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Gauntlet.toml
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Gauntlet.toml
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[repositories."ENCODE-DCC/chip-seq-pipeline2"]
identifier = "ENCODE-DCC/chip-seq-pipeline2"
commit_hash = "26eeda81a0540dc793fc69b0c390d232ca7ca50a"
[repositories."PacificBiosciences/HiFi-human-WGS-WDL"]
identifier = "PacificBiosciences/HiFi-human-WGS-WDL"
commit_hash = "9a1a2846443e4b621f1dca0259fd3fa21885156a"
[repositories."aws-samples/amazon-omics-tutorials"]
identifier = "aws-samples/amazon-omics-tutorials"
commit_hash = "136ecf7e5aaee18619e14ee65a97acc6d6704bef"
[repositories."biowdl/tasks"]
identifier = "biowdl/tasks"
commit_hash = "2bf875300d90a3c9c8d670b3d99026452d5dbae2"
[repositories."broadinstitute/gatk-tool-wdls"]
identifier = "broadinstitute/gatk-tool-wdls"
commit_hash = "4536dd2c6719b86f4c50348f0ce354818260cadb"
[repositories."broadinstitute/palantir-workflows"]
identifier = "broadinstitute/palantir-workflows"
commit_hash = "1e32078d3b57dcb2291534d0caa30f600d40967e"
[repositories."broadinstitute/warp"]
identifier = "broadinstitute/warp"
commit_hash = "4c62783f441ac7405f7c720ffd1059b066e3640e"
[repositories."chanzuckerberg/czid-workflows"]
identifier = "chanzuckerberg/czid-workflows"
commit_hash = "a7c54be041e9fbd4cfdd9fac99226e6b4f6f3bfd"
[repositories."getwilds/ww-fastq-to-cram"]
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commit_hash = "7dd6c4c7c8c9fc6dcd4eb5ff8f3262cd26d5e7cc"
[repositories."getwilds/ww-star-deseq2"]
identifier = "getwilds/ww-star-deseq2"
commit_hash = "3de83fa91db1b2d1b0d91dfc20e3ca71303c8d15"
[repositories."getwilds/ww-vc-trio"]
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commit_hash = "ee08634f28810e5d6fd1a904fc83f4e67821550e"
[repositories."stjudecloud/workflows"]
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filters = ["/template/task-templates.wdl"]
[repositories."theiagen/public_health_bioinformatics"]
identifier = "theiagen/public_health_bioinformatics"
commit_hash = "d0377e139855252e15b57d7699aa6f5abb510996"
[[diagnostics]]
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[[diagnostics]]
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[[diagnostics]]
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message = "mutec2.wdl:114:41: error: expected struct member name, but found string"
permalink = "https://github.com/aws-samples/amazon-omics-tutorials/blob/136ecf7e5aaee18619e14ee65a97acc6d6704bef/example-workflows/gatk-best-practices/workflows/somatic-snps-and-indels/mutec2.wdl/#L114"
[[diagnostics]]
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message = "mutec2.wdl:115:41: error: expected struct member name, but found string"
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[[diagnostics]]
document = "aws-samples/amazon-omics-tutorials:/example-workflows/protein-folding/workflows/alphafold/alphafold-600.wdl"
message = "alphafold-600.wdl:110:29: error: expected runtime key, but found `,`"
permalink = "https://github.com/aws-samples/amazon-omics-tutorials/blob/136ecf7e5aaee18619e14ee65a97acc6d6704bef/example-workflows/protein-folding/workflows/alphafold/alphafold-600.wdl/#L110"
[[diagnostics]]
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message = "alphafold-600.wdl:111:23: error: expected runtime key, but found `,`"
permalink = "https://github.com/aws-samples/amazon-omics-tutorials/blob/136ecf7e5aaee18619e14ee65a97acc6d6704bef/example-workflows/protein-folding/workflows/alphafold/alphafold-600.wdl/#L111"
[[diagnostics]]
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permalink = "https://github.com/aws-samples/amazon-omics-tutorials/blob/136ecf7e5aaee18619e14ee65a97acc6d6704bef/example-workflows/protein-folding/workflows/alphafold/alphafold-600.wdl/#L142"
[[diagnostics]]
