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Szilveszter Juhos
authored
Merge pull request nf-core#638 from MaxUlysse/Tests
Update tests
2 parents 432661d + b11fb96 commit 24673f2

7 files changed

Lines changed: 64 additions & 101 deletions

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‎.travis.yml‎

Lines changed: 3 additions & 9 deletions
Original file line numberDiff line numberDiff line change
@@ -11,19 +11,13 @@ env:
1111
global:
1212
- NXF_VER=0.31.0 SGT_VER=2.5.1
1313
matrix:
14-
- CE=singularity TEST=TOOLS
15-
- CE=singularity TEST=MANTA
16-
- CE=docker TEST=MANTA
17-
- CE=docker TEST=TOOLS
14+
- CE=singularity TEST=SOMATIC
15+
- CE=docker TEST=SOMATIC
1816
- CE=docker TEST=ANNOTATEVEP
1917
- CE=singularity TEST=ANNOTATESNPEFF
20-
- CE=singularity TEST=STEP
21-
- CE=singularity TEST=GERMLINE
22-
- CE=singularity TEST=DIR
2318
- CE=docker TEST=ANNOTATESNPEFF
24-
- CE=docker TEST=STEP
19+
- CE=singularity TEST=GERMLINE
2520
- CE=docker TEST=GERMLINE
26-
- CE=docker TEST=DIR
2721

2822
install:
2923
# Install Nextflow (and Singularity if needed)

‎CHANGELOG.md‎

Lines changed: 3 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -17,12 +17,13 @@ and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.
1717
- [#608](https://github.com/SciLifeLab/Sarek/pull/608) - Update Nextflow required version
1818
- [#616](https://github.com/SciLifeLab/Sarek/pull/616) - Update CHANGELOG
1919
- [#615](https://github.com/SciLifeLab/Sarek/pull/615) - Use `splitCsv` instead of `readlines`
20-
- [#621](https://github.com/SciLifeLab/Sarek/pull/621) - Improve install script
21-
- [#621](https://github.com/SciLifeLab/Sarek/pull/621) - Simplify tests
20+
- [#621](https://github.com/SciLifeLab/Sarek/pull/621), [#638](https://github.com/SciLifeLab/Sarek/pull/638) - Improve install script
21+
- [#621](https://github.com/SciLifeLab/Sarek/pull/621), [#638](https://github.com/SciLifeLab/Sarek/pull/638) - Simplify tests
2222
- [#627](https://github.com/SciLifeLab/Sarek/pull/627), [#629](https://github.com/SciLifeLab/Sarek/pull/629), [#637](https://github.com/SciLifeLab/Sarek/pull/637) - Refactor docs
2323
- [#629](https://github.com/SciLifeLab/Sarek/pull/629) - Refactor config
2424
- [#632](https://github.com/SciLifeLab/Sarek/pull/632) - Use 2 threads and 2 cpus FastQC processes
2525
- [#637](https://github.com/SciLifeLab/Sarek/pull/637) - Update tool version gathering
26+
- [#638](https://github.com/SciLifeLab/Sarek/pull/638) - Use correct `.simg` extension for Singularity images
2627

2728
### `Removed`
2829
- [#616](https://github.com/SciLifeLab/Sarek/pull/616) - Remove old Issue Template

‎buildContainers.nf‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -98,7 +98,7 @@ process PullSingularityContainers {
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script:
100100
"""
101-
singularity pull --name ${container}-${params.tag}.img docker://${params.repository}/${container}:${params.tag}
101+
singularity build ${container}-${params.tag}.simg docker://${params.repository}/${container}:${params.tag}
102102
"""
103103
}
104104

‎conf/singularity-path.config‎

Lines changed: 36 additions & 36 deletions
Original file line numberDiff line numberDiff line change
@@ -14,111 +14,111 @@ singularity {
1414

