diff --git a/tools/dorado/.shed.yml b/tools/dorado/.shed.yml new file mode 100644 index 00000000..6015e875 --- /dev/null +++ b/tools/dorado/.shed.yml @@ -0,0 +1,23 @@ +--- +auto_tool_repositories: + name_template: "{{ tool_id }}" + description_template: "{{ tool_name }} from the dorado suite" +categories: + - Sequence Analysis +description: Dorado is a high-performance, easy-to-use, open source basecaller for Oxford Nanopore reads. +exclude: + - tool_test_output.html + - tool_test_output.json +homepage_url: https://github.com/nanoporetech/dorado +long_description: > + Dorado is a high-performance, easy-to-use, open source basecaller for Oxford Nanopore reads. +name: dorado +owner: galaxy-australia +remote_repository_url: https://github.com/usegalaxy-au/tools-au/tree/main/tools/dorado +suite: + name: suite_dorado + description: > + Dorado is a high-performance, easy-to-use, open source basecaller for Oxford Nanopore reads. + long_description: > + Dorado is a high-performance, easy-to-use, open source basecaller for Oxford Nanopore reads. +type: unrestricted diff --git a/tools/dorado/README.md b/tools/dorado/README.md new file mode 100644 index 00000000..218e90f9 --- /dev/null +++ b/tools/dorado/README.md @@ -0,0 +1,48 @@ + +## Tool versions + +Dorado is distributed on +[DockerHub](https://hub.docker.com/r/nanoporetech/dorado/tags) by nanoporetech. +The containers are identified by sha256 hash, but not tagged with a version. + +We can still use the containers and display the dorado version by hard-coding +both dorado version and container hash into the wrapper (see `macros.xml`). +Unfortunately you have to pull a >6 GB container and run `dorado --version` just +to check the tool version. This also prevents auto-updates of this wrapper. + +You can update the list of models at the same time (see +below). **You must do this when you update the wrapper**. + +## Basecalling models + +The models are bundled in the container at `/models` and made available by the +`dorado_models.loc` file. + +The columns are `value`, `container_hash`, `name` and `path`. + +To update the list, modify `tool-data/dorado_models.loc.sample`. + +Because models can be added and removed, models are listed **per container** in +the loc file. + +Here's some code to **append** the models from the container with hash +`1c65eb070a9fc1d88710c4dc09b06541f96fdd28` to the loc file. + +```bash +export DORADO_HASH="1c65eb070a9fc1d88710c4dc09b06541f96fdd28" + +apptainer exec "docker://nanoporetech/dorado:sha${DORADO_HASH}" \ + ls /models | \ + awk -v hash="${DORADO_HASH}" '{print hash "_" $0 "\t" hash "\t" $0 "\t/models/" $0}' \ + >> tool-data/dorado_models.loc.sample +``` + +The loc file doesn't have a header, so you can keep it sorted. + +```bash +cp tool-data/dorado_models.loc.sample \ + tool-data/dorado_models.loc.sample.old && +sort -t$'\t' -k1,1V tool-data/dorado_models.loc.sample.old \ + > tool-data/dorado_models.loc +``` + diff --git a/tools/dorado/dorado.xml b/tools/dorado/dorado.xml new file mode 100644 index 00000000..aee04635 --- /dev/null +++ b/tools/dorado/dorado.xml @@ -0,0 +1,186 @@ + + basecaller for raw Oxford Nanopore data + + macros.xml + + + + calls.bam + +&& + +dorado summary +calls.bam +> summary.tsv + + ]]> + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + `__ basecaller. + +The input is pod5 format. If you have older data in fast5 format, you +can convert them using the ``fast5 to pod5`` convert tool. + +Basecalling models +------------------ + +**TLDR: to decide which model to use, see Oxford Nanopore’s** `table of +basecalling +models `__. + +The names of Dorado models are structured with each segment +corresponding to a different aspect of the model separated by +underscores. + +For example, the model ``dna_r10.4.1_e8.2_400bps_hac@v4.3.0`` can be +decoded as follows: + +Analyte Type (``dna``): + - For DNA sequencing, it is represented as dna. If you are using a + Direct RNA Sequencing Kit, this will be rna002 or rna004, + depending on