CDS 1
36 2 197585 AC079779.7 28.0 CDS 1
37 2 197586 AC079779.7 28.0 CDS 1
38 2 197587 AC079779.7 28.0 CDS 1
39 2 197588 AC079779.7 28.0 CDS 1
40 2 197589 AC079779.7 28.0 CDS 1
41 2 197590 AC079779.7 28.0 CDS 1
42 2 197591 AC079779.7 28.0 CDS 1
43 2 197592 AC079779.7 28.0 CDS 1
44 2 197593 AC079779.7 27.0 CDS 1
45 2 197594 AC079779.7 26.0 CDS 1
46 2 197595 AC079779.7 26.0 CDS 1
47 2 197596 AC079779.7 26.0 CDS 1
48 2 197597 AC079779.7 25.0 CDS 1
49 2 197598 AC079779.7 25.0 CDS 1
52329 Y 2803782 ZFY 0.0 CDS 1
52330 Y 2803783 ZFY 0.0 CDS 1
52331 Y 2803784 ZFY 0.0 CDS 1
52332 Y 2803785 ZFY 0.0 CDS 1
52333 Y 2803786 ZFY 0.0 CDS 1
52334 Y 2803787 ZFY 0.0 CDS 1
52335 Y 2803788 ZFY 0.0 CDS 1
52336 Y 2803789 ZFY 0.0 CDS 1
52337 Y 2803790 ZFY 0.0 CDS 1
52338 Y 2803791 ZFY 0.0 CDS 1
52339 Y 2803792 ZFY 0.0 CDS 1
52340 Y 2803793 ZFY 0.0 CDS 1
52341 Y 2803794 ZFY 0.0 CDS 1
52342 Y 2803795 ZFY 0.0 CDS 1
52343 Y 2803796 ZFY 0.0 CDS 1
52344 Y 2803797 ZFY 0.0 CDS 1
52345 Y 2803798 ZFY 0.0 CDS 1
52346 Y 2803799 ZFY 0.0 CDS 1
52347 Y 2803800 ZFY 0.0 CDS 1
52348 Y 2803801 ZFY 0.0 CDS 1
52349 Y 2803802 ZFY 0.0 CDS 1
52350 Y 2803803 ZFY 0.0 CDS 1
52351 Y 2803804 ZFY 0.0 CDS 1
52352 Y 2803805 ZFY 0.0 CDS 1
52353 Y 2803806 ZFY 0.0 CDS 1
52354 Y 2803807 ZFY 0.0 CDS 1
52355 Y 2803808 ZFY 0.0 CDS 1
52356 Y 2803809 ZFY 0.0 CDS 1
52357 Y 2803810 ZFY 0.0 CDS 1
52358 Y 2803811 ZFY 0.0 CDS 1
52359 Y 2803812 ZFY 0.0 CDS 1
52360 Y 2803813 ZFY 0.0 CDS 1
52361 Y 2803814 ZFY 0.0 CDS 1
52362 Y 2803815 ZFY 0.0 CDS 1
52363 Y 2803816 ZFY 0.0 CDS 1
52364 Y 2803817 ZFY 0.0 CDS 1
52365 Y 2803818 ZFY 0.0 CDS 1
52366 Y 2803819 ZFY 0.0 CDS 1
52367 Y 2803820 ZFY 0.0 CDS 1
52368 Y 2803821 ZFY 0.0 CDS 1
52369 Y 2803822 ZFY 0.0 CDS 1
52370 Y 2803823 ZFY 0.0 CDS 1
52371 Y 2803824 ZFY 0.0 CDS 1
52372 Y 2803825 ZFY 0.0 CDS 1
52373 Y 2803826 ZFY 0.0 CDS 1
52374 Y 2803827 ZFY 0.0 CDS 1
52375 Y 2803828 ZFY 0.0 CDS 1
52376 Y 2803829 ZFY 0.0 CDS 1
52377 Y 2803830 ZFY 0.0 CDS 1
52378 Y 2803831 ZFY 0.0 CDS 1
1 2 197550 AC079779.7 33 CDS 1
2 2 197551 AC079779.7 33 CDS 1
3 2 197552 AC079779.7 33 CDS 1
4 2 197553 AC079779.7 33 CDS 1
5 2 197554 AC079779.7 33 CDS 1
6 2 197555 AC079779.7 33 CDS 1
7 2 197556 AC079779.7 33 CDS 1
8 2 197557 AC079779.7 33 CDS 1
9 2 197558 AC079779.7 33 CDS 1
10 2 197559 AC079779.7 33 CDS 1
11 2 197560 AC079779.7 33 CDS 1
12 2 197561 AC079779.7 33 CDS 1
13 2 197562 AC079779.7 33 CDS 1
14 2 197563 AC079779.7 33 CDS 1
15 2 197564 AC079779.7 36 CDS 1
16 2 197565 AC079779.7 36 CDS 1
17 2 197566 AC079779.7 36 CDS 1
18 2 197567 AC079779.7 36 CDS 1
19 2 197568 AC079779.7 31 CDS 1
20 2 197569 AC079779.7 31 CDS 1
21 2 197570 AC079779.7 31 CDS 1
22 2 197571 AC079779.7 31 CDS 1
23 2 197572 AC079779.7 31 CDS 1
24 2 197573 AC079779.7 31 CDS 1
25 2 197574 AC079779.7 31 CDS 1
26 2 197575 AC079779.7 31 CDS 1
27 2 197576 AC079779.7 31 CDS 1
28 2 197577 AC079779.7 31 CDS 1
29 2 197578 AC079779.7 31 CDS 1
30 2 197579 AC079779.7 31 CDS 1
31 2 197580 AC079779.7 31 CDS 1
32 2 197581 AC079779.7 31 CDS 1
33 2 197582 AC079779.7 31 CDS 1
