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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 = "0a2dd537383b137ebc888695c0ecd6d13d75761b"
[repositories."aws-samples/amazon-omics-tutorials"]
identifier = "aws-samples/amazon-omics-tutorials"
commit_hash = "74fc4a99034645db92fb9016cecea18f7f52d17b"
[repositories."biowdl/tasks"]
identifier = "biowdl/tasks"
commit_hash = "2bf875300d90a3c9c8d670b3d99026452d5dbae2"
[repositories."broadinstitute/gatk-tool-wdls"]
identifier = "broadinstitute/gatk-tool-wdls"
commit_hash = "980883d87ee81df7925cd60dd04140e9fd01e317"
[repositories."broadinstitute/palantir-workflows"]
identifier = "broadinstitute/palantir-workflows"
commit_hash = "58f72308bdf511a760dea92dbf2ac21eb2c7dc0e"
[repositories."broadinstitute/warp"]
identifier = "broadinstitute/warp"
commit_hash = "158772d35e6e83ecbdd43450e6cd2d7f3519bfc7"
[repositories."chanzuckerberg/czid-workflows"]
identifier = "chanzuckerberg/czid-workflows"
commit_hash = "a04293a5271176885ce7f876b6353b20da3f7b98"
[repositories."getwilds/ww-fastq-to-cram"]
identifier = "getwilds/ww-fastq-to-cram"
commit_hash = "2d1e1989a57402642c06d15f4b623ac66fd9ed7d"
[repositories."getwilds/ww-star-deseq2"]
identifier = "getwilds/ww-star-deseq2"
commit_hash = "6d81ede0ad963115697c3f707f073177ddde7013"
[repositories."getwilds/ww-vc-trio"]
identifier = "getwilds/ww-vc-trio"
commit_hash = "c2c13e85efda8ac7aca7f8765fbaa7c2cacb08b2"
[repositories."stjudecloud/workflows"]
identifier = "stjudecloud/workflows"
commit_hash = "d6b826dd4deafaf7e94254ab8623e7e7316220c4"
filters = ["/template/task-templates.wdl"]
[repositories."theiagen/public_health_bioinformatics"]
identifier = "theiagen/public_health_bioinformatics"
commit_hash = "ad49a36614ab3a5a4713318c429ccd07f5486318"
[[diagnostics]]
document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl"
message = "chip.wdl:1357:64: error: type mismatch: argument to function `defined` expects type `X` where `X`: any optional type, but found type `File`"
permalink = "https://github.com/ENCODE-DCC/chip-seq-pipeline2/blob/26eeda81a0540dc793fc69b0c390d232ca7ca50a/chip.wdl/#L1357"
[[diagnostics]]
document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl"
message = "chip.wdl:1604:13: warning[UnusedDeclaration]: unused declaration `has_all_inputs_of_pool_ta_pr2`"
permalink = "https://github.com/ENCODE-DCC/chip-seq-pipeline2/blob/26eeda81a0540dc793fc69b0c390d232ca7ca50a/chip.wdl/#L1604"
[[diagnostics]]
document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl"
message = "chip.wdl:176:17: warning[UnusedInput]: unused input `use_filt_pe_ta_for_xcor`"
permalink = "https://github.com/ENCODE-DCC/chip-seq-pipeline2/blob/26eeda81a0540dc793fc69b0c390d232ca7ca50a/chip.wdl/#L176"
[[diagnostics]]
document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl"
message = "chip.wdl:2169:15: warning[UnusedInput]: unused input `ref_fa`"
permalink = "https://github.com/ENCODE-DCC/chip-seq-pipeline2/blob/26eeda81a0540dc793fc69b0c390d232ca7ca50a/chip.wdl/#L2169"
[[diagnostics]]
document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl"
message = "chip.wdl:2619:40: error: type mismatch: expected type `Array[Int]`, but found type `Array[String]`"
permalink = "https://github.com/ENCODE-DCC/chip-seq-pipeline2/blob/26eeda81a0540dc793fc69b0c390d232ca7ca50a/chip.wdl/#L2619"
[[diagnostics]]
document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl"
message = "chip.wdl:2620:46: error: type mismatch: expected type `Array[Int]`, but found type `Array[String]`"
permalink = "https://github.com/ENCODE-DCC/chip-seq-pipeline2/blob/26eeda81a0540dc793fc69b0c390d232ca7ca50a/chip.wdl/#L2620"
[[diagnostics]]
document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_bam2ta.wdl"
message = "test_bam2ta.wdl:79:25: warning[UnusedCall]: unused call `compare_md5sum`"
permalink = "https://github.com/ENCODE-DCC/chip-seq-pipeline2/blob/26eeda81a0540dc793fc69b0c390d232ca7ca50a/dev/test/test_task/test_bam2ta.wdl/#L79"
[[diagnostics]]
document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_bam_to_pbam.wdl"
message = "test_bam_to_pbam.wdl:79:25: warning[UnusedCall]: unused call `compare_md5sum`"
