diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml index cdb6322e6..710ab8060 100644 --- a/.gitlab-ci.yml +++ b/.gitlab-ci.yml @@ -527,6 +527,7 @@ build_archive:macos:x64: MODEL_SPEED: hac MODEL_VERSION: v4.2.0 NO_TEST_DORADO_CORRECT: 0 + NO_TEST_DUPLEX: 0 script: # Do everything inside a newly created folder, since some runners only run # tests and hence never perform a git clean. @@ -600,6 +601,7 @@ test:linux:arm64:bionic: MODEL_SPEED: hac MODEL_VERSION: v4.2.0 NO_TEST_DORADO_CORRECT: 1 + NO_TEST_DUPLEX: 1 needs: - build:linux:arm64:bionic @@ -631,6 +633,8 @@ test:macos:x64: BATCH: 0 MODEL_SPEED: hac MODEL_VERSION: v4.2.0 + NO_TEST_DORADO_CORRECT: 1 + NO_TEST_DUPLEX: 1 timeout: 1h 30m # Test that you can run dorado in a clean cuda 20.04 environment diff --git a/README.md b/README.md index afd613ac9..ca105117e 100644 --- a/README.md +++ b/README.md @@ -388,7 +388,7 @@ The versioning of modification models is bound to the basecalling model. This me | :-------- | :------- | :--- | :--- | | **dna_r10.4.1_e8.2_400bps_fast@v5.0.0** | | | 5 kHz | | **dna_r10.4.1_e8.2_400bps_hac@v5.0.0** | 4mC_5mC
5mCG_5hmCG
5mC_5hmC
6mA
| v2
v2
v2
v2 | 5 kHz | -| **dna_r10.4.1_e8.2_400bps_sup@v5.0.0** | 4mC_5mC
5mCG_5hmCG
5mC_5hmC
6mA
| v2
v2
v2
v2 | 5 kHz | +| **dna_r10.4.1_e8.2_400bps_sup@v5.0.0** | 4mC_5mC
5mCG_5hmCG
5mC_5hmC
6mA
| v2
v2.0.1
v2.0.1
v2 | 5 kHz | | dna_r10.4.1_e8.2_400bps_fast@v4.3.0 | | | 5 kHz | | dna_r10.4.1_e8.2_400bps_hac@v4.3.0 | 5mCG_5hmCG
5mC_5hmC
6mA
| v1
v1
v2 | 5 kHz | | dna_r10.4.1_e8.2_400bps_sup@v4.3.0 | 5mCG_5hmCG
5mC_5hmC
6mA
| v1
v1
v2 | 5 kHz | diff --git a/dorado/models/metadata.cpp b/dorado/models/metadata.cpp index 6d83ab58d..d94018ec2 100644 --- a/dorado/models/metadata.cpp +++ b/dorado/models/metadata.cpp @@ -49,14 +49,14 @@ const std::unordered_map map = { {"v0.0.0", ModelVersion::v0_0_0}, {"v0.1.0", ModelVersion::v0_1_0}, {"v1.0.0", ModelVersion::v1_0_0}, {"v1.1.0", ModelVersion::v1_1_0}, {"v1.2.0", ModelVersion::v1_2_0}, {"v2.0.0", ModelVersion::v2_0_0}, - {"v3.0.0", ModelVersion::v3_0_0}, {"v3.0.1", ModelVersion::v3_0_1}, - {"v3.1.0", ModelVersion::v3_1_0}, {"v3.3.0", ModelVersion::v3_3_0}, - {"v3.4.0", ModelVersion::v3_4_0}, {"v3.5.0", ModelVersion::v3_5_0}, - {"v3.5.2", ModelVersion::v3_5_2}, {"v3.6.0", ModelVersion::v3_6_0}, - {"v4.0.0", ModelVersion::v4_0_0}, {"v4.1.0", ModelVersion::v4_1_0}, - {"v4.2.0", ModelVersion::v4_2_0}, {"v4.3.0", ModelVersion::v4_3_0}, - {"v5.0.0", ModelVersion::v5_0_0}, {"v5.1.0", ModelVersion::v5_1_0}, - {"latest", ModelVersion::NONE}}; + {"v2.0.1", ModelVersion::v2_0_1}, {"v3.0.0", ModelVersion::v3_0_0}, + {"v3.0.1", ModelVersion::v3_0_1}, {"v3.1.0", ModelVersion::v3_1_0}, + {"v3.3.0", ModelVersion::v3_3_0}, {"v3.4.0", ModelVersion::v3_4_0}, + {"v3.5.0", ModelVersion::v3_5_0}, {"v3.5.2", ModelVersion::v3_5_2}, + {"v3.6.0", ModelVersion::v3_6_0}, {"v4.0.0", ModelVersion::v4_0_0}, + {"v4.1.0", ModelVersion::v4_1_0}, {"v4.2.0", ModelVersion::v4_2_0}, + {"v4.3.0", ModelVersion::v4_3_0}, {"v5.0.0", ModelVersion::v5_0_0}, + {"v5.1.0", ModelVersion::v5_1_0}, {"latest", ModelVersion::NONE}}; } // namespace version const std::unordered_map& model_variants_map() { diff --git a/dorado/models/metadata.h b/dorado/models/metadata.h index 22c76b3c9..0aa97b846 100644 --- a/dorado/models/metadata.h +++ b/dorado/models/metadata.h @@ -42,6 +42,7 @@ enum class ModelVersion : uint8_t { v1_1_0, v1_2_0, v2_0_0, + v2_0_1, v3_0_0, v3_0_1, v3_1_0, diff --git a/dorado/models/models.cpp b/dorado/models/models.cpp index e0a934aa8..3808999bd 100644 --- a/dorado/models/models.cpp +++ b/dorado/models/models.cpp @@ -863,11 +863,11 @@ const std::vector models = { ModsVariantPair{ModsVariant::M_5mC_5hmC, VV::v2_0_0}, }, ModelInfo{ - "dna_r10.4.1_e8.2_400bps_sup@v5.0.0_5mC_5hmC@v2", - "36de2e58edaf1e1a53bca0ebf029164112b9dbaad413672dde45efb093b7fcf6", + "dna_r10.4.1_e8.2_400bps_sup@v5.0.0_5mC_5hmC@v2.0.1", + "757dabc280e25f1c442fcfeb3e1f4d44a2d445e0ea89bb30c15e4757879111be", CC::DNA_R10_4_1_E8_2_400BPS_5KHZ, ModelVariantPair{ModelVariant::SUP, VV::v5_0_0}, - ModsVariantPair{ModsVariant::M_5mC_5hmC, VV::v2_0_0}, + ModsVariantPair{ModsVariant::M_5mC_5hmC, VV::v2_0_1}, }, // 5mC+5hmC CG-context HAC and SUP ModelInfo{ @@ -892,11 +892,11 @@ const std::vector models = { ModsVariantPair{ModsVariant::M_5mCG_5hmCG, VV::v2_0_0}, }, ModelInfo{ - "dna_r10.4.1_e8.2_400bps_sup@v5.0.0_5mCG_5hmCG@v2", - "2e2d4de2ec1df90b37c50b3367bea90f7b9dfab11b90e98ee6963876589be4cc", + "dna_r10.4.1_e8.2_400bps_sup@v5.0.0_5mCG_5hmCG@v2.0.1", + "c8ebafd13008a919232cd45514e07ea929509a5e20254c73b9eff2cd0e5a4786", CC::DNA_R10_4_1_E8_2_400BPS_5KHZ, ModelVariantPair{ModelVariant::SUP, VV::v5_0_0}, - ModsVariantPair{ModsVariant::M_5mCG_5hmCG, VV::v2_0_0}, + ModsVariantPair{ModsVariant::M_5mCG_5hmCG, VV::v2_0_1}, }, // 6mA all-context HAC and SUP ModelInfo{ diff --git a/tests/test_simple_basecaller_execution.sh b/tests/test_simple_basecaller_execution.sh index ebd4eb01d..416f080fd 100755 --- a/tests/test_simple_basecaller_execution.sh +++ b/tests/test_simple_basecaller_execution.sh @@ -188,7 +188,8 @@ dorado_aligner_options_test() ( ) dorado_aligner_options_test -if ! uname -r | grep -q -E 'tegra|minit'; then +# Skip duplex tests if NO_TEST_DUPLEX is set. +if [[ "${NO_TEST_DUPLEX}" -ne "1" ]]; then echo dorado duplex basespace test stage $dorado_bin duplex basespace $data_dir/basespace/pairs.bam --threads 1 --pairs $data_dir/basespace/pairs.txt > $output_dir/calls.bam