document = "aws-samples/amazon-omics-tutorials:/example-workflows/protein-folding/workflows/alphafold/alphafold-600.wdl"
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[[diagnostics]]
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[[diagnostics]]
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permalink = "https://github.com/aws-samples/amazon-omics-tutorials/blob/136ecf7e5aaee18619e14ee65a97acc6d6704bef/example-workflows/protein-folding/workflows/alphafold/alphafold-600.wdl/#L175"
[[diagnostics]]
document = "aws-samples/amazon-omics-tutorials:/example-workflows/protein-folding/workflows/alphafold/alphafold-600.wdl"
message = "alphafold-600.wdl:210:29: error: expected runtime key, but found `,`"
permalink = "https://github.com/aws-samples/amazon-omics-tutorials/blob/136ecf7e5aaee18619e14ee65a97acc6d6704bef/example-workflows/protein-folding/workflows/alphafold/alphafold-600.wdl/#L210"
[[diagnostics]]
document = "aws-samples/amazon-omics-tutorials:/example-workflows/protein-folding/workflows/alphafold/alphafold-600.wdl"
message = "alphafold-600.wdl:211:23: error: expected runtime key, but found `,`"
permalink = "https://github.com/aws-samples/amazon-omics-tutorials/blob/136ecf7e5aaee18619e14ee65a97acc6d6704bef/example-workflows/protein-folding/workflows/alphafold/alphafold-600.wdl/#L211"
[[diagnostics]]
document = "aws-samples/amazon-omics-tutorials:/example-workflows/protein-folding/workflows/alphafold/alphafold-600.wdl"
message = "alphafold-600.wdl:244:29: error: expected runtime key, but found `,`"
permalink = "https://github.com/aws-samples/amazon-omics-tutorials/blob/136ecf7e5aaee18619e14ee65a97acc6d6704bef/example-workflows/protein-folding/workflows/alphafold/alphafold-600.wdl/#L244"
[[diagnostics]]
document = "aws-samples/amazon-omics-tutorials:/example-workflows/protein-folding/workflows/alphafold/alphafold-600.wdl"
message = "alphafold-600.wdl:245:23: error: expected runtime key, but found `,`"
permalink = "https://github.com/aws-samples/amazon-omics-tutorials/blob/136ecf7e5aaee18619e14ee65a97acc6d6704bef/example-workflows/protein-folding/workflows/alphafold/alphafold-600.wdl/#L245"
[[diagnostics]]
document = "aws-samples/amazon-omics-tutorials:/example-workflows/protein-folding/workflows/alphafold/alphafold-600.wdl"
message = "alphafold-600.wdl:284:29: error: expected runtime key, but found `,`"
permalink = "https://github.com/aws-samples/amazon-omics-tutorials/blob/136ecf7e5aaee18619e14ee65a97acc6d6704bef/example-workflows/protein-folding/workflows/alphafold/alphafold-600.wdl/#L284"
[[diagnostics]]
document = "aws-samples/amazon-omics-tutorials:/example-workflows/protein-folding/workflows/alphafold/alphafold-600.wdl"
message = "alphafold-600.wdl:285:23: error: expected runtime key, but found `,`"
permalink = "https://github.com/aws-samples/amazon-omics-tutorials/blob/136ecf7e5aaee18619e14ee65a97acc6d6704bef/example-workflows/protein-folding/workflows/alphafold/alphafold-600.wdl/#L285"
[[diagnostics]]
document = "aws-samples/amazon-omics-tutorials:/example-workflows/protein-folding/workflows/alphafold/alphafold-600.wdl"
message = "alphafold-600.wdl:323:29: error: expected runtime key, but found `,`"
permalink = "https://github.com/aws-samples/amazon-omics-tutorials/blob/136ecf7e5aaee18619e14ee65a97acc6d6704bef/example-workflows/protein-folding/workflows/alphafold/alphafold-600.wdl/#L323"
[[diagnostics]]
document = "aws-samples/amazon-omics-tutorials:/example-workflows/protein-folding/workflows/alphafold/alphafold-600.wdl"
message = "alphafold-600.wdl:324:23: error: expected runtime key, but found `,`"
permalink = "https://github.com/aws-samples/amazon-omics-tutorials/blob/136ecf7e5aaee18619e14ee65a97acc6d6704bef/example-workflows/protein-folding/workflows/alphafold/alphafold-600.wdl/#L324"
[[diagnostics]]
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[[diagnostics]]