1515
process {
1616
withName:BuildBWAindexes {
17-
container = "${params.containerPath}/sarek-${params.tag}.img"
17+
container = "${params.containerPath}/sarek-${params.tag}.simg"
1818
}
1919
withName:BuildReferenceIndex {
20-
container = "${params.containerPath}/sarek-${params.tag}.img"
20+
container = "${params.containerPath}/sarek-${params.tag}.simg"
2121
}
2222
withName:BuildSAMToolsIndex {
23-
container = "${params.containerPath}/sarek-${params.tag}.img"
23+
container = "${params.containerPath}/sarek-${params.tag}.simg"
2424
}
2525
withName:BuildVCFIndex {
26-
container = "${params.containerPath}/sarek-${params.tag}.img"
26+
container = "${params.containerPath}/sarek-${params.tag}.simg"
2727
}
2828
withName:CompressVCF {
29-
container = "${params.containerPath}/sarek-${params.tag}.img"
29+
container = "${params.containerPath}/sarek-${params.tag}.simg"
3030
}
3131
withName:ConcatVCF {
32-
container = "${params.containerPath}/sarek-${params.tag}.img"
32+
container = "${params.containerPath}/sarek-${params.tag}.simg"
3333
}
3434
withName:CreateRecalibrationTable {
35-
container = "${params.containerPath}/sarek-${params.tag}.img"
35+
container = "${params.containerPath}/sarek-${params.tag}.simg"
3636
}
3737
withName:GetVersionAll {
38-
container = "${params.containerPath}/sarek-${params.tag}.img"
38+
container = "${params.containerPath}/sarek-${params.tag}.simg"
3939
}
4040
withName:GetVersionAlleleCount {
41-
container = "${params.containerPath}/runallelecount-${params.tag}.img"
41+
container = "${params.containerPath}/runallelecount-${params.tag}.simg"
4242
}
4343
withName:GetVersionASCAT {
44-
container = "${params.containerPath}/r-base-${params.tag}.img"
44+
container = "${params.containerPath}/r-base-${params.tag}.simg"
4545
}
4646
withName:GetVersionSnpeff {
47-
container = {params.genome == 'GRCh38' ? "${params.containerPath}/snpeffgrch38-${params.tag}.img" : "${params.containerPath}/snpeffgrch37-${params.tag}.img"}
47+
container = {params.genome == 'GRCh38' ? "${params.containerPath}/snpeffgrch38-${params.tag}.simg" : "${params.containerPath}/snpeffgrch37-${params.tag}.simg"}
4848
}
4949
withName:GetVersionVEP {
50-
container = {params.genome == 'GRCh38' ? "${params.containerPath}/vepgrch38-${params.tag}.img" : "${params.containerPath}/vepgrch37-${params.tag}.img"}
50+
container = {params.genome == 'GRCh38' ? "${params.containerPath}/vepgrch38-${params.tag}.simg" : "${params.containerPath}/vepgrch37-${params.tag}.simg"}
5151
}
5252
withName:MapReads {
53-
container = "${params.containerPath}/sarek-${params.tag}.img"
53+
container = "${params.containerPath}/sarek-${params.tag}.simg"
5454
}
5555
withName:MarkDuplicates {
56-
container = "${params.containerPath}/sarek-${params.tag}.img"
56+
container = "${params.containerPath}/sarek-${params.tag}.simg"
5757
}
5858
withName:MergeBams {
59-
container = "${params.containerPath}/sarek-${params.tag}.img"
59+
container = "${params.containerPath}/sarek-${params.tag}.simg"
6060
}
6161
withName:RecalibrateBam {
62-
container = "${params.containerPath}/sarek-${params.tag}.img"
62+
container = "${params.containerPath}/sarek-${params.tag}.simg"
6363
}
6464
withName:RunAlleleCount {
65-
container = "${params.containerPath}/runallelecount-${params.tag}.img"
65+
container = "${params.containerPath}/runallelecount-${params.tag}.simg"
6666
}
6767
withName:RunAscat {
68-
container = "${params.containerPath}/r-base-${params.tag}.img"
68+
container = "${params.containerPath}/r-base-${params.tag}.simg"