permalink = "https://github.com/ENCODE-DCC/chip-seq-pipeline2/blob/26eeda81a0540dc793fc69b0c390d232ca7ca50a/dev/test/test_task/test_bam_to_pbam.wdl/#L79"
[[diagnostics]]
document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_bam_to_pbam.wdl"
message = "test_bam_to_pbam.wdl:9:17: warning[UnusedInput]: unused input `no_dup_removal`"
permalink = "https://github.com/ENCODE-DCC/chip-seq-pipeline2/blob/26eeda81a0540dc793fc69b0c390d232ca7ca50a/dev/test/test_task/test_bam_to_pbam.wdl/#L9"
[[diagnostics]]
document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_bowtie2.wdl"
message = "test_bowtie2.wdl:111:25: warning[UnusedCall]: unused call `compare_md5sum`"
permalink = "https://github.com/ENCODE-DCC/chip-seq-pipeline2/blob/26eeda81a0540dc793fc69b0c390d232ca7ca50a/dev/test/test_task/test_bowtie2.wdl/#L111"
[[diagnostics]]
document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_bwa.wdl"
message = "test_bwa.wdl:70:25: warning[UnusedCall]: unused call `compare_md5sum`"
permalink = "https://github.com/ENCODE-DCC/chip-seq-pipeline2/blob/26eeda81a0540dc793fc69b0c390d232ca7ca50a/dev/test/test_task/test_bwa.wdl/#L70"
[[diagnostics]]
document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_choose_ctl.wdl"
message = "test_choose_ctl.wdl:196:24: error: type mismatch: expected type `Array[String]?`, but found type `Array[Int]+`"
permalink = "https://github.com/ENCODE-DCC/chip-seq-pipeline2/blob/26eeda81a0540dc793fc69b0c390d232ca7ca50a/dev/test/test_task/test_choose_ctl.wdl/#L196"
[[diagnostics]]
document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_choose_ctl.wdl"
message = "test_choose_ctl.wdl:3:32: warning[UnusedImport]: unused import namespace `compare_md5sum`"
permalink = "https://github.com/ENCODE-DCC/chip-seq-pipeline2/blob/26eeda81a0540dc793fc69b0c390d232ca7ca50a/dev/test/test_task/test_choose_ctl.wdl/#L3"
[[diagnostics]]
document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_count_signal_track.wdl"
message = "test_count_signal_track.wdl:27:25: warning[UnusedCall]: unused call `compare_md5sum`"
permalink = "https://github.com/ENCODE-DCC/chip-seq-pipeline2/blob/26eeda81a0540dc793fc69b0c390d232ca7ca50a/dev/test/test_task/test_count_signal_track.wdl/#L27"
[[diagnostics]]
document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_filter.wdl"
message = "test_filter.wdl:106:25: warning[UnusedCall]: unused call `compare_md5sum`"
permalink = "https://github.com/ENCODE-DCC/chip-seq-pipeline2/blob/26eeda81a0540dc793fc69b0c390d232ca7ca50a/dev/test/test_task/test_filter.wdl/#L106"
[[diagnostics]]
document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_filter.wdl"
message = "test_filter.wdl:9:17: warning[UnusedInput]: unused input `no_dup_removal`"
permalink = "https://github.com/ENCODE-DCC/chip-seq-pipeline2/blob/26eeda81a0540dc793fc69b0c390d232ca7ca50a/dev/test/test_task/test_filter.wdl/#L9"
[[diagnostics]]
document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_gc_bias.wdl"
message = "test_gc_bias.wdl:33:25: warning[UnusedCall]: unused call `compare_md5sum`"
permalink = "https://github.com/ENCODE-DCC/chip-seq-pipeline2/blob/26eeda81a0540dc793fc69b0c390d232ca7ca50a/dev/test/test_task/test_gc_bias.wdl/#L33"
[[diagnostics]]
document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_idr.wdl"
message = "test_idr.wdl:48:25: warning[UnusedCall]: unused call `compare_md5sum`"
permalink = "https://github.com/ENCODE-DCC/chip-seq-pipeline2/blob/26eeda81a0540dc793fc69b0c390d232ca7ca50a/dev/test/test_task/test_idr.wdl/#L48"
[[diagnostics]]
document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_jsd.wdl"
message = "test_jsd.wdl:50:25: warning[UnusedCall]: unused call `compare_md5sum`"
permalink = "https://github.com/ENCODE-DCC/chip-seq-pipeline2/blob/26eeda81a0540dc793fc69b0c390d232ca7ca50a/dev/test/test_task/test_jsd.wdl/#L50"
[[diagnostics]]
document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_macs2.wdl"
message = "test_macs2.wdl:55:25: warning[UnusedCall]: unused call `compare_md5sum`"
permalink = "https://github.com/ENCODE-DCC/chip-seq-pipeline2/blob/26eeda81a0540dc793fc69b0c390d232ca7ca50a/dev/test/test_task/test_macs2.wdl/#L55"