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[[diagnostics]]
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[[diagnostics]]
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[[diagnostics]]
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[[diagnostics]]
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[[diagnostics]]
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[[diagnostics]]
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[[diagnostics]]
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[[diagnostics]]
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[[diagnostics]]
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[[diagnostics]]
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[[diagnostics]]
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[[diagnostics]]
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permalink = "https://github.com/biowdl/tasks/blob/2bf875300d90a3c9c8d670b3d99026452d5dbae2/bowtie.wdl/#L75"
[[diagnostics]]
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[[diagnostics]]
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permalink = "https://github.com/biowdl/tasks/blob/2bf875300d90a3c9c8d670b3d99026452d5dbae2/centrifuge.wdl/#L122"
[[diagnostics]]
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[[diagnostics]]
document = "biowdl/tasks:/centrifuge.wdl"
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[[diagnostics]]
document = "biowdl/tasks:/centrifuge.wdl"
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permalink = "https://github.com/biowdl/tasks/blob/2bf875300d90a3c9c8d670b3d99026452d5dbae2/centrifuge.wdl/#L256"
[[diagnostics]]
document = "biowdl/tasks:/centrifuge.wdl"
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permalink = "https://github.com/biowdl/tasks/blob/2bf875300d90a3c9c8d670b3d99026452d5dbae2/centrifuge.wdl/#L256"
[[diagnostics]]
document = "biowdl/tasks:/common.wdl"
message = 'common.wdl:275:45: error: unknown escape sequence `\.`'
permalink = "https://github.com/biowdl/tasks/blob/2bf875300d90a3c9c8d670b3d99026452d5dbae2/common.wdl/#L275"
[[diagnostics]]
document = "biowdl/tasks:/fastqc.wdl"
message = 'fastqc.wdl:59:42: error: unknown escape sequence `\.`'
permalink = "https://github.com/biowdl/tasks/blob/2bf875300d90a3c9c8d670b3d99026452d5dbae2/fastqc.wdl/#L59"
[[diagnostics]]
document = "biowdl/tasks:/fastqc.wdl"
message = 'fastqc.wdl:63:54: error: unknown escape sequence `\.`'
permalink = "https://github.com/biowdl/tasks/blob/2bf875300d90a3c9c8d670b3d99026452d5dbae2/fastqc.wdl/#L63"
[[diagnostics]]
document = "biowdl/tasks:/fastqc.wdl"
message = 'fastqc.wdl:63:58: error: unknown escape sequence `\.`'
permalink = "https://github.com/biowdl/tasks/blob/2bf875300d90a3c9c8d670b3d99026452d5dbae2/fastqc.wdl/#L63"
[[diagnostics]]
document = "biowdl/tasks:/gatk.wdl"
message = 'gatk.wdl:127:57: error: unknown escape sequence `\.`'
permalink = "https://github.com/biowdl/tasks/blob/2bf875300d90a3c9c8d670b3d99026452d5dbae2/gatk.wdl/#L127"
[[diagnostics]]
document = "biowdl/tasks:/gatk.wdl"
message = 'gatk.wdl:1597:41: error: unknown escape sequence `\.`'
permalink = "https://github.com/biowdl/tasks/blob/2bf875300d90a3c9c8d670b3d99026452d5dbae2/gatk.wdl/#L1597"
[[diagnostics]]
document = "biowdl/tasks:/hisat2.wdl"
message = 'hisat2.wdl:60:34: error: unknown escape sequence `\.`'
permalink = "https://github.com/biowdl/tasks/blob/2bf875300d90a3c9c8d670b3d99026452d5dbae2/hisat2.wdl/#L60"
[[diagnostics]]
document = "biowdl/tasks:/hisat2.wdl"
message = 'hisat2.wdl:60:41: error: unknown escape sequence `\.`'
permalink = "https://github.com/biowdl/tasks/blob/2bf875300d90a3c9c8d670b3d99026452d5dbae2/hisat2.wdl/#L60"
[[diagnostics]]
document = "biowdl/tasks:/multiqc.wdl"
message = 'multiqc.wdl:133:45: error: unknown escape sequence `\.`'
permalink = "https://github.com/biowdl/tasks/blob/2bf875300d90a3c9c8d670b3d99026452d5dbae2/multiqc.wdl/#L133"