6969
}
7070
withName:RunBamQC {
71-
container = "${params.containerPath}/sarek-${params.tag}.img"
71+
container = "${params.containerPath}/sarek-${params.tag}.simg"
7272
}
7373
withName:RunBcftoolsStats {
74-
container = "${params.containerPath}/sarek-${params.tag}.img"
74+
container = "${params.containerPath}/sarek-${params.tag}.simg"
7575
}
7676
withName:RunConvertAlleleCounts {
77-
container = "${params.containerPath}/r-base-${params.tag}.img"
77+
container = "${params.containerPath}/r-base-${params.tag}.simg"
7878
}
7979
withName:RunFastQC {
80-
container = "${params.containerPath}/sarek-${params.tag}.img"
80+
container = "${params.containerPath}/sarek-${params.tag}.simg"
8181
}
8282
withName:RunFreeBayes {
83-
container = "${params.containerPath}/sarek-${params.tag}.img"
83+
container = "${params.containerPath}/sarek-${params.tag}.simg"
8484
}
8585
withName:RunGenotypeGVCFs {
86-
container = "${params.containerPath}/sarek-${params.tag}.img"
86+
container = "${params.containerPath}/sarek-${params.tag}.simg"
8787
}
8888
withName:RunHaplotypecaller {
89-
container = "${params.containerPath}/sarek-${params.tag}.img"
89+
container = "${params.containerPath}/sarek-${params.tag}.simg"
9090
}
9191
withName:RunManta {
92-
container = "${params.containerPath}/sarek-${params.tag}.img"
92+
container = "${params.containerPath}/sarek-${params.tag}.simg"
9393
}
9494
withName:RunMultiQC {
95-
container = "${params.containerPath}/sarek-${params.tag}.img"
95+
container = "${params.containerPath}/sarek-${params.tag}.simg"
9696
}
9797
withName:RunMutect2 {
98-
container = "${params.containerPath}/sarek-${params.tag}.img"
98+
container = "${params.containerPath}/sarek-${params.tag}.simg"
9999
}
100100
withName:RunSamtoolsStats {
101-
container = "${params.containerPath}/sarek-${params.tag}.img"
101+
container = "${params.containerPath}/sarek-${params.tag}.simg"
102102
}
103103
withName:RunSingleManta {
104-
container = "${params.containerPath}/sarek-${params.tag}.img"
104+
container = "${params.containerPath}/sarek-${params.tag}.simg"
105105
}
106106
withName:RunSingleStrelka {
107-
container = "${params.containerPath}/sarek-${params.tag}.img"
107+
container = "${params.containerPath}/sarek-${params.tag}.simg"
108108
}
109109
withName:RunSnpeff {
110-
container = {params.genome == 'GRCh38' ? "${params.containerPath}/snpeffgrch38-${params.tag}.img" : "${params.containerPath}/snpeffgrch37-${params.tag}.img"}
110+
container = {params.genome == 'GRCh38' ? "${params.containerPath}/snpeffgrch38-${params.tag}.simg" : "${params.containerPath}/snpeffgrch37-${params.tag}.simg"}
111111
}
112112
withName:RunStrelka {
113-
container = "${params.containerPath}/sarek-${params.tag}.img"
113+
container = "${params.containerPath}/sarek-${params.tag}.simg"
114114
}
115115
withName:RunStrelkaBP {
116-
container = "${params.containerPath}/sarek-${params.tag}.img"
116+
container = "${params.containerPath}/sarek-${params.tag}.simg"
117117
}
118118
withName:RunVcftools {
119-
container = "${params.containerPath}/sarek-${params.tag}.img"
119+
container = "${params.containerPath}/sarek-${params.tag}.simg"
120120
}
121121
withName:RunVEP {
122-
container = {params.genome == 'GRCh38' ? "${params.containerPath}/vepgrch38-${params.tag}.img" : "${params.containerPath}/vepgrch37-${params.tag}.img"}
122+
container = {params.genome == 'GRCh38' ? "${params.containerPath}/vepgrch38-${params.tag}.simg" : "${params.containerPath}/vepgrch37-${params.tag}.simg"}
123123
}
124124
}