[[diagnostics]]
document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_macs2_signal_track.wdl"
message = "test_macs2_signal_track.wdl:42:25: warning[UnusedCall]: unused call `compare_md5sum`"
permalink = "https://github.com/ENCODE-DCC/chip-seq-pipeline2/blob/26eeda81a0540dc793fc69b0c390d232ca7ca50a/dev/test/test_task/test_macs2_signal_track.wdl/#L42"
[[diagnostics]]
document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_overlap.wdl"
message = "test_overlap.wdl:45:25: warning[UnusedCall]: unused call `compare_md5sum`"
permalink = "https://github.com/ENCODE-DCC/chip-seq-pipeline2/blob/26eeda81a0540dc793fc69b0c390d232ca7ca50a/dev/test/test_task/test_overlap.wdl/#L45"
[[diagnostics]]
document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_pool_ta.wdl"
message = "test_pool_ta.wdl:24:25: warning[UnusedCall]: unused call `compare_md5sum`"
permalink = "https://github.com/ENCODE-DCC/chip-seq-pipeline2/blob/26eeda81a0540dc793fc69b0c390d232ca7ca50a/dev/test/test_task/test_pool_ta.wdl/#L24"
[[diagnostics]]
document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_reproducibility.wdl"
message = "test_reproducibility.wdl:32:25: warning[UnusedCall]: unused call `compare_md5sum`"
permalink = "https://github.com/ENCODE-DCC/chip-seq-pipeline2/blob/26eeda81a0540dc793fc69b0c390d232ca7ca50a/dev/test/test_task/test_reproducibility.wdl/#L32"
[[diagnostics]]
document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_spp.wdl"
message = "test_spp.wdl:54:25: warning[UnusedCall]: unused call `compare_md5sum`"
permalink = "https://github.com/ENCODE-DCC/chip-seq-pipeline2/blob/26eeda81a0540dc793fc69b0c390d232ca7ca50a/dev/test/test_task/test_spp.wdl/#L54"
[[diagnostics]]
document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_spr.wdl"
message = "test_spr.wdl:61:25: warning[UnusedCall]: unused call `compare_md5sum`"
permalink = "https://github.com/ENCODE-DCC/chip-seq-pipeline2/blob/26eeda81a0540dc793fc69b0c390d232ca7ca50a/dev/test/test_task/test_spr.wdl/#L61"
[[diagnostics]]
document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_subsample_ctl.wdl"
message = "test_subsample_ctl.wdl:64:25: warning[UnusedCall]: unused call `compare_md5sum`"
permalink = "https://github.com/ENCODE-DCC/chip-seq-pipeline2/blob/26eeda81a0540dc793fc69b0c390d232ca7ca50a/dev/test/test_task/test_subsample_ctl.wdl/#L64"
[[diagnostics]]
document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_trimmomatic.wdl"
message = "test_trimmomatic.wdl:117:25: warning[UnusedCall]: unused call `compare_md5sum`"
permalink = "https://github.com/ENCODE-DCC/chip-seq-pipeline2/blob/26eeda81a0540dc793fc69b0c390d232ca7ca50a/dev/test/test_task/test_trimmomatic.wdl/#L117"
[[diagnostics]]
document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_xcor.wdl"
message = "test_xcor.wdl:79:25: warning[UnusedCall]: unused call `compare_md5sum`"
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[[diagnostics]]
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[[diagnostics]]
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message = "joint.wdl:94:30: error: type mismatch: expected type `Int`, but found type `Int?`"
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[[diagnostics]]
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[[diagnostics]]
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[[diagnostics]]
document = "PacificBiosciences/HiFi-human-WGS-WDL:/workflows/wdl-common/wdl/workflows/backend_configuration/backend_configuration.wdl"
message = "backend_configuration.wdl:101:28: error: type mismatch: a type common to both type `String` and type `Int` does not exist"
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message = "backend_configuration.wdl:102:22: error: type mismatch: a type common to both type `String` and type `Int` does not exist"
permalink = "https://github.com/PacificBiosciences/HiFi-human-WGS-WDL/blob/0a2dd537383b137ebc888695c0ecd6d13d75761b/workflows/wdl-common/wdl/workflows/backend_configuration/backend_configuration.wdl/#L102"
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message = "backend_configuration.wdl:112:48: error: type mismatch: expected type `RuntimeAttributes`, but found type `Map[String, String]`"
