upstream v3#7
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yttria-aniseia merged 64 commits intoyttria-aniseia:mainfrom Sep 9, 2025
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- remove the deepvariant_version option and hard-code the default into the subworkflow - remove the custom_deepvariant_model_tar option - update the version to 1.8.0 - modify task command calls to 1.8.0 options - use generic tfrecord filenames Remove the pharmcat_version option and provide the default directly within the subworkflow.
PEDigree file syntax is generated directly within WDL for each sample independently. PED files are written within tasks by `write_tsv()` by concatenating sample lines. `is_duo_kid` and `is_trio_kid` arrays are generated for convenience in preparation for duo-/trio-specific secondary/tertiary analyses. Move phenotype lookup to tertiary subworkflow. Adjust tests for changes to write_phrank. Fix write_phrank test. If sex cannot be inferred by mosdepth, output is empty string. Change `pedigree_sex["UNKNOWN"]` to `pedigree_sex[""]`.
- now accepts phased small variant and structural variant VCFs
…r than the reported sex. Inferred sex is compared to the reported sex, and if there is a disagreement, a new `String qc_sex` message is emitted by upstream. These messages are gathered at top level `Array[String?] qc_messages` and emitted as output.
…ate through the BAM once. (#198) * Refactor tasks that extract stats from BAM files so that we only iterate through the BAM once. - remove components from pbmm2_align taskthat gather stats about read length and quality - remove task to merge per-bam stats and plot read length and quality - remove components from hiphasse task that gather stats about mapping and alignment - add a new bam_stats task that extracts all tasks in a single pass through the BAM and replaces the outputs from the removed components * update wdl-ci config file after successful tests --------- Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
…se memory/cpu attributes for some tasks based on typical available cloud node types.
…P zones that lack n1 nodes. (#207) * Add the `cpuPlatform` runtime attribute to support the workflow in GCP zones that lack n1 nodes. - add cpuPlatform to every task - add cpuPlatform to backend_configuration - add cpuPlatform input to family and singleton entrypoints - document input in singleton and family docs - document input in backend-gcp doc * update wdl-ci config file after successful tests * Fix spacing for runtime.zones. Add cpuPlatform to subworkflow inputs. * update wdl-ci config file after successful tests --------- Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Change `msg` syntax.
Change `msg` concept so that task output `msg` is always `Array[String]`. Any empty messages are pruned by the `Utilities.consolidate_stats` task, which outputs all raised messages to a text file.
* Parallelize alignment by chunking input.
- the split_input_bam task:
- checks inputs for alignments and kinetics/basemod tags
- resets alignments and kinetics tags
- if max_reads_per_chunk is greater than 0, the input is indexed and split into chunks of no more than max_reads_per_chunk records
Note: We are investigating native chunking features in pbmm2, so this implementation may change.
* Update to sawfish 0.12.10
bump: update trgt to v3.0.0
* bump: update mitorsaw to v0.2.0
* bump: update paraphase to v3.3.1
* bump: Upgrade DeepVariant to v1.9.0
- also make Paraphase outputs optional to allow it to fail without ending workflow in cases where the coverage is very low - updated docs - updated image manifest - add msg output to Paraphase to capture errors.
Update to StarPhase 1.4.1
…222) * feat: Update to sawfish v2.0.1, replace hificnv functionality - annotate ALU/L1/SVA annotations with sawshark - add gc_bias_corrected_depth.bw output
* Updated LoF metrics to use gnomAD v4.1 gene constraint metrics. TSVs will now be annotated with pLI, oe.lof, LOEUF, and LOEUF_decile. More details on these metrics [here](https://gnomad.broadinstitute.org/news/2024-03-gnomad-v4-0-gene-constraint/).
* bump: update mitorsaw to v0.2.1
- update static resources to v3.0.0 bundle - update to CoLoRSdb v1.2.0 - update ClinVar lookup - update gene constraint lookup to gnomAD v4.1 - update reference/tertiary map templates - update input templates - update image manifest script to pull DeepVariant 1.9.0 - update image manifest - update version numbers in README and WDLs
* fix: Add pbtk to the image manifest.
…ss_variants. (#235) * fix: Add example_tfrecord_tars to disk_size for deepvariant_postprocess_variants.
* bump: update sawfish to 2.0.3 and sawshark to 0.3.0
* bump: update mitorsaw to 0.2.2
Co-authored-by: Helena <hexylena@galaxians.org>
* bump: Update mitorsaw to v0.2.3
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summary:
prepull.shand many other things that will probably break things :)