Merge pull request #1242 from nf-core/sentieon-license-fixing3

Simplify sentieon test license server usage
nf-core · Sep 18, 2023 · 647b664 · 647b664
2 parents 607ecd6 + c12ed5b
commit 647b664
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -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

diff --git a/conf/test/cache.config b/conf/test/cache.config
@@ -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 = {

diff --git a/docs/usage.md b/docs/usage.md
@@ -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:

diff --git a/tests/config/tags.yml b/tests/config/tags.yml
@@ -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
 
 ## markduplicates
 gatk4/markduplicates:

diff --git a/tests/test_aligner_sentieon_bwamem.yml → tests/test_sentieon_aligner_bwamem.yml b/tests/test_aligner_sentieon_bwamem.yml → tests/test_sentieon_aligner_bwamem.yml
@@ -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
   tags:
     - aligner
     - sentieon/bwamem
@@ -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
@@ -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
@@ -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

diff --git a/tests/test_sentieon_dedup_from_bam.yml b/tests/test_sentieon_dedup_from_bam.yml
@@ -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

diff --git a/tests/test_sentieon_dedup_from_cram.yml b/tests/test_sentieon_dedup_from_cram.yml
@@ -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

diff --git a/tests/test_sentieon_haplotyper.yml b/tests/test_sentieon_haplotyper.yml
@@ -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
@@ -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
@@ -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
@@ -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

diff --git a/tests/test_sentieon_haplotyper_skip_filter.yml b/tests/test_sentieon_haplotyper_skip_filter.yml
@@ -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
@@ -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

diff --git a/tests/test_sentieon_joint_germline.yml b/tests/test_sentieon_joint_germline.yml
@@ -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
@@ -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
@@ -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

diff --git a/tests/test_umi.yml b/tests/test_umi.yml
@@ -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