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document = "PacificBiosciences/HiFi-human-WGS-WDL:/workflows/wdl-common/wdl/workflows/backend_configuration/backend_configuration.wdl"
message = "backend_configuration.wdl:114:28: error: type mismatch: a type common to both type `String` and type `Int` does not exist"
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document = "PacificBiosciences/HiFi-human-WGS-WDL:/workflows/wdl-common/wdl/workflows/backend_configuration/backend_configuration.wdl"
message = "backend_configuration.wdl:115:22: error: type mismatch: a type common to both type `String` and type `Int` does not exist"
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message = "backend_configuration.wdl:46:53: error: type mismatch: expected type `RuntimeAttributes`, but found type `Map[String, String]`"
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message = "backend_configuration.wdl:48:28: error: type mismatch: a type common to both type `String` and type `Int` does not exist"
permalink = "https://github.com/PacificBiosciences/HiFi-human-WGS-WDL/blob/0a2dd537383b137ebc888695c0ecd6d13d75761b/workflows/wdl-common/wdl/workflows/backend_configuration/backend_configuration.wdl/#L48"
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document = "PacificBiosciences/HiFi-human-WGS-WDL:/workflows/wdl-common/wdl/workflows/backend_configuration/backend_configuration.wdl"
message = "backend_configuration.wdl:49:22: error: type mismatch: a type common to both type `String` and type `Int` does not exist"
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message = "backend_configuration.wdl:55:58: error: type mismatch: expected type `RuntimeAttributes`, but found type `Map[String, String]`"
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message = "backend_configuration.wdl:57:28: error: type mismatch: a type common to both type `String` and type `Int` does not exist"
permalink = "https://github.com/PacificBiosciences/HiFi-human-WGS-WDL/blob/0a2dd537383b137ebc888695c0ecd6d13d75761b/workflows/wdl-common/wdl/workflows/backend_configuration/backend_configuration.wdl/#L57"
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document = "PacificBiosciences/HiFi-human-WGS-WDL:/workflows/wdl-common/wdl/workflows/backend_configuration/backend_configuration.wdl"
message = "backend_configuration.wdl:58:22: error: type mismatch: a type common to both type `String` and type `Int` does not exist"
permalink = "https://github.com/PacificBiosciences/HiFi-human-WGS-WDL/blob/0a2dd537383b137ebc888695c0ecd6d13d75761b/workflows/wdl-common/wdl/workflows/backend_configuration/backend_configuration.wdl/#L58"
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document = "PacificBiosciences/HiFi-human-WGS-WDL:/workflows/wdl-common/wdl/workflows/backend_configuration/backend_configuration.wdl"
message = "backend_configuration.wdl:70:55: error: type mismatch: expected type `RuntimeAttributes`, but found type `Map[String, String]`"
permalink = "https://github.com/PacificBiosciences/HiFi-human-WGS-WDL/blob/0a2dd537383b137ebc888695c0ecd6d13d75761b/workflows/wdl-common/wdl/workflows/backend_configuration/backend_configuration.wdl/#L70"
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document = "PacificBiosciences/HiFi-human-WGS-WDL:/workflows/wdl-common/wdl/workflows/backend_configuration/backend_configuration.wdl"
message = "backend_configuration.wdl:72:28: error: type mismatch: a type common to both type `String` and type `Int` does not exist"
permalink = "https://github.com/PacificBiosciences/HiFi-human-WGS-WDL/blob/0a2dd537383b137ebc888695c0ecd6d13d75761b/workflows/wdl-common/wdl/workflows/backend_configuration/backend_configuration.wdl/#L72"
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message = "backend_configuration.wdl:73:22: error: type mismatch: a type common to both type `String` and type `Int` does not exist"
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message = "backend_configuration.wdl:79:60: error: type mismatch: expected type `RuntimeAttributes`, but found type `Map[String, String]`"