[[diagnostics]]
document = "biowdl/tasks:/picard.wdl"
message = 'picard.wdl:1021:48: error: unknown escape sequence `\.`'
permalink = "https://github.com/biowdl/tasks/blob/2bf875300d90a3c9c8d670b3d99026452d5dbae2/picard.wdl/#L1021"
[[diagnostics]]
document = "biowdl/tasks:/picard.wdl"
message = 'picard.wdl:1191:48: error: unknown escape sequence `\.`'
permalink = "https://github.com/biowdl/tasks/blob/2bf875300d90a3c9c8d670b3d99026452d5dbae2/picard.wdl/#L1191"
[[diagnostics]]
document = "biowdl/tasks:/picard.wdl"
message = 'picard.wdl:643:51: error: unknown escape sequence `\.`'
permalink = "https://github.com/biowdl/tasks/blob/2bf875300d90a3c9c8d670b3d99026452d5dbae2/picard.wdl/#L643"
[[diagnostics]]
document = "biowdl/tasks:/picard.wdl"
message = 'picard.wdl:785:51: error: unknown escape sequence `\.`'
permalink = "https://github.com/biowdl/tasks/blob/2bf875300d90a3c9c8d670b3d99026452d5dbae2/picard.wdl/#L785"
[[diagnostics]]
document = "biowdl/tasks:/picard.wdl"
message = 'picard.wdl:900:46: error: unknown escape sequence `\.`'
permalink = "https://github.com/biowdl/tasks/blob/2bf875300d90a3c9c8d670b3d99026452d5dbae2/picard.wdl/#L900"
[[diagnostics]]
document = "biowdl/tasks:/picard.wdl"
message = 'picard.wdl:901:46: error: unknown escape sequence `\.`'
permalink = "https://github.com/biowdl/tasks/blob/2bf875300d90a3c9c8d670b3d99026452d5dbae2/picard.wdl/#L901"
[[diagnostics]]
document = "biowdl/tasks:/picard.wdl"
message = 'picard.wdl:902:49: error: unknown escape sequence `\.`'
permalink = "https://github.com/biowdl/tasks/blob/2bf875300d90a3c9c8d670b3d99026452d5dbae2/picard.wdl/#L902"
[[diagnostics]]
document = "biowdl/tasks:/sambamba.wdl"
message = 'sambamba.wdl:145:49: error: unknown escape sequence `\.`'
permalink = "https://github.com/biowdl/tasks/blob/2bf875300d90a3c9c8d670b3d99026452d5dbae2/sambamba.wdl/#L145"
[[diagnostics]]
document = "biowdl/tasks:/sambamba.wdl"
message = 'sambamba.wdl:157:60: error: unknown escape sequence `\.`'
permalink = "https://github.com/biowdl/tasks/blob/2bf875300d90a3c9c8d670b3d99026452d5dbae2/sambamba.wdl/#L157"
[[diagnostics]]
document = "biowdl/tasks:/sambamba.wdl"
message = 'sambamba.wdl:91:44: error: unknown escape sequence `\.`'
permalink = "https://github.com/biowdl/tasks/blob/2bf875300d90a3c9c8d670b3d99026452d5dbae2/sambamba.wdl/#L91"
[[diagnostics]]
document = "biowdl/tasks:/samtools.wdl"
message = 'samtools.wdl:238:53: error: unknown escape sequence `\.`'
permalink = "https://github.com/biowdl/tasks/blob/2bf875300d90a3c9c8d670b3d99026452d5dbae2/samtools.wdl/#L238"
[[diagnostics]]
document = "biowdl/tasks:/samtools.wdl"
message = 'samtools.wdl:326:44: error: unknown escape sequence `\.`'
permalink = "https://github.com/biowdl/tasks/blob/2bf875300d90a3c9c8d670b3d99026452d5dbae2/samtools.wdl/#L326"
[[diagnostics]]
document = "biowdl/tasks:/samtools.wdl"
message = 'samtools.wdl:414:44: error: unknown escape sequence `\.`'
permalink = "https://github.com/biowdl/tasks/blob/2bf875300d90a3c9c8d670b3d99026452d5dbae2/samtools.wdl/#L414"
[[diagnostics]]
document = "biowdl/tasks:/samtools.wdl"
message = 'samtools.wdl:458:49: error: unknown escape sequence `\.`'
permalink = "https://github.com/biowdl/tasks/blob/2bf875300d90a3c9c8d670b3d99026452d5dbae2/samtools.wdl/#L458"
[[diagnostics]]
document = "biowdl/tasks:/samtools.wdl"
message = 'samtools.wdl:470:60: error: unknown escape sequence `\.`'
permalink = "https://github.com/biowdl/tasks/blob/2bf875300d90a3c9c8d670b3d99026452d5dbae2/samtools.wdl/#L470"
[[diagnostics]]
document = "biowdl/tasks:/samtools.wdl"
message = 'samtools.wdl:80:42: error: unknown escape sequence `\.`'
permalink = "https://github.com/biowdl/tasks/blob/2bf875300d90a3c9c8d670b3d99026452d5dbae2/samtools.wdl/#L80"
[[diagnostics]]
document = "biowdl/tasks:/umi-tools.wdl"
