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Simplify sentieon test license server usage #1242

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merged 13 commits into from
Sep 18, 2023
Merged

Simplify sentieon test license server usage #1242

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a3d57b4
remove usage of sentieon secrets in cache.config
asp8200 Sep 15, 2023
bede8ab
introducing profile sentieon_test_licence
asp8200 Sep 15, 2023
137e2ca
Forgot profile sentieon_test_licence in some tests
asp8200 Sep 15, 2023
a774c91
Fix typo in nf secrets cmd
asp8200 Sep 18, 2023
3c568e7
Merge branch 'sentieon-license-fixing2' of github.com:nf-core/sarek i…
maxulysse Sep 18, 2023
a55df91
use profile from configs
maxulysse Sep 18, 2023
2882b0c
update CHANGELOG
maxulysse Sep 18, 2023
0298c65
forgot this test
maxulysse Sep 18, 2023
a071f26
update tests
maxulysse Sep 18, 2023
83da7c0
renamed file
maxulysse Sep 18, 2023
8617e92
Merge branch 'dev' into sentieon-license-fixing3
maxulysse Sep 18, 2023
56c1916
Apply suggestions from code review
maxulysse Sep 18, 2023
c12ed5b
Update tests/test_umi.yml
maxulysse Sep 18, 2023
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1 change: 1 addition & 0 deletions CHANGELOG.md
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Expand Up @@ -13,6 +13,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0

### Changed

- [#1242](https://github.com/nf-core/sarek/pull/1242) - Simplify sentieon nf-core test license usage
- [#1243](https://github.com/nf-core/sarek/pull/1243) - Improve json schema usage for input

### Fixed
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5 changes: 0 additions & 5 deletions conf/test/cache.config
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Expand Up @@ -58,11 +58,6 @@ params {
}

process {
withLabel: 'sentieon' {
ext.sentieon_auth_mech_base64 = secrets.SENTIEON_AUTH_MECH_BASE64
ext.sentieon_auth_data_base64 = secrets.SENTIEON_AUTH_DATA_BASE64
}

// This must contain .* in order to properly overwrite the standard config in test cases
withName:'.*:FREEC_SOMATIC'{
ext.args = {
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2 changes: 1 addition & 1 deletion docs/usage.md
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Expand Up @@ -1062,7 +1062,7 @@ In particular, Sentieon contains what may be view as speedup version of some sta
Sentieon supply license in the form of a string-value (a url) or a file. It should be base64-encoded and stored in a nextflow secret named `SENTIEON_LICENSE_BASE64`. If a license string (url) is supplied, then the nextflow secret should be set like this:
```bash
nextflow secret set SENTIEON_LICENSE_BASE64 $(echo -n <sentieon_license_string> | base64 -w 0)
nextflow secrets set SENTIEON_LICENSE_BASE64 $(echo -n <sentieon_license_string> | base64 -w 0)
```
If a license file is supplied, then the nextflow secret should be set like this:
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2 changes: 1 addition & 1 deletion tests/config/tags.yml
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Expand Up @@ -138,7 +138,7 @@ sentieon/bwamem:
- modules/nf-core/sentieon/bwamem/main.nf
- subworkflows/local/fastq_align_bwamem_mem2_dragmap_sentieon/main.nf
- tests/csv/3.0/fastq_single.csv
- tests/test_aligner_sentieon_bwamem.yml
- tests/test_sentieon_aligner_bwamem.yml
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The aligner is called "sentieon bwamem" hence the order of the words in the filename.

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yeah, I know, but when renamed this way all the sentieon tests files are nicely grouped together