the kit. +Pore Type (``r10.4.1``): + - The type of flow cell used. +Chemistry Type (``e8.2``): + - The chemistry type, which corresponds to the kit used for + sequencing. For example, Kit 14 chemistry is denoted by e8.2 and + Kit 10 or Kit 9 are denoted by e8. +Translocation Speed (``400bps``): + - The speed of translocation selected at the run setup in MinKNOW +Model Type (``hac``): + - The size of the model, where larger models yield more accurate + basecalls but take more time. The three types of models are fast, + hac, and sup. The fast model is the quickest, sup is the most + accurate, and hac provides a balance between speed and accuracy. +Model Version Number (``v4.3.0``): + - The version of the model. Model updates are regularly released, + and higher version numbers typically signify greater accuracy. + + ]]> + diff --git a/tools/dorado/dorado_pod5_convert.xml b/tools/dorado/dorado_pod5_convert.xml new file mode 100644 index 00000000..a7a21d39 --- /dev/null +++ b/tools/dorado/dorado_pod5_convert.xml @@ -0,0 +1,60 @@ + + converter for raw Oxford Nanopore data + + macros.xml + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + `__ for basecalling with Dorado. + + Combine all your fast5 files into a single tar archive, and optionally + compress the archive with Gzip, Bzip2 or XZ, before uploading it to + Galaxy. + + ]]> + diff --git a/tools/dorado/macros.xml b/tools/dorado/macros.xml new file mode 100644 index 00000000..38fc7b1a --- /dev/null +++ b/tools/dorado/macros.xml @@ -0,0 +1,15 @@ + + + 0.7.1+80da5f5 + 1c65eb070a9fc1d88710c4dc09b06541f96fdd28 + + + nanoporetech/dorado:sha@CONTAINER_HASH@ + + + + + dorado + + + diff --git a/tools/dorado/test-data/FAL00375_473bf0ed_0.ten_reads.0_0.fast5.tar b/tools/dorado/test-data/FAL00375_473bf0ed_0.ten_reads.0_0.fast5.tar new file mode 100644 index 00000000..be486454 Binary files /dev/null and b/tools/dorado/test-data/FAL00375_473bf0ed_0.ten_reads.0_0.fast5.tar differ diff --git a/tools/dorado/test-data/FAL00375_473bf0ed_0.ten_reads.pod5 b/tools/dorado/test-data/FAL00375_473bf0ed_0.ten_reads.pod5 new file mode 100644 index 00000000..41d4e9a2 Binary files /dev/null and b/tools/dorado/test-data/FAL00375_473bf0ed_0.ten_reads.pod5 differ diff --git a/tools/dorado/test-data/SQK-RBK114_BC01_BC04_unclassified.pod5 b/tools/dorado/test-data/SQK-RBK114_BC01_BC04_unclassified.pod5 new file mode 100644 index 00000000..00f79382 Binary files /dev/null and b/tools/dorado/test-data/SQK-RBK114_BC01_BC04_unclassified.pod5 differ diff --git a/tools/dorado/test-data/dorado_models.loc b/tools/dorado/test-data/dorado_models.loc new file mode 120000 index 00000000..fb6fc000 --- /dev/null +++ b/tools/dorado/test-data/dorado_models.loc @@ -0,0 +1 @@ +../tool-data/dorado_models.loc.sample \ No newline at end of file diff --git a/tools/dorado/test-data/reads_in_directories.tar.gz b/tools/dorado/test-data/reads_in_directories.tar.gz new file mode 100644 index 00000000..be390542 Binary files /dev/null and b/tools/dorado/test-data/reads_in_directories.tar.gz differ diff --git a/tools/dorado/tool-data/dorado_models.loc.sample b/tools/dorado/tool-data/dorado_models.loc.sample new file mode 100644 index 00000000..e84d214e --- /dev/null +++ b/tools/dorado/tool-data/dorado_models.loc.sample @@ -0,0 +1,58 @@ +1c65eb070a9fc1d88710c4dc09b06541f96fdd28_dna_r10.4.1_e8.2_260bps_fast@v4.1.0 1c65eb070a9fc1d88710c4dc09b06541f96fdd28 dna_r10.4.1_e8.2_260bps_fast@v4.1.0 /models/dna_r10.4.1_e8.2_260bps_fast@v4.1.0 +1c65eb070a9fc1d88710c4dc09b06541f96fdd28_dna_r10.4.1_e8.2_260bps_fast@v4.1.0_5mCG_5hmCG@v2 1c65eb070a9fc1d88710c4dc09b06541f96fdd28 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+ \ No newline at end of file diff --git a/tools/dorado/tool_data_table_conf.xml.test b/tools/dorado/tool_data_table_conf.xml.test new file mode 100644 index 00000000..27816e66 --- /dev/null +++ b/tools/dorado/tool_data_table_conf.xml.test @@ -0,0 +1,6 @@ + + + value, tool_version, name, path + +
+ \ No newline at end of file