‎docs/TESTS.md‎

Lines changed: 2 additions & 10 deletions
Original file line numberDiff line numberDiff line change
@@ -24,11 +24,6 @@ nextflow run main.nf --sampleDir Sarek-data/testdata/manta/normal \
2424
--step mapping --genome smallGRCh37 --genome_base References/smallGRCh37 \
2525
--tag latest -profile singularity
2626

27-
# Testing to restart from `realign`
28-
nextflow run main.nf --step realign \
29-
--genome smallGRCh37 --genome_base References/smallGRCh37 \
30-
--tag latest -profile singularity
31-
3227
# Testing to restart from `recalibrate`
3328
nextflow run main.nf --step recalibrate \
3429
--genome smallGRCh37 --genome_base References/smallGRCh37 \
@@ -93,11 +88,8 @@ Four optional arguments are supported:
9388
- `-s` || `--sample`:
9489
Use to change the test sample (default=`Sarek-data/testdata/tsv/tiny.tsv`)
9590
- `-t` || `--test`:
96-
- `DIR`: test `mapping` with an input directory
97-
- `STEP`: test `mapping`, `realign` and `recalibrate`
98-
- `GERMLINE`: test `mapping` and Variant Calling with `HaplotypeCaller`
99-
- `TOOLS`: test `mapping` and Variant Calling with `FreeBayes`, `HaplotypeCaller`, `MuTect1`, `MuTect2`, `Strelka`
100-
- `MANTA`: test `mapping` and Variant Calling with `Manta`
91+
- `GERMLINE`: test `mapping`, `recalibrate` and Variant Calling with `HaplotypeCaller`
92+
- `SOMATIC`: test `mapping` and Variant Calling with `FreeBayes`, `HaplotypeCaller`, `MuTect2`, `Strelka` and `Manta`
10193
- `ANNOTATESNPEFF`: test annotation using `snpEFF`
10294
- `ANNOTATEVEP`: test annotation using `VEP`
10395
- `BUILDCONTAINERS`: test building all containers except `snpeffgrch37`, `snpeffgrch38`, `vepgrch37` and `vepgrch38`

‎scripts/containers.sh‎

Lines changed: 15 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -5,6 +5,9 @@ PROFILE=singularity
55
TEST=ALL
66
TRAVIS=${TRAVIS:-false}
77

8+
TMPDIR=`pwd`/tmp
9+
mkdir -p $TMPDIR
10+
811
while [[ $# -gt 0 ]]
912
do
1013
key=$1
@@ -25,7 +28,17 @@ do
2528
esac
2629
done
2730

28-
if [[ $TEST = ANNOTATEVEP ]] && [[ $PROFILE = docker ]] && [[ $TRAVIS == true ]]
31+
if [[ $PROFILE = docker ]] && [[ $TRAVIS == true ]]
32+
then
33+
if [[ $TEST = ANNOTATEVEP ]]
34+
then
35+
docker pull maxulysse/vepgrch37:latest
36+
else
37+
docker pull maxulysse/snpeffgrch37:latest
38+
fi
39+
fi
40+
41+
if [[ $TEST = ANNOTATESNPEFF ]] && [[ $PROFILE = singularity ]] && [[ $TRAVIS == true ]]
2942
then
30-
docker pull maxulysse/vepgrch37:latest
43+
singularity build $TMPDIR/maxulysse-snpeffgrch37-latest.simg docker://maxulysse/snpeffgrch37:latest
3144
fi

‎scripts/test.sh‎

Lines changed: 4 additions & 41 deletions
Original file line numberDiff line numberDiff line change
@@ -13,10 +13,8 @@ TMPDIR=`pwd`/tmp
1313
mkdir -p $TMPDIR
1414
export NXF_SINGULARITY_CACHEDIR=$TMPDIR
1515
export NXF_TEMP=$TMPDIR
16-
17-
export SINGULARITY_TMPDIR=$TMPDIR
1816
export SINGULARITY_CACHEDIR=$TMPDIR
19-
17+
export SINGULARITY_TMPDIR=$TMPDIR
2018

