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fix: update tiddit_sv tests (#272)

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Maxime Garcia 2021-03-15 15:02:20 +01:00 committed by GitHub
parent 9b99b33401
commit 66fd57a8bc
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GPG key ID: 4AEE18F83AFDEB23
2 changed files with 10 additions and 14 deletions
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16
tests/software/tiddit/sv/main.nf
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@ -7,24 +7,20 @@ include { SAMTOOLS_FAIDX } from '../../../../software/samtools/faidx/main.nf' ad
workflow test_tiddit_sv { workflow test_tiddit_sv {
def input = [] def input = []
def fasta = file("${launchDir}/tests/data/fasta/E_coli/NC_010473.fa", checkIfExists: true) def fasta = file("${launchDir}/tests/data/genomics/sarscov2/fasta/test_genome.fasta", checkIfExists: true)
def fai = file("${launchDir}/tests/data/genomics/sarscov2/fasta/test_genome.fasta.fai", checkIfExists: true)
input = [ [ id:'test' ], // meta map input = [ [ id:'test' ], // meta map
[ file("${launchDir}/tests/data/bam/test.paired_end.sorted.bam", checkIfExists: true) ] ] [ file("${launchDir}/tests/data/genomics/sarscov2/bam/test_paired_end.sorted.bam", checkIfExists: true) ] ]
SAMTOOLS_FAIDX ( fasta ) TIDDIT_SV ( input, fasta, fai )
TIDDIT_SV ( input, fasta, SAMTOOLS_FAIDX.out.fai )
} }
workflow test_tiddit_sv_no_ref { workflow test_tiddit_sv_no_ref {
def input = [] def input = []
def dummy_file = file("${launchDir}/tests/data/dummy/dummy_file.txt", checkIfExists: true)
def dummy_file2 = file("${launchDir}/tests/data/dummy/dummy_file2.txt", checkIfExists: true)
input = [ [ id:'test' ], // meta map input = [ [ id:'test' ], // meta map
[ file("${launchDir}/tests/data/bam/test.paired_end.sorted.bam", checkIfExists: true) ] ] [ file("${launchDir}/tests/data/genomics/sarscov2/bam/test_paired_end.sorted.bam", checkIfExists: true) ] ]
TIDDIT_SV ( input, [], [] )
TIDDIT_SV ( input, dummy_file, dummy_file2 )
} }

8
tests/software/tiddit/sv/test.yml
View file

@ -6,9 +6,9 @@
- vcf - vcf
files: files:
- path: output/tiddit/test.ploidy.tab - path: output/tiddit/test.ploidy.tab
md5sum: 207bd22e75de82160f98bedc2d3d262d md5sum: 45e050b0e204f0a5a3a99627cc440eaa
- path: output/tiddit/test.signals.tab - path: output/tiddit/test.signals.tab
md5sum: 67e041b737fe0fe1a33119c3109e9eff md5sum: 25408a43dbdd01c08e33a6d670f2bb84
- path: output/tiddit/test.vcf - path: output/tiddit/test.vcf
should_exist: true should_exist: true
@ -20,8 +20,8 @@
- vcf - vcf
files: files:
- path: output/tiddit/test.ploidy.tab - path: output/tiddit/test.ploidy.tab
md5sum: 207bd22e75de82160f98bedc2d3d262d md5sum: 45e050b0e204f0a5a3a99627cc440eaa
- path: output/tiddit/test.signals.tab - path: output/tiddit/test.signals.tab
md5sum: 67e041b737fe0fe1a33119c3109e9eff md5sum: 25408a43dbdd01c08e33a6d670f2bb84
- path: output/tiddit/test.vcf - path: output/tiddit/test.vcf
should_exist: true should_exist: true