message = 'umi-tools.wdl:95:49: error: unknown escape sequence `\.`'
permalink = "https://github.com/biowdl/tasks/blob/2bf875300d90a3c9c8d670b3d99026452d5dbae2/umi-tools.wdl/#L95"
[[diagnostics]]
document = "biowdl/tasks:/umi.wdl"
message = 'umi.wdl:39:60: error: unknown escape sequence `\.`'
permalink = "https://github.com/biowdl/tasks/blob/2bf875300d90a3c9c8d670b3d99026452d5dbae2/umi.wdl/#L39"
[[diagnostics]]
document = "broadinstitute/gatk-tool-wdls:/wdls/ApplyBQSR.wdl"
message = "ApplyBQSR.wdl:104:6: error: conflicting task name `ApplyBQSR`"
permalink = "https://github.com/broadinstitute/gatk-tool-wdls/blob/4536dd2c6719b86f4c50348f0ce354818260cadb/wdls/ApplyBQSR.wdl/#L104"
[[diagnostics]]
document = "broadinstitute/gatk-tool-wdls:/wdls/ApplyBQSRAllArgs.wdl"
message = "ApplyBQSRAllArgs.wdl:291:6: error: conflicting task name `ApplyBQSR`"
permalink = "https://github.com/broadinstitute/gatk-tool-wdls/blob/4536dd2c6719b86f4c50348f0ce354818260cadb/wdls/ApplyBQSRAllArgs.wdl/#L291"
[[diagnostics]]
document = "broadinstitute/gatk-tool-wdls:/wdls/BaseRecalibrator.wdl"
message = "BaseRecalibrator.wdl:111:6: error: conflicting task name `BaseRecalibrator`"
permalink = "https://github.com/broadinstitute/gatk-tool-wdls/blob/4536dd2c6719b86f4c50348f0ce354818260cadb/wdls/BaseRecalibrator.wdl/#L111"
[[diagnostics]]
document = "broadinstitute/gatk-tool-wdls:/wdls/BaseRecalibratorAllArgs.wdl"
message = "BaseRecalibratorAllArgs.wdl:318:6: error: conflicting task name `BaseRecalibrator`"
permalink = "https://github.com/broadinstitute/gatk-tool-wdls/blob/4536dd2c6719b86f4c50348f0ce354818260cadb/wdls/BaseRecalibratorAllArgs.wdl/#L318"
[[diagnostics]]
document = "broadinstitute/gatk-tool-wdls:/wdls/ClipReads.wdl"
message = "ClipReads.wdl:100:6: error: conflicting task name `ClipReads`"
permalink = "https://github.com/broadinstitute/gatk-tool-wdls/blob/4536dd2c6719b86f4c50348f0ce354818260cadb/wdls/ClipReads.wdl/#L100"
[[diagnostics]]
document = "broadinstitute/gatk-tool-wdls:/wdls/ClipReadsAllArgs.wdl"
message = "ClipReadsAllArgs.wdl:304:6: error: conflicting task name `ClipReads`"
permalink = "https://github.com/broadinstitute/gatk-tool-wdls/blob/4536dd2c6719b86f4c50348f0ce354818260cadb/wdls/ClipReadsAllArgs.wdl/#L304"
[[diagnostics]]
document = "broadinstitute/gatk-tool-wdls:/wdls/CollectReadCounts.wdl"
message = "CollectReadCounts.wdl:99:6: error: conflicting task name `CollectReadCounts`"
permalink = "https://github.com/broadinstitute/gatk-tool-wdls/blob/4536dd2c6719b86f4c50348f0ce354818260cadb/wdls/CollectReadCounts.wdl/#L99"
[[diagnostics]]
document = "broadinstitute/gatk-tool-wdls:/wdls/CollectReadCountsAllArgs.wdl"
message = "CollectReadCountsAllArgs.wdl:266:6: error: conflicting task name `CollectReadCounts`"
permalink = "https://github.com/broadinstitute/gatk-tool-wdls/blob/4536dd2c6719b86f4c50348f0ce354818260cadb/wdls/CollectReadCountsAllArgs.wdl/#L266"
[[diagnostics]]
document = "broadinstitute/gatk-tool-wdls:/wdls/CombineGVCFs.wdl"
message = "CombineGVCFs.wdl:112:6: error: conflicting task name `CombineGVCFs`"
permalink = "https://github.com/broadinstitute/gatk-tool-wdls/blob/4536dd2c6719b86f4c50348f0ce354818260cadb/wdls/CombineGVCFs.wdl/#L112"
[[diagnostics]]
document = "broadinstitute/gatk-tool-wdls:/wdls/CombineGVCFsAllArgs.wdl"
message = "CombineGVCFsAllArgs.wdl:323:6: error: conflicting task name `CombineGVCFs`"
permalink = "https://github.com/broadinstitute/gatk-tool-wdls/blob/4536dd2c6719b86f4c50348f0ce354818260cadb/wdls/CombineGVCFsAllArgs.wdl/#L323"
[[diagnostics]]
document = "broadinstitute/gatk-tool-wdls:/wdls/CountBases.wdl"
message = "CountBases.wdl:91:6: error: conflicting task name `CountBases`"
permalink = "https://github.com/broadinstitute/gatk-tool-wdls/blob/4536dd2c6719b86f4c50348f0ce354818260cadb/wdls/CountBases.wdl/#L91"
[[diagnostics]]
document = "broadinstitute/gatk-tool-wdls:/wdls/CountBasesAllArgs.wdl"
