Merge pull request #1411 from maxulysse/remove_tests_until_fix

update triggered tests

.github/workflows/ci.yml

@@ -52,6 +52,15 @@ jobs:
         NXF_VER:
           - "23.04.0"
           - "latest-everything"
+        exclude:
+          - tags: "sentieon/bwamem"
+          - tags: "sentieon/dedup"
+          - tags: "sentieon/dnascope"
+          - tags: "sentieon/dnascope_joint_germline"
+          - tags: "sentieon/dnascope_skip_filter"
+          - tags: "sentieon/haplotyper"
+          - tags: "sentieon/haplotyper_joint_germline"
+          - tags: "sentieon/haplotyper_skip_filter"
     env:
       NXF_ANSI_LOG: false
       TEST_DATA_BASE: "${{ github.workspace }}/test-datasets"

CHANGELOG.md

@@ -14,6 +14,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - [#1335](https://github.com/nf-core/sarek/pull/1335) - Add index computation of `bcftools_annotations`, if not provided
 - [#1340](https://github.com/nf-core/sarek/pull/1340) - Adds Azure test profiles and megatests.
 - [#1372](https://github.com/nf-core/sarek/pull/1372) - Add NCBench test profile for Agilent datasets
+- [#1409](https://github.com/nf-core/sarek/pull/1409) - Add params `modules_testdata_base_path` to test profile
 
 ### Changed
 
@@ -22,6 +23,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - [#1359](https://github.com/nf-core/sarek/pull/1359) - Removing params usage from local modules
 - [#1359](https://github.com/nf-core/sarek/pull/1359) - Removing params usage from local subworkflows
 - [#1360](https://github.com/nf-core/sarek/pull/1360) - Sync `TEMPLATE` with `tools` `2.11`
+- [#1411](https://github.com/nf-core/sarek/pull/1411) - Temporally disable sentieon related tests
 
 ### Fixed
 

tests/config/pytesttags.yml

@@ -327,7 +327,7 @@ sentieon/dnascope:
   - tests/csv/3.0/mapped_single_bam.csv
   - tests/test_sentieon_dnascope.yml
 
-sentieon_dnascope_skip_filter:
+sentieon/dnascope_skip_filter:
   - conf/modules/sentieon_dnascope.config
   - modules/nf-core/sentieon/dnascope/**
   - modules/nf-core/gatk4/mergevcfs/**
@@ -355,7 +355,7 @@ sentieon/haplotyper:
   - tests/csv/3.0/mapped_single_bam.csv
   - tests/test_sentieon_haplotyper.yml
 
-sentieon_haplotyper_skip_filter:
+sentieon/haplotyper_skip_filter:
   - conf/modules/sentieon_haplotyper.config
   - modules/nf-core/sentieon/haplotyper/**
   - modules/nf-core/gatk4/mergevcfs/**
@@ -390,7 +390,7 @@ joint_germline:
   - tests/test_joint_germline.yml
 
 ## sentieon_dnascope_joint_germline
-sentieon_dnascope_joint_germline:
+sentieon/dnascope_joint_germline:
   - conf/modules/prepare_genome.config
   - conf/modules/sentieon_dnascope.config
   - conf/modules/sentieon_dnascope_joint_germline.config
@@ -401,7 +401,7 @@ sentieon_dnascope_joint_germline:
   - tests/test_sentieon_dnascop_joint_germline.yml
 
 ## sentieon_haplotyper_joint_germline
-sentieon_haplotyper_joint_germline:
+sentieon/haplotyper_joint_germline:
   - conf/modules/prepare_genome.config
   - conf/modules/sentieon_haplotyper.config
   - conf/modules/sentieon_haplotyper_joint_germline.config

tests/test_sentieon_dnascope_joint_germline.yml

@@ -2,7 +2,7 @@
   command: nextflow run main.nf -profile test_cache,targeted,software_license --sentieon_extension --input ./tests/csv/3.0/mapped_joint_bam.csv --tools sentieon_dnascope --step variant_calling --joint_germline --outdir results --sentieon_dnascope_emit_mode gvcf
   tags:
     - germline
-    - sentieon_dnascope_joint_germline
+    - sentieon/dnascope_joint_germline
     - variant_calling
   files:
     - path: results/csv/variantcalled.csv
@@ -64,7 +64,7 @@
   command: nextflow run main.nf -profile test_cache,targeted,software_license --sentieon_extension --input ./tests/csv/3.0/mapped_joint_bam.csv --tools sentieon_dnascope --step variant_calling --joint_germline --outdir results --sentieon_dnascope_emit_mode gvcf --nucleotides_per_second 100
   tags:
     - germline
-    - sentieon_dnascope_joint_germline
+    - sentieon/dnascope_joint_germline
     - variant_calling
   files:
     - path: results/csv/variantcalled.csv

tests/test_sentieon_dnascope_skip_filter.yml

@@ -2,7 +2,7 @@
   command: nextflow run main.nf -profile test_cache,targeted,software_license --sentieon_extension --input ./tests/csv/3.0/mapped_single_bam.csv --tools sentieon_dnascope --step variant_calling --skip_tools dnascope_filter --outdir results
   tags:
     - germline
-    - sentieon_dnascope_skip_filter
+    - sentieon/dnascope_skip_filter
     - variant_calling
   files:
     - path: results/csv/variantcalled.csv
@@ -46,7 +46,7 @@
   command: nextflow run main.nf -profile test_cache,targeted,software_license --sentieon_extension --input ./tests/csv/3.0/mapped_single_bam.csv --tools sentieon_dnascope --step variant_calling --skip_tools dnascope_filter --no_intervals --outdir results
   tags:
     - germline
-    - sentieon_dnascope_skip_filter
+    - sentieon/dnascope_skip_filter
     - no_intervals
     - variant_calling
   files:

tests/test_sentieon_haplotyper_joint_germline.yml

@@ -2,9 +2,8 @@
   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_haplotyper_joint_germline
+    - sentieon/haplotyper_joint_germline
     - variant_calling
-    - sentieon/haplotyper
   files:
     - path: results/csv/variantcalled.csv
       md5sum: 6ec10f6455c2b5290c7f6fc687c529ca
@@ -53,9 +52,8 @@
   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_haplotyper_joint_germline
+    - sentieon/haplotyper_joint_germline
     - variant_calling
-    - sentieon/haplotyper
   files:
     - path: results/csv/variantcalled.csv
       md5sum: 6ec10f6455c2b5290c7f6fc687c529ca
@@ -102,7 +100,7 @@
   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_haplotyper_joint_germline
+    - sentieon/haplotyper_joint_germline
     - variant_calling
     - vqsr
   files:

tests/test_sentieon_haplotyper_skip_filter.yml

@@ -2,9 +2,8 @@
   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
+    - sentieon/haplotyper_skip_filter
     - variant_calling
-    - sentieon/haplotyper
   files:
     - path: results/csv/variantcalled.csv
       md5sum: e08d6aa77d914bc2c933e70696b74cdd
@@ -48,10 +47,9 @@
   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
+    - sentieon/haplotyper_skip_filter
     - no_intervals
     - variant_calling
-    - sentieon/haplotyper
   files:
     - path: results/csv/variantcalled.csv
       md5sum: e08d6aa77d914bc2c933e70696b74cdd