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Adding wdl-ci tests.#157

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williamrowell merged 41 commits intomainPacificBiosciences/HiFi-human-WGS-WDL:mainfrom develop-v2PacificBiosciences/HiFi-human-WGS-WDL:develop-v2Copy head branch name to clipboardNov 21, 2024

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Commits

Commits on Nov 19, 2024

• Added tests for merge_bam_stats, pbmm2_align_wgs, pbsv_discover, pbsv_call.

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• update wdl-ci config file after successful tests

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• Fixed error in pbmm2_align_wgs-3

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• Remove md5sum tests for gzipped files.

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• Add count_columns tests for tabular files.

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• update wdl-ci config file after successful tests

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Commits on Nov 20, 2024

• Added cpg_pileup tests.

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• Added glnexus test.

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• Added hificnv tests.

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• Added mosdepth tests.

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• update wdl-ci config file after successful tests

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• Fix paths for hificnv and glnexus tests.

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• update wdl-ci config file after successful tests

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• Added tests for paraphase and pbstarphase_diplotype.

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• Added test for samtools_merge.

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• Added tests for split_string and consolidate_stats.

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• Fix output key name for split_string

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• update wdl-ci config file after successful tests

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• Added concat_pbsv_vcf test.

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• Added tests for split_vcf_by_sample

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• Added tests for split_vcf_by_sample

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• Added bcftools_merge tests.

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• Added sv_stats test.

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• update wdl-ci config file after successful tests

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• Formatting.

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• Added tests for bcftools_stats_roh_small_variants.

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• Added hiphase tests.

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• Added trgt tests.

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• Added write_ped_phrank tests.

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• Fix hiphase bam test.

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• update wdl-ci config file after successful tests

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• Fix for write_ped_phrank cromwell failure.

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• update wdl-ci config file after successful tests

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• Remove calculate_md5sum tests for bcftools_stats_roh_small_variants

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• update wdl-ci config file after successful tests

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• Added deepvariant tests.

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• Added pharmcat tests.

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• Added tests for tertary.wdl.

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• Removed vcf_validator test for pharmcat_preprocess, because the vcf emitted by this ask is not strictly valid.

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Commits on Nov 21, 2024

• update wdl-ci config file after successful tests

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• Updated version numbers.

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