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message = "backend_configuration.wdl:81:28: error: type mismatch: a type common to both type `String` and type `Int` does not exist"
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message = "backend_configuration.wdl:82:22: error: type mismatch: a type common to both type `String` and type `Int` does not exist"
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message = "backend_configuration.wdl:99:70: error: type mismatch: expected type `RuntimeAttributes`, but found type `Map[String, String]`"
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[[diagnostics]]
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message = "processing-for-variant-discovery-gatk4.wdl:573:40: error: this use of function `sep` requires a minimum WDL version of 1.1"
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[[diagnostics]]
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message = "processing-for-variant-discovery-gatk4.wdl:574:43: error: this use of function `sep` requires a minimum WDL version of 1.1"
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[[diagnostics]]
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message = "processing-for-variant-discovery-gatk4.wdl:703:9: warning[UnusedInput]: unused input `compression_level`"
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[[diagnostics]]
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[[diagnostics]]
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message = "mutec2.wdl:112:32: error: struct `Runtime` requires a value for members `gatk_docker`, `cpu`, `machine_mem`, and `command_mem`"
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[[diagnostics]]
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message = "mutec2.wdl:112:41: error: expected struct member name, but found string"
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[[diagnostics]]
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message = "mutec2.wdl:113:41: error: expected struct member name, but found string"
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[[diagnostics]]
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message = "mutec2.wdl:114:41: error: expected struct member name, but found string"
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[[diagnostics]]
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message = "mutec2.wdl:115:41: error: expected struct member name, but found string"
permalink = "https://github.com/aws-samples/amazon-omics-tutorials/blob/74fc4a99034645db92fb9016cecea18f7f52d17b/example-workflows/gatk-best-practices/workflows/somatic-snps-and-indels/mutec2.wdl/#L115"
[[diagnostics]]
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message = "mutec2.wdl:198:21: error: type mismatch: argument to function `defined` expects type `X` where `X`: any optional type, but found type `File`"
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[[diagnostics]]
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message = "mutec2.wdl:99:13: warning[UnusedInput]: unused input `small_task_cpu`"
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[[diagnostics]]
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message = "hla_from_fastq.wdl:59:16: warning[UnusedInput]: unused input `aws_region`"
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[[diagnostics]]
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message = "alphafold-600.wdl:110:29: error: expected runtime key, but found `,`"
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[[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/74fc4a99034645db92fb9016cecea18f7f52d17b/example-workflows/protein-folding/workflows/alphafold/alphafold-600.wdl/#L111"
[[diagnostics]]
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message = "alphafold-600.wdl:142:29: error: expected runtime key, but found `,`"
permalink = "https://github.com/aws-samples/amazon-omics-tutorials/blob/74fc4a99034645db92fb9016cecea18f7f52d17b/example-workflows/protein-folding/workflows/alphafold/alphafold-600.wdl/#L142"
[[diagnostics]]
