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Support for BAMs that lack basemods.
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@williamrowell
williamrowell committed Dec 9, 2024
1 parent 2a08c81 commit b6f702a
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Showing 7 changed files with 76 additions and 46 deletions.
18 changes: 9 additions & 9 deletions docs/family.md
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Expand Up @@ -223,15 +223,15 @@ The `Sample` struct contains sample specific data and metadata. The struct has t

| Type | Name | Description | Notes |
| ---- | ---- | ----------- | ----- |
| Array\[File\] | cpg_hap1_bed | CpG hap1 BED | |
| Array\[File\] | cpg_hap1_bed_index | | |
| Array\[File\] | cpg_hap2_bed | CpG hap2 BED | |
| Array\[File\] | cpg_hap2_bed_index | | |
| Array\[File\] | cpg_combined_bed | CpG combined BED | |
| Array\[File\] | cpg_combined_bed_index | | |
| Array\[File\] | cpg_hap1_bw | CpG hap1 BigWig | |
| Array\[File\] | cpg_hap2_bw | CpG hap2 BigWig | |
| Array\[File\] | cpg_combined_bw | CpG combined BigWig | |
| Array\[File?\] | cpg_hap1_bed | CpG hap1 BED | |
| Array\[File?\] | cpg_hap1_bed_index | | |
| Array\[File?\] | cpg_hap2_bed | CpG hap2 BED | |
| Array\[File?\] | cpg_hap2_bed_index | | |
| Array\[File?\] | cpg_combined_bed | CpG combined BED | |
| Array\[File?\] | cpg_combined_bed_index | | |
| Array\[File?\] | cpg_hap1_bw | CpG hap1 BigWig | |
| Array\[File?\] | cpg_hap2_bw | CpG hap2 BigWig | |
| Array\[File?\] | cpg_combined_bw | CpG combined BigWig | |
| Array\[String\] | stat_cpg_hap1_count | Hap1 CpG count | |
| Array\[String\] | stat_cpg_hap2_count | Hap2 CpG count | |
| Array\[String\] | stat_cpg_combined_count | Combined CpG count | |
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18 changes: 9 additions & 9 deletions docs/singleton.md
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Expand Up @@ -182,15 +182,15 @@ flowchart TD

| Type | Name | Description | Notes |
| ---- | ---- | ----------- | ----- |
| File | cpg_hap1_bed | CpG hap1 BED | |
| File | cpg_hap1_bed_index | | |
| File | cpg_hap2_bed | CpG hap2 BED | |
| File | cpg_hap2_bed_index | | |
| File | cpg_combined_bed | CpG combined BED | |
| File | cpg_combined_bed_index | | |
| File | cpg_hap1_bw | CpG hap1 BigWig | |
| File | cpg_hap2_bw | CpG hap2 BigWig | |
| File | cpg_combined_bw | CpG combined BigWig | |
| File? | cpg_hap1_bed | CpG hap1 BED | |
| File? | cpg_hap1_bed_index | | |
| File? | cpg_hap2_bed | CpG hap2 BED | |
| File? | cpg_hap2_bed_index | | |
| File? | cpg_combined_bed | CpG combined BED | |
| File? | cpg_combined_bed_index | | |
| File? | cpg_hap1_bw | CpG hap1 BigWig | |
| File? | cpg_hap2_bw | CpG hap2 BigWig | |
| File? | cpg_combined_bw | CpG combined BigWig | |
| String | stat_cpg_hap1_count | Hap1 CpG count | |
| String | stat_cpg_hap2_count | Hap2 CpG count | |
| String | stat_cpg_combined_count | Combined CpG count | |
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30 changes: 30 additions & 0 deletions wdl-ci.config.json
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Expand Up @@ -665,6 +665,36 @@
]
}
}
},
{
"inputs": {
"haplotagged_bam": "${resources_file_path}/inputs/NA19238.GRCh38.chr6_10000000_20000000.haplotagged.bam",
"haplotagged_bam_index": "${resources_file_path}/inputs/NA19238.GRCh38.chr6_10000000_20000000.haplotagged.bam.bai",
"out_prefix": "NA19238.GRCh38",
"ref_fasta": "${ref_fasta}",
"ref_index": "${ref_index}",
"runtime_attributes": "${default_runtime_attributes}"
},
"output_tests": {
"stat_hap1_cpg_count": {
"value": "0",
"test_tasks": [
"compare_string"
]
},
"stat_hap2_cpg_count": {
"value": "0",
"test_tasks": [
"compare_string"
]
},
"stat_combined_cpg_count": {
"value": "0",
"test_tasks": [
"compare_string"
]
}
}
}
]
}
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18 changes: 9 additions & 9 deletions workflows/downstream/downstream.wdl
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Expand Up @@ -198,15 +198,15 @@ workflow downstream {
String stat_sv_BND_count = sv_stats.stat_sv_BND_count