message = "CountBasesAllArgs.wdl:262:6: error: conflicting task name `CountBases`"
permalink = "https://github.com/broadinstitute/gatk-tool-wdls/blob/4536dd2c6719b86f4c50348f0ce354818260cadb/wdls/CountBasesAllArgs.wdl/#L262"
[[diagnostics]]
document = "broadinstitute/gatk-tool-wdls:/wdls/CountReads.wdl"
message = "CountReads.wdl:91:6: error: conflicting task name `CountReads`"
permalink = "https://github.com/broadinstitute/gatk-tool-wdls/blob/4536dd2c6719b86f4c50348f0ce354818260cadb/wdls/CountReads.wdl/#L91"
[[diagnostics]]
document = "broadinstitute/gatk-tool-wdls:/wdls/CountReadsAllArgs.wdl"
message = "CountReadsAllArgs.wdl:262:6: error: conflicting task name `CountReads`"
permalink = "https://github.com/broadinstitute/gatk-tool-wdls/blob/4536dd2c6719b86f4c50348f0ce354818260cadb/wdls/CountReadsAllArgs.wdl/#L262"
[[diagnostics]]
document = "broadinstitute/gatk-tool-wdls:/wdls/FixMisencodedBaseQualityReads.wdl"
message = "FixMisencodedBaseQualityReads.wdl:100:6: error: conflicting task name `FixMisencodedBaseQualityReads`"
permalink = "https://github.com/broadinstitute/gatk-tool-wdls/blob/4536dd2c6719b86f4c50348f0ce354818260cadb/wdls/FixMisencodedBaseQualityReads.wdl/#L100"
[[diagnostics]]
document = "broadinstitute/gatk-tool-wdls:/wdls/FixMisencodedBaseQualityReadsAllArgs.wdl"
message = "FixMisencodedBaseQualityReadsAllArgs.wdl:267:6: error: conflicting task name `FixMisencodedBaseQualityReads`"
permalink = "https://github.com/broadinstitute/gatk-tool-wdls/blob/4536dd2c6719b86f4c50348f0ce354818260cadb/wdls/FixMisencodedBaseQualityReadsAllArgs.wdl/#L267"
[[diagnostics]]
document = "broadinstitute/gatk-tool-wdls:/wdls/FlagStat.wdl"
message = "FlagStat.wdl:91:6: error: conflicting task name `FlagStat`"
permalink = "https://github.com/broadinstitute/gatk-tool-wdls/blob/4536dd2c6719b86f4c50348f0ce354818260cadb/wdls/FlagStat.wdl/#L91"
[[diagnostics]]
document = "broadinstitute/gatk-tool-wdls:/wdls/FlagStatAllArgs.wdl"
message = "FlagStatAllArgs.wdl:262:6: error: conflicting task name `FlagStat`"
permalink = "https://github.com/broadinstitute/gatk-tool-wdls/blob/4536dd2c6719b86f4c50348f0ce354818260cadb/wdls/FlagStatAllArgs.wdl/#L262"
[[diagnostics]]
document = "broadinstitute/gatk-tool-wdls:/wdls/GatherTranches.wdl"
message = "GatherTranches.wdl:95:6: error: conflicting task name `GatherTranches`"
permalink = "https://github.com/broadinstitute/gatk-tool-wdls/blob/4536dd2c6719b86f4c50348f0ce354818260cadb/wdls/GatherTranches.wdl/#L95"
[[diagnostics]]
document = "broadinstitute/gatk-tool-wdls:/wdls/GatherTranchesAllArgs.wdl"
message = "GatherTranchesAllArgs.wdl:146:6: error: conflicting task name `GatherTranches`"
permalink = "https://github.com/broadinstitute/gatk-tool-wdls/blob/4536dd2c6719b86f4c50348f0ce354818260cadb/wdls/GatherTranchesAllArgs.wdl/#L146"
[[diagnostics]]
document = "broadinstitute/gatk-tool-wdls:/wdls/LeftAlignIndels.wdl"
message = "LeftAlignIndels.wdl:112:6: error: conflicting task name `LeftAlignIndels`"
permalink = "https://github.com/broadinstitute/gatk-tool-wdls/blob/4536dd2c6719b86f4c50348f0ce354818260cadb/wdls/LeftAlignIndels.wdl/#L112"
[[diagnostics]]
document = "broadinstitute/gatk-tool-wdls:/wdls/LeftAlignIndelsAllArgs.wdl"
message = "LeftAlignIndelsAllArgs.wdl:267:6: error: conflicting task name `LeftAlignIndels`"
permalink = "https://github.com/broadinstitute/gatk-tool-wdls/blob/4536dd2c6719b86f4c50348f0ce354818260cadb/wdls/LeftAlignIndelsAllArgs.wdl/#L267"
[[diagnostics]]
document = "broadinstitute/gatk-tool-wdls:/wdls/PrintReads.wdl"
message = "PrintReads.wdl:100:6: error: conflicting task name `PrintReads`"
permalink = "https://github.com/broadinstitute/gatk-tool-wdls/blob/4536dd2c6719b86f4c50348f0ce354818260cadb/wdls/PrintReads.wdl/#L100"
[[diagnostics]]
document = "broadinstitute/gatk-tool-wdls:/wdls/PrintReadsAllArgs.wdl"