34 2 197583 AC079779.7 31 CDS 1
35 2 197584 AC079779.7 28 CDS 1
36 2 197585 AC079779.7 28 CDS 1
37 2 197586 AC079779.7 28 CDS 1
38 2 197587 AC079779.7 28 CDS 1
39 2 197588 AC079779.7 28 CDS 1
40 2 197589 AC079779.7 28 CDS 1
41 2 197590 AC079779.7 28 CDS 1
42 2 197591 AC079779.7 28 CDS 1
43 2 197592 AC079779.7 28 CDS 1
44 2 197593 AC079779.7 27 CDS 1
45 2 197594 AC079779.7 26 CDS 1
46 2 197595 AC079779.7 26 CDS 1
47 2 197596 AC079779.7 26 CDS 1
48 2 197597 AC079779.7 25 CDS 1
49 2 197598 AC079779.7 25 CDS 1
52329 Y 2803782 ZFY 0 CDS 1
52330 Y 2803783 ZFY 0 CDS 1
52331 Y 2803784 ZFY 0 CDS 1
52332 Y 2803785 ZFY 0 CDS 1
52333 Y 2803786 ZFY 0 CDS 1
52334 Y 2803787 ZFY 0 CDS 1
52335 Y 2803788 ZFY 0 CDS 1
52336 Y 2803789 ZFY 0 CDS 1
52337 Y 2803790 ZFY 0 CDS 1
52338 Y 2803791 ZFY 0 CDS 1
52339 Y 2803792 ZFY 0 CDS 1
52340 Y 2803793 ZFY 0 CDS 1
52341 Y 2803794 ZFY 0 CDS 1
52342 Y 2803795 ZFY 0 CDS 1
52343 Y 2803796 ZFY 0 CDS 1
52344 Y 2803797 ZFY 0 CDS 1
52345 Y 2803798 ZFY 0 CDS 1
52346 Y 2803799 ZFY 0 CDS 1
52347 Y 2803800 ZFY 0 CDS 1
52348 Y 2803801 ZFY 0 CDS 1
52349 Y 2803802 ZFY 0 CDS 1
52350 Y 2803803 ZFY 0 CDS 1
52351 Y 2803804 ZFY 0 CDS 1
52352 Y 2803805 ZFY 0 CDS 1
52353 Y 2803806 ZFY 0 CDS 1
52354 Y 2803807 ZFY 0 CDS 1
52355 Y 2803808 ZFY 0 CDS 1
52356 Y 2803809 ZFY 0 CDS 1
52357 Y 2803810 ZFY 0 CDS 1
52358 Y 2803811 ZFY 0 CDS 1
52359 Y 2803812 ZFY 0 CDS 1
52360 Y 2803813 ZFY 0 CDS 1
52361 Y 2803814 ZFY 0 CDS 1
52362 Y 2803815 ZFY 0 CDS 1
52363 Y 2803816 ZFY 0 CDS 1
52364 Y 2803817 ZFY 0 CDS 1
52365 Y 2803818 ZFY 0 CDS 1
52366 Y 2803819 ZFY 0 CDS 1
52367 Y 2803820 ZFY 0 CDS 1
52368 Y 2803821 ZFY 0 CDS 1
52369 Y 2803822 ZFY 0 CDS 1
52370 Y 2803823 ZFY 0 CDS 1
52371 Y 2803824 ZFY 0 CDS 1
52372 Y 2803825 ZFY 0 CDS 1
52373 Y 2803826 ZFY 0 CDS 1
52374 Y 2803827 ZFY 0 CDS 1
52375 Y 2803828 ZFY 0 CDS 1
52376 Y 2803829 ZFY 0 CDS 1
52377 Y 2803830 ZFY 0 CDS 1
52378 Y 2803831 ZFY 0 CDS 1
4 changes: 2 additions & 2 deletions workflow_DRAGEN.csv
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@@ -1,9 +1,9 @@
step,protocol,dependencies
s01_PrepareDragenData,protocols/PrepareDragenData.sh,
s01b_processDragenTrendAnalysis,protocols/processDragenTrendAnalysis.sh,s01_PrepareDragenData
s01b_ProcessDragenTrendAnalysis,protocols/ProcessDragenTrendAnalysis.sh,s01_PrepareDragenData
s02_CoverageCalculations,protocols/CoverageCalculations_gvcf.sh,s01_PrepareDragenData;variantCalls=sampleDragenRawVariantCalls;merge=noMerge
s03_AnnotateVcf,protocols/AnnotateVcf_perSample.sh,s01_PrepareDragenData;variantCalls=sampleDragenVariantCalls
s04_SnpEff,protocols/SnpEff_perSample.sh,s03_AnnotateVcf
s08_Gavin,protocols/Gavin.sh,s04_SnpEff;inputFile=sampleVariantCallsSnpEff_Annotated
s09_ReheaderVcf,protocols/ReheaderVCF.sh,s08_Gavin
s10_PipelineFinished,protocols/PipelineFinished.sh,s01b_processDragenTrendAnalysis;s02_CoverageCalculations;s09_ReheaderVcf
s10_PipelineFinished,protocols/PipelineFinished.sh,s01b_ProcessDragenTrendAnalysis;s02_CoverageCalculations;s09_ReheaderVcf

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