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message = "alphafold-600.wdl:143:23: error: expected runtime key, but found `,`"
permalink = "https://github.com/aws-samples/amazon-omics-tutorials/blob/74fc4a99034645db92fb9016cecea18f7f52d17b/example-workflows/protein-folding/workflows/alphafold/alphafold-600.wdl/#L143"
[[diagnostics]]
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message = "alphafold-600.wdl:174:29: error: expected runtime key, but found `,`"
permalink = "https://github.com/aws-samples/amazon-omics-tutorials/blob/74fc4a99034645db92fb9016cecea18f7f52d17b/example-workflows/protein-folding/workflows/alphafold/alphafold-600.wdl/#L174"
[[diagnostics]]
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message = "alphafold-600.wdl:175:23: error: expected runtime key, but found `,`"
permalink = "https://github.com/aws-samples/amazon-omics-tutorials/blob/74fc4a99034645db92fb9016cecea18f7f52d17b/example-workflows/protein-folding/workflows/alphafold/alphafold-600.wdl/#L175"
[[diagnostics]]
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message = "alphafold-600.wdl:210:29: error: expected runtime key, but found `,`"
permalink = "https://github.com/aws-samples/amazon-omics-tutorials/blob/74fc4a99034645db92fb9016cecea18f7f52d17b/example-workflows/protein-folding/workflows/alphafold/alphafold-600.wdl/#L210"
[[diagnostics]]
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message = "alphafold-600.wdl:211:23: error: expected runtime key, but found `,`"
permalink = "https://github.com/aws-samples/amazon-omics-tutorials/blob/74fc4a99034645db92fb9016cecea18f7f52d17b/example-workflows/protein-folding/workflows/alphafold/alphafold-600.wdl/#L211"
[[diagnostics]]
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[[diagnostics]]
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message = "alphafold-600.wdl:245:23: error: expected runtime key, but found `,`"
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[[diagnostics]]
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message = "alphafold-600.wdl:284:29: error: expected runtime key, but found `,`"
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[[diagnostics]]
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message = "alphafold-600.wdl:285:23: error: expected runtime key, but found `,`"
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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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[[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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[[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/hmftools.wdl/#L1079"
[[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]]
document = "biowdl/tasks:/hmftools.wdl"
message = "hmftools.wdl:901:14: warning[UnusedInput]: unused input `transSpliceDataCsv`"
permalink = "https://github.com/biowdl/tasks/blob/2bf875300d90a3c9c8d670b3d99026452d5dbae2/hmftools.wdl/#L901"
[[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]]
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[[diagnostics]]
document = "biowdl/tasks:/ncbi.wdl"
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permalink = "https://github.com/biowdl/tasks/blob/2bf875300d90a3c9c8d670b3d99026452d5dbae2/ncbi.wdl/#L98"
[[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:753:27: error: type mismatch: expected type `String`, but found type `Int`"
permalink = "https://github.com/biowdl/tasks/blob/2bf875300d90a3c9c8d670b3d99026452d5dbae2/picard.wdl/#L753"
[[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:157:44: error: type mismatch: argument to function `select_first` expects type `Array[X]` where `X`: any optional type, but found type `Array[String]+`"
permalink = "https://github.com/biowdl/tasks/blob/2bf875300d90a3c9c8d670b3d99026452d5dbae2/sambamba.wdl/#L157"
[[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:470:44: error: type mismatch: argument to function `select_first` expects type `Array[X]` where `X`: any optional type, but found type `Array[String]+`"
permalink = "https://github.com/biowdl/tasks/blob/2bf875300d90a3c9c8d670b3d99026452d5dbae2/samtools.wdl/#L470"