message = "PrintReadsAllArgs.wdl:267:6: error: conflicting task name `PrintReads`"
permalink = "https://github.com/broadinstitute/gatk-tool-wdls/blob/4536dd2c6719b86f4c50348f0ce354818260cadb/wdls/PrintReadsAllArgs.wdl/#L267"
[[diagnostics]]
document = "broadinstitute/gatk-tool-wdls:/wdls/ReadAnonymizer.wdl"
message = "ReadAnonymizer.wdl:112:6: error: conflicting task name `ReadAnonymizer`"
permalink = "https://github.com/broadinstitute/gatk-tool-wdls/blob/4536dd2c6719b86f4c50348f0ce354818260cadb/wdls/ReadAnonymizer.wdl/#L112"
[[diagnostics]]
document = "broadinstitute/gatk-tool-wdls:/wdls/ReadAnonymizerAllArgs.wdl"
message = "ReadAnonymizerAllArgs.wdl:275:6: error: conflicting task name `ReadAnonymizer`"
permalink = "https://github.com/broadinstitute/gatk-tool-wdls/blob/4536dd2c6719b86f4c50348f0ce354818260cadb/wdls/ReadAnonymizerAllArgs.wdl/#L275"
[[diagnostics]]
document = "broadinstitute/gatk-tool-wdls:/wdls/RevertBaseQualityScores.wdl"
message = "RevertBaseQualityScores.wdl:100:6: error: conflicting task name `RevertBaseQualityScores`"
permalink = "https://github.com/broadinstitute/gatk-tool-wdls/blob/4536dd2c6719b86f4c50348f0ce354818260cadb/wdls/RevertBaseQualityScores.wdl/#L100"
[[diagnostics]]
document = "broadinstitute/gatk-tool-wdls:/wdls/RevertBaseQualityScoresAllArgs.wdl"
message = "RevertBaseQualityScoresAllArgs.wdl:267:6: error: conflicting task name `RevertBaseQualityScores`"
permalink = "https://github.com/broadinstitute/gatk-tool-wdls/blob/4536dd2c6719b86f4c50348f0ce354818260cadb/wdls/RevertBaseQualityScoresAllArgs.wdl/#L267"
[[diagnostics]]
document = "broadinstitute/gatk-tool-wdls:/wdls/SplitNCigarReads.wdl"
message = "SplitNCigarReads.wdl:112:6: error: conflicting task name `SplitNCigarReads`"
permalink = "https://github.com/broadinstitute/gatk-tool-wdls/blob/4536dd2c6719b86f4c50348f0ce354818260cadb/wdls/SplitNCigarReads.wdl/#L112"
[[diagnostics]]
document = "broadinstitute/gatk-tool-wdls:/wdls/SplitNCigarReadsAllArgs.wdl"
message = "SplitNCigarReadsAllArgs.wdl:291:6: error: conflicting task name `SplitNCigarReads`"
permalink = "https://github.com/broadinstitute/gatk-tool-wdls/blob/4536dd2c6719b86f4c50348f0ce354818260cadb/wdls/SplitNCigarReadsAllArgs.wdl/#L291"
[[diagnostics]]
document = "broadinstitute/gatk-tool-wdls:/wdls/SplitReads.wdl"
message = "SplitReads.wdl:95:6: error: conflicting task name `SplitReads`"
permalink = "https://github.com/broadinstitute/gatk-tool-wdls/blob/4536dd2c6719b86f4c50348f0ce354818260cadb/wdls/SplitReads.wdl/#L95"
[[diagnostics]]
document = "broadinstitute/gatk-tool-wdls:/wdls/SplitReadsAllArgs.wdl"
message = "SplitReadsAllArgs.wdl:274:6: error: conflicting task name `SplitReads`"
permalink = "https://github.com/broadinstitute/gatk-tool-wdls/blob/4536dd2c6719b86f4c50348f0ce354818260cadb/wdls/SplitReadsAllArgs.wdl/#L274"
[[diagnostics]]
document = "broadinstitute/gatk-tool-wdls:/wdls/UnmarkDuplicates.wdl"
message = "UnmarkDuplicates.wdl:100:6: error: conflicting task name `UnmarkDuplicates`"
permalink = "https://github.com/broadinstitute/gatk-tool-wdls/blob/4536dd2c6719b86f4c50348f0ce354818260cadb/wdls/UnmarkDuplicates.wdl/#L100"
[[diagnostics]]
document = "broadinstitute/gatk-tool-wdls:/wdls/UnmarkDuplicatesAllArgs.wdl"
message = "UnmarkDuplicatesAllArgs.wdl:267:6: error: conflicting task name `UnmarkDuplicates`"
permalink = "https://github.com/broadinstitute/gatk-tool-wdls/blob/4536dd2c6719b86f4c50348f0ce354818260cadb/wdls/UnmarkDuplicatesAllArgs.wdl/#L267"
[[diagnostics]]
document = "broadinstitute/palantir-workflows:/BenchmarkSVs/WittyerTasks.wdl"
message = "WittyerTasks.wdl:74:14: error: conflicting declaration name `wittyer_config`"
permalink = "https://github.com/broadinstitute/palantir-workflows/blob/1e32078d3b57dcb2291534d0caa30f600d40967e/BenchmarkSVs/WittyerTasks.wdl/#L74"
[[diagnostics]]
document = "broadinstitute/palantir-workflows:/BenchmarkVCFs/BenchmarkAndCompareVCFs.wdl"