2119
# remove Reference directory
2220
rm -rf References
@@ -84,48 +82,22 @@ then
8482
echo "$(tput setaf 1)Building references$(tput sgr0)"
8583
nextflow run buildReferences.nf --refDir Sarek-data/reference --outDir References/$GENOME -profile $PROFILE --genome $GENOME --verbose
8684
fi
87-
# Remove images only on TRAVIS
88-
if [[ $PROFILE == docker ]] && [[ $TRAVIS == true ]]
89-
then
90-
docker rmi -f maxulysse/igvtools:latest
91-
elif [[ $PROFILE == singularity ]] && [[ $TRAVIS == true ]]
92-
then
93-
rm -rf work/singularity/igvtools-latest.img
94-
fi
95-
fi
96-
97-
if [[ ALL,DIR =~ $TEST ]]
98-
then
99-
run_wrapper --germline --sampleDir Sarek-data/testdata/tiny/normal
100-
clean_repo
101-
fi
102-
103-
if [[ ALL,STEP =~ $TEST ]]
104-
then
105-
run_wrapper --germline --sampleDir Sarek-data/testdata/tiny/normal
106-
run_wrapper --germline --step recalibrate --noReports
107-
clean_repo
10885
fi
10986

11087
if [[ ALL,GERMLINE =~ $TEST ]]
11188
then
11289
run_wrapper --germline --sampleDir Sarek-data/testdata/tiny/normal --variantCalling --tools HaplotypeCaller
90+
run_wrapper --germline --step recalibrate --noReports
11391
clean_repo
11492
fi
11593

116-
if [[ ALL,TOOLS =~ $TEST ]]
117-
then
118-
run_wrapper --somatic --sample $SAMPLE --variantCalling --tools FreeBayes,HaplotypeCaller,Mutect2
119-
fi
120-
121-
if [[ ALL,MANTA =~ $TEST ]]
94+
if [[ ALL,SOMATIC =~ $TEST ]]
12295
then
123-
run_wrapper --somatic --sample Sarek-data/testdata/tsv/tiny-manta.tsv --variantCalling --tools Manta --noReports
96+
run_wrapper --somatic --sample Sarek-data/testdata/tsv/tiny-manta.tsv --variantCalling --tools FreeBayes,HaplotypeCaller,Manta,Mutect2 --noReports
12497
run_wrapper --somatic --sample Sarek-data/testdata/tsv/tiny-manta.tsv --variantCalling --tools Manta,Strelka --noReports --strelkaBP
12598
clean_repo
12699
fi
127100

128-
129101
if [[ ALL,ANNOTATEALL,ANNOTATESNPEFF,ANNOTATEVEP =~ $TEST ]]
130102
then
131103
if [[ $TEST = ANNOTATESNPEFF ]]
@@ -138,15 +110,6 @@ then
138110
then
139111
ANNOTATOR=merge,snpEFF,VEP
140112
fi
141-
if [[ $PROFILE == docker ]] && [[ $TRAVIS == true ]]
142-
then
143-
docker rmi -f maxulysse/sarek:latest
144-
docker rmi -f maxulysse/picard:latest
145-
elif [[ $PROFILE == singularity ]] && [[ $TRAVIS == true ]]
146-
then
147-
rm -rf work/singularity/sarek-latest.img
148-
rm -rf work/singularity/picard-latest.img
149-
fi
150113
run_wrapper --annotate --tools ${ANNOTATOR} --annotateVCF Sarek-data/testdata/vcf/Strelka_1234N_variants.vcf.gz --noReports
151114
run_wrapper --annotate --tools ${ANNOTATOR} --annotateVCF Sarek-data/testdata/vcf/Strelka_1234N_variants.vcf.gz,Sarek-data/testdata/vcf/Strelka_9876T_variants.vcf.gz
152115
clean_repo

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