[[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"
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permalink = "https://github.com/biowdl/tasks/blob/2bf875300d90a3c9c8d670b3d99026452d5dbae2/samtools.wdl/#L72"
[[diagnostics]]
document = "biowdl/tasks:/samtools.wdl"
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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]]
document = "biowdl/tasks:/umi.wdl"
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[[diagnostics]]
document = "biowdl/tasks:/umi.wdl"
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[[diagnostics]]
document = "biowdl/tasks:/unicycler.wdl"
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[[diagnostics]]
document = "biowdl/tasks:/vardict.wdl"
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[[diagnostics]]
document = "biowdl/tasks:/whatshap.wdl"
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[[diagnostics]]
document = "biowdl/tasks:/whatshap.wdl"
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[[diagnostics]]
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[[diagnostics]]
document = "broadinstitute/gatk-tool-wdls:/wdls/ApplyBQSR.wdl"
message = "ApplyBQSR.wdl:51:8: error: cannot recursively call workflow `ApplyBQSR`"
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[[diagnostics]]
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message = "ApplyBQSRAllArgs.wdl:144:8: error: cannot recursively call workflow `ApplyBQSR`"
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[[diagnostics]]
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message = "ApplyBQSRAllArgs.wdl:291:6: error: conflicting task name `ApplyBQSR`"
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[[diagnostics]]
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[[diagnostics]]
document = "broadinstitute/gatk-tool-wdls:/wdls/BaseRecalibrator.wdl"
message = "BaseRecalibrator.wdl:55:8: error: cannot recursively call workflow `BaseRecalibrator`"
permalink = "https://github.com/broadinstitute/gatk-tool-wdls/blob/980883d87ee81df7925cd60dd04140e9fd01e317/wdls/BaseRecalibrator.wdl/#L55"
[[diagnostics]]
document = "broadinstitute/gatk-tool-wdls:/wdls/BaseRecalibratorAllArgs.wdl"
message = "BaseRecalibratorAllArgs.wdl:158:8: error: cannot recursively call workflow `BaseRecalibrator`"
permalink = "https://github.com/broadinstitute/gatk-tool-wdls/blob/980883d87ee81df7925cd60dd04140e9fd01e317/wdls/BaseRecalibratorAllArgs.wdl/#L158"
[[diagnostics]]
document = "broadinstitute/gatk-tool-wdls:/wdls/BaseRecalibratorAllArgs.wdl"
message = "BaseRecalibratorAllArgs.wdl:318:6: error: conflicting task name `BaseRecalibrator`"
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[[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/980883d87ee81df7925cd60dd04140e9fd01e317/wdls/ClipReads.wdl/#L100"
[[diagnostics]]
document = "broadinstitute/gatk-tool-wdls:/wdls/ClipReads.wdl"
message = "ClipReads.wdl:49:8: error: cannot recursively call workflow `ClipReads`"
permalink = "https://github.com/broadinstitute/gatk-tool-wdls/blob/980883d87ee81df7925cd60dd04140e9fd01e317/wdls/ClipReads.wdl/#L49"
[[diagnostics]]
document = "broadinstitute/gatk-tool-wdls:/wdls/ClipReadsAllArgs.wdl"
message = "ClipReadsAllArgs.wdl:150:8: error: cannot recursively call workflow `ClipReads`"
permalink = "https://github.com/broadinstitute/gatk-tool-wdls/blob/980883d87ee81df7925cd60dd04140e9fd01e317/wdls/ClipReadsAllArgs.wdl/#L150"
[[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/980883d87ee81df7925cd60dd04140e9fd01e317/wdls/ClipReadsAllArgs.wdl/#L304"
[[diagnostics]]
document = "broadinstitute/gatk-tool-wdls:/wdls/CollectReadCounts.wdl"
message = "CollectReadCounts.wdl:49:8: error: cannot recursively call workflow `CollectReadCounts`"
permalink = "https://github.com/broadinstitute/gatk-tool-wdls/blob/980883d87ee81df7925cd60dd04140e9fd01e317/wdls/CollectReadCounts.wdl/#L49"
[[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/980883d87ee81df7925cd60dd04140e9fd01e317/wdls/CollectReadCounts.wdl/#L99"
[[diagnostics]]
document = "broadinstitute/gatk-tool-wdls:/wdls/CollectReadCountsAllArgs.wdl"