message = "BenchmarkAndCompareVCFs.wdl:43:14: error: conflicting declaration name `preemptible`"
permalink = "https://github.com/broadinstitute/palantir-workflows/blob/1e32078d3b57dcb2291534d0caa30f600d40967e/BenchmarkVCFs/BenchmarkAndCompareVCFs.wdl/#L43"
[[diagnostics]]
document = "broadinstitute/palantir-workflows:/HaplotypeMap/BuildHaplotypeMap.wdl"
message = "BuildHaplotypeMap.wdl:17:1: error: a WDL document must start with a version statement"
permalink = "https://github.com/broadinstitute/palantir-workflows/blob/1e32078d3b57dcb2291534d0caa30f600d40967e/HaplotypeMap/BuildHaplotypeMap.wdl/#L17"
[[diagnostics]]
document = "broadinstitute/palantir-workflows:/LongReadRNABenchmark/IsoformDiscoveryBenchmark.wdl"
message = "IsoformDiscoveryBenchmark.wdl:147:13: error: conflicting scatter variable name `gtf`"
permalink = "https://github.com/broadinstitute/palantir-workflows/blob/1e32078d3b57dcb2291534d0caa30f600d40967e/LongReadRNABenchmark/IsoformDiscoveryBenchmark.wdl/#L147"
[[diagnostics]]
document = "broadinstitute/warp:/pipelines/broad/dna_seq/somatic/single_sample/wgs/gdc_genome/GDCWholeGenomeSomaticSingleSample.wdl"
message = "GDCWholeGenomeSomaticSingleSample.wdl:672:14: error: conflicting scatter variable name `ubam`"
permalink = "https://github.com/broadinstitute/warp/blob/4c62783f441ac7405f7c720ffd1059b066e3640e/pipelines/broad/dna_seq/somatic/single_sample/wgs/gdc_genome/GDCWholeGenomeSomaticSingleSample.wdl/#L672"
[[diagnostics]]
document = "broadinstitute/warp:/pipelines/skylab/scATAC/scATAC.wdl"
message = "scATAC.wdl:203:9: error: duplicate key `cpu` in runtime section"
permalink = "https://github.com/broadinstitute/warp/blob/4c62783f441ac7405f7c720ffd1059b066e3640e/pipelines/skylab/scATAC/scATAC.wdl/#L203"
[[diagnostics]]
document = "broadinstitute/warp:/tasks/broad/GermlineVariantDiscovery.wdl"
message = "GermlineVariantDiscovery.wdl:137:32: error: expected string, but found integer"
permalink = "https://github.com/broadinstitute/warp/blob/4c62783f441ac7405f7c720ffd1059b066e3640e/tasks/broad/GermlineVariantDiscovery.wdl/#L137"
[[diagnostics]]
document = "broadinstitute/warp:/tasks/broad/GermlineVariantDiscovery.wdl"
message = "GermlineVariantDiscovery.wdl:65:32: error: expected string, but found integer"
permalink = "https://github.com/broadinstitute/warp/blob/4c62783f441ac7405f7c720ffd1059b066e3640e/tasks/broad/GermlineVariantDiscovery.wdl/#L65"
[[diagnostics]]
document = "broadinstitute/warp:/tasks/broad/UltimaGenomicsWholeGenomeGermlineTasks.wdl"
message = "UltimaGenomicsWholeGenomeGermlineTasks.wdl:814:27: error: expected string, but found integer"
permalink = "https://github.com/broadinstitute/warp/blob/4c62783f441ac7405f7c720ffd1059b066e3640e/tasks/broad/UltimaGenomicsWholeGenomeGermlineTasks.wdl/#L814"
[[diagnostics]]
document = "broadinstitute/warp:/tasks/broad/UltimaGenomicsWholeGenomeGermlineTasks.wdl"
message = "UltimaGenomicsWholeGenomeGermlineTasks.wdl:866:27: error: expected string, but found integer"
permalink = "https://github.com/broadinstitute/warp/blob/4c62783f441ac7405f7c720ffd1059b066e3640e/tasks/broad/UltimaGenomicsWholeGenomeGermlineTasks.wdl/#L866"
[[diagnostics]]
document = "broadinstitute/warp:/tests/cemba/pr/CheckCembaOutputs.wdl"
message = "CheckCembaOutputs.wdl:1:1: error: a WDL document must start with a version statement"
permalink = "https://github.com/broadinstitute/warp/blob/4c62783f441ac7405f7c720ffd1059b066e3640e/tests/cemba/pr/CheckCembaOutputs.wdl/#L1"
[[diagnostics]]
document = "chanzuckerberg/czid-workflows:/workflows/index-generation/index-generation.wdl"
message = "index-generation.wdl:1:9: error: unsupported WDL version `development`"
permalink = "https://github.com/chanzuckerberg/czid-workflows/blob/a7c54be041e9fbd4cfdd9fac99226e6b4f6f3bfd/workflows/index-generation/index-generation.wdl/#L1"