## markduplicates
gatk4/markduplicates:
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8 changes: 4 additions & 4 deletions tests/test_aligner_sentieon_bwamem.yml → tests/test_sentieon_aligner_bwamem.yml
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@@ -1,5 +1,5 @@
- name: Run sentieon bwamem
command: nextflow run main.nf -profile test_cache --aligner sentieon-bwamem --save_reference --outdir results
command: nextflow run main.nf -profile test_cache,software_license --sentieon_extension --aligner sentieon-bwamem --save_reference --outdir results
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tags:
- aligner
- sentieon/bwamem
Expand Down Expand Up @@ -74,7 +74,7 @@
- path: results/reports/samtools/test/test.recal.cram.stats
# conda changes md5sums for test
- name: Build only index with sentieon bwa
command: nextflow run main.nf -profile test_cache --aligner sentieon-bwamem --build_only_index --outdir results
command: nextflow run main.nf -profile test_cache,software_license --sentieon_extension --aligner sentieon-bwamem --build_only_index --outdir results
tags:
- aligner
- build_only_index
Expand Down Expand Up @@ -106,7 +106,7 @@
- path: results/reference/known_indels/mills_and_1000G.indels.vcf.gz.tbi
# conda changes md5sums for test
- name: Run sentieon bwamem save bam
command: nextflow run main.nf -profile test_cache --aligner sentieon-bwamem --save_mapped --save_output_as_bam --outdir results
command: nextflow run main.nf -profile test_cache,software_license --sentieon_extension --aligner sentieon-bwamem --save_mapped --save_output_as_bam --outdir results
tags:
- aligner
- sentieon/bwamem
Expand Down Expand Up @@ -160,7 +160,7 @@
- path: results/reports/samtools/test/test.recal.cram.stats
# conda changes md5sums for test
- name: Run sentieon bwamem save cram
command: nextflow run main.nf -profile test_cache --aligner sentieon-bwamem --save_mapped --outdir results
command: nextflow run main.nf -profile test_cache,software_license --sentieon_extension --aligner sentieon-bwamem --save_mapped --outdir results
tags:
- aligner
- sentieon/bwamem
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2 changes: 1 addition & 1 deletion tests/test_sentieon_dedup_from_bam.yml
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@@ -1,5 +1,5 @@
- name: Run sentieon dedup starting from BAM
command: nextflow run main.nf -profile test_cache,sentieon_dedup_bam --outdir results
command: nextflow run main.nf -profile test_cache,software_license,sentieon_dedup_bam --sentieon_extension --outdir results
tags:
- input_bam
- preprocessing
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2 changes: 1 addition & 1 deletion tests/test_sentieon_dedup_from_cram.yml
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@@ -1,5 +1,5 @@
- name: Run sentieon dedup starting from CRAM
command: nextflow run main.nf -profile test_cache,sentieon_dedup_cram --outdir results
command: nextflow run main.nf -profile test_cache,software_license,sentieon_dedup_cram --sentieon_extension --outdir results
tags:
- input_cram
- preprocessing
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8 changes: 4 additions & 4 deletions tests/test_sentieon_haplotyper.yml
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@@ -1,5 +1,5 @@
- name: Run variant calling on germline sample with sentieons haplotyper
command: nextflow run main.nf -profile test_cache,targeted --input ./tests/csv/3.0/mapped_single_bam.csv --tools sentieon_haplotyper --step variant_calling --outdir results
command: nextflow run main.nf -profile test_cache,software_license,targeted --sentieon_extension --input ./tests/csv/3.0/mapped_single_bam.csv --tools sentieon_haplotyper --step variant_calling --outdir results
tags:
- germline
- sentieon/haplotyper
Expand Down Expand Up @@ -35,7 +35,7 @@
- path: results/haplotyper
should_exist: false
- name: Run variant calling on germline sample with sentieons haplotyper without intervals
command: nextflow run main.nf -profile test_cache,targeted --input ./tests/csv/3.0/mapped_single_bam.csv --tools sentieon_haplotyper --step variant_calling --no_intervals --outdir results
command: nextflow run main.nf -profile test_cache,software_license,targeted --sentieon_extension --input ./tests/csv/3.0/mapped_single_bam.csv --tools sentieon_haplotyper --step variant_calling --no_intervals --outdir results
tags:
- germline
- sentieon/haplotyper
Expand Down Expand Up @@ -78,7 +78,7 @@
- path: results/sentieon_haplotyper
should_exist: false
- name: Run variant calling on germline sample with sentieons haplotyper output gvcf
command: nextflow run main.nf -profile test_cache,targeted --input ./tests/csv/3.0/mapped_single_bam.csv --tools sentieon_haplotyper --step variant_calling --outdir results --sentieon_haplotyper_emit_mode gvcf
command: nextflow run main.nf -profile test_cache,software_license,targeted --sentieon_extension --input ./tests/csv/3.0/mapped_single_bam.csv --tools sentieon_haplotyper --step variant_calling --outdir results --sentieon_haplotyper_emit_mode gvcf
tags:
- germline
- sentieon/haplotyper
