Basic workflow for basecalling ONT pod5 files. Does not yet include demultiplexing. #61
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…WIP things (e.g., want to automate nanopore_run extraction, rename pod5_dir, remove defining default run.nf parameters that I'm not using but that always get flagged when I execute the basecall workflow.
Yeah this is a known issue that someone (possibly me) should look into fixing. If we're going to have multiple workflows running from the same start point this is going to keep coming up.
Sorry, I don't understand what you mean by this. |
When the s3 address is s3://foo/bar, I want the nanopore run identifier to be bar. After trying for 5 min I didn't figure out how to do this. |
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@simonleandergrimm can you put this in the appropriate module directory? We're using module binaries now.
| // TODO: Add optional paramter for ONT kit | ||
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| // Files | ||
| pod5_dir = "${base_dir}/pod5_small/" |
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Do these need to be in the config file? If they'll always be the same except for the base_dir you can hardcode them in the pipeline and save the user some thinking.
| calls_bam = "${base_dir}/bam/calls.bam" | ||
| fastq_file = "${base_dir}/raw/${nanopore_run}.fastq.gz" | ||
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| // Default values for undefined run.nf parameters. Adding them here because they always get triggered |
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I think this should be fixed now that I've removed all the addParams statements. Try it again after merging in the changes from master?
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| includeConfig "${projectDir}/configs/containers.config" | ||
| includeConfig "${projectDir}/configs/resources.config" | ||
| includeConfig "${projectDir}/configs/profiles.config" |
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Some missing standard configs to add once you've merged in master.
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| // Run parameters | ||
| // TODO: Automate getting run name from base_dir | ||
| nanopore_run = "NAO-ONT-20240905-DCS_RNA2_Test" |
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If this value is always equivalent to the basename of base_dir, you can do this with Groovy: https://www.nextflow.io/docs/latest/working-with-files.html#getting-file-attributes
| @@ -63,4 +63,12 @@ process { | |||
| withLabel: fastp { | |||
| container = "staphb/fastp:0.23.4" | |||
| } | |||
| withLabel: dorado { | |||
| container = "ontresearch/dorado:latest" | |||
| // NB: For now going with latest version, maybe the version switching with new updates will break things in the future. | |||
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I would recommend locking in a version soon
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| publish: |
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These need to be compatible with the output structure specified in main.nf (@simonleandergrimm look into this more after merging in master)
This PR creates the necessary files to basecall Oxford Nanopore pod5 files. Running the basecaller (dorado) requires a g5.xlarge machine, with an AMI that is both ECS-optimized and contains GPU-drivers (link). The Instance template can be found here
@willbradshaw I had to specify default values for undefined run.nf parameters as I always got warnings that they were not defined (even though I wasn't running run.nf). I will resolve this in future, though let me know if I can suppress these warnings in some other way.
Also, let me know if there is a more efficient way to get the base_dir leaf, which I'd need to define the name of the nanopore_run: