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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.
Update to DeepVariant v1.8.0
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[""]`.
Feature/colors-v1.2
…gree Feature/refactor-pedigree
Updated to StarPhase 1.3.1. - accepts phased SV vcf as input
… where it can take advantage of the phased reads to report haplotype dropouts.
…-dropouts-downstream Move coverage_dropouts to downstream.
…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.
…red-to-reported-sex Compare inferred to reported sex for QC
…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
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* Update to sawfish and sv_stats. sawfish: - Remove sex from inputs. - Add `--verbose` to all fs operations. - Switch to long form arguments. - Clean up compressed/decompressed files at the end of each task. - Pass supporting_reads_json up to main workflow outputs. sv_stats: - Remove InversionBND filtered events. - Require that all events are FILTER="PASS" and non REF genotypes. - Parameterize minimum variant size and maximum "scar" size (for sequence swaps) - Filter "sequence swap" (len(REF) and len(ALT) both >10bp) complex variants from the INS and DEL counts, and put them in a separate SWAP category. These are variants where both the REF and ALT are longer than 1bp. * update wdl-ci config file after successful tests --------- Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
…facts on tags that match semantic versions (only numerical versions).
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Added new GitHub workflow:
This should only run for releases with simple semantic versioning, like
'v[0-9]+.[0-9]+.[0-9]+'.alpha/prerelease/rc*-dockstorereleases