Expand Down Expand Up @@ -116,7 +116,7 @@
- path: results/haplotyper
should_exist: false
- name: Run variant calling on germline sample with sentieons haplotyper output both gvcf and vcf
command: nextflow run main.nf -profile test_cache,targeted --input ./tests/csv/3.0/mapped_single_bam.csv --tools sentieon_haplotyper --step variant_calling --outdir results --sentieon_haplotyper_emit_mode variant,gvcf
command: nextflow run main.nf -profile test_cache,software_license,targeted --sentieon_extension --input ./tests/csv/3.0/mapped_single_bam.csv --tools sentieon_haplotyper --step variant_calling --outdir results --sentieon_haplotyper_emit_mode variant,gvcf
tags:
- germline
- sentieon/haplotyper
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4 changes: 2 additions & 2 deletions tests/test_sentieon_haplotyper_skip_filter.yml
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@@ -1,5 +1,5 @@
- name: Run variant calling on germline sample with sentieon haplotyper and skip filter
command: nextflow run main.nf -profile test_cache,targeted --input ./tests/csv/3.0/mapped_single_bam.csv --tools sentieon_haplotyper --step variant_calling --skip_tools haplotyper_filter --outdir results
command: nextflow run main.nf -profile test_cache,software_license,targeted --sentieon_extension --input ./tests/csv/3.0/mapped_single_bam.csv --tools sentieon_haplotyper --step variant_calling --skip_tools haplotyper_filter --outdir results
tags:
- germline
- sentieon_haplotyper_skip_filter
Expand Down Expand Up @@ -36,7 +36,7 @@
- path: results/sentieon_haplotyper
should_exist: false
- name: Run variant calling on germline sample with sentieon haplotyper without intervals and skip filter
command: nextflow run main.nf -profile test_cache,targeted --input ./tests/csv/3.0/mapped_single_bam.csv --tools sentieon_haplotyper --step variant_calling --skip_tools haplotyper_filter --no_intervals --outdir results
command: nextflow run main.nf -profile test_cache,software_license,targeted --sentieon_extension --input ./tests/csv/3.0/mapped_single_bam.csv --tools sentieon_haplotyper --step variant_calling --skip_tools haplotyper_filter --no_intervals --outdir results
tags:
- germline
- sentieon_haplotyper_skip_filter
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6 changes: 3 additions & 3 deletions tests/test_sentieon_joint_germline.yml
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@@ -1,5 +1,5 @@
- name: Run joint germline variant calling with sentieon haplotyper
command: nextflow run main.nf -profile test_cache,targeted --input ./tests/csv/3.0/mapped_joint_bam.csv --tools sentieon_haplotyper --step variant_calling --joint_germline --outdir results --sentieon_haplotyper_emit_mode gvcf
command: nextflow run main.nf -profile test_cache,software_license,targeted --sentieon_extension --input ./tests/csv/3.0/mapped_joint_bam.csv --tools sentieon_haplotyper --step variant_calling --joint_germline --outdir results --sentieon_haplotyper_emit_mode gvcf
tags:
- germline
- sentieon_joint_germline
Expand Down Expand Up @@ -28,7 +28,7 @@
- path: results/haplotyper
should_exist: false
- name: Run joint germline variant calling with sentieon haplotyper all intervals at once
command: nextflow run main.nf -profile test_cache,targeted --input ./tests/csv/3.0/mapped_joint_bam.csv --tools sentieon_haplotyper --step variant_calling --joint_germline --outdir results --sentieon_haplotyper_emit_mode gvcf --nucleotides_per_second 100
command: nextflow run main.nf -profile test_cache,software_license,targeted --sentieon_extension --input ./tests/csv/3.0/mapped_joint_bam.csv --tools sentieon_haplotyper --step variant_calling --joint_germline --outdir results --sentieon_haplotyper_emit_mode gvcf --nucleotides_per_second 100
tags:
- germline
- sentieon_joint_germline
Expand All @@ -55,7 +55,7 @@
- path: results/haplotyper
should_exist: false
- name: Run joint germline variant calling with sentieon haplotyper with stub for VQSR
command: nextflow run main.nf -profile test_cache,tools_germline --input ./tests/csv/3.0/mapped_joint_bam.csv --tools sentieon_haplotyper --step variant_calling --joint_germline --outdir results --sentieon_haplotyper_emit_mode gvcf -stub-run
command: nextflow run main.nf -profile test_cache,software_license,tools_germline --sentieon_extension --input ./tests/csv/3.0/mapped_joint_bam.csv --tools sentieon_haplotyper --step variant_calling --joint_germline --outdir results --sentieon_haplotyper_emit_mode gvcf -stub-run
tags:
- germline
- sentieon_joint_germline
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2 changes: 1 addition & 1 deletion tests/test_umi.yml
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Expand Up @@ -52,7 +52,7 @@
# text-based file changes md5sums on reruns

- name: Run Sentieon-FGBio UMI combination test
command: nextflow run main.nf -profile test_cache,umi --outdir results --aligner "sentieon-bwamem"
command: nextflow run main.nf -profile test_cache,software_license,umi --sentieon_extension --outdir results --aligner "sentieon-bwamem"
tags:
- preprocessing
- umi
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