# cpg_pileup outputs
File cpg_combined_bed = cpg_pileup.combined_bed
File cpg_combined_bed_index = cpg_pileup.combined_bed_index
File cpg_hap1_bed = cpg_pileup.hap1_bed
File cpg_hap1_bed_index = cpg_pileup.hap1_bed_index
File cpg_hap2_bed = cpg_pileup.hap2_bed
File cpg_hap2_bed_index = cpg_pileup.hap2_bed_index
File cpg_combined_bw = cpg_pileup.combined_bw
File cpg_hap1_bw = cpg_pileup.hap1_bw
File cpg_hap2_bw = cpg_pileup.hap2_bw
File? cpg_combined_bed = cpg_pileup.combined_bed
File? cpg_combined_bed_index = cpg_pileup.combined_bed_index
File? cpg_hap1_bed = cpg_pileup.hap1_bed
File? cpg_hap1_bed_index = cpg_pileup.hap1_bed_index
File? cpg_hap2_bed = cpg_pileup.hap2_bed
File? cpg_hap2_bed_index = cpg_pileup.hap2_bed_index
File? cpg_combined_bw = cpg_pileup.combined_bw
File? cpg_hap1_bw = cpg_pileup.hap1_bw
File? cpg_hap2_bw = cpg_pileup.hap2_bw
String stat_hap1_cpg_count = cpg_pileup.stat_hap1_cpg_count
String stat_hap2_cpg_count = cpg_pileup.stat_hap2_cpg_count
String stat_combined_cpg_count = cpg_pileup.stat_combined_cpg_count
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18 changes: 9 additions & 9 deletions workflows/family.wdl
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Expand Up @@ -304,15 +304,15 @@ workflow humanwgs_family {
Array[String] stat_phase_block_ng50 = downstream.stat_phase_block_ng50

# cpg_pileup outputs
Array[File] cpg_combined_bed = downstream.cpg_combined_bed
Array[File] cpg_combined_bed_index = downstream.cpg_combined_bed_index
Array[File] cpg_hap1_bed = downstream.cpg_hap1_bed
Array[File] cpg_hap1_bed_index = downstream.cpg_hap1_bed_index
Array[File] cpg_hap2_bed = downstream.cpg_hap2_bed
Array[File] cpg_hap2_bed_index = downstream.cpg_hap2_bed_index
Array[File] cpg_combined_bw = downstream.cpg_combined_bw
Array[File] cpg_hap1_bw = downstream.cpg_hap1_bw
Array[File] cpg_hap2_bw = downstream.cpg_hap2_bw
Array[File?] cpg_combined_bed = downstream.cpg_combined_bed
Array[File?] cpg_combined_bed_index = downstream.cpg_combined_bed_index
Array[File?] cpg_hap1_bed = downstream.cpg_hap1_bed
Array[File?] cpg_hap1_bed_index = downstream.cpg_hap1_bed_index
Array[File?] cpg_hap2_bed = downstream.cpg_hap2_bed
Array[File?] cpg_hap2_bed_index = downstream.cpg_hap2_bed_index
Array[File?] cpg_combined_bw = downstream.cpg_combined_bw
Array[File?] cpg_hap1_bw = downstream.cpg_hap1_bw
Array[File?] cpg_hap2_bw = downstream.cpg_hap2_bw
Array[String] stat_cpg_hap1_count = downstream.stat_hap1_cpg_count
Array[String] stat_cpg_hap2_count = downstream.stat_hap2_cpg_count
Array[String] stat_cpg_combined_count = downstream.stat_combined_cpg_count
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18 changes: 9 additions & 9 deletions workflows/singleton.wdl
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Expand Up @@ -244,15 +244,15 @@ workflow humanwgs_singleton {
String stat_phase_block_ng50 = downstream.stat_phase_block_ng50

# cpg_pileup outputs
File cpg_combined_bed = downstream.cpg_combined_bed
File cpg_combined_bed_index = downstream.cpg_combined_bed_index
File cpg_hap1_bed = downstream.cpg_hap1_bed
File cpg_hap1_bed_index = downstream.cpg_hap1_bed_index
File cpg_hap2_bed = downstream.cpg_hap2_bed
File cpg_hap2_bed_index = downstream.cpg_hap2_bed_index
File cpg_combined_bw = downstream.cpg_combined_bw
File cpg_hap1_bw = downstream.cpg_hap1_bw
File cpg_hap2_bw = downstream.cpg_hap2_bw
File? cpg_combined_bed = downstream.cpg_combined_bed
File? cpg_combined_bed_index = downstream.cpg_combined_bed_index
File? cpg_hap1_bed = downstream.cpg_hap1_bed
File? cpg_hap1_bed_index = downstream.cpg_hap1_bed_index
File? cpg_hap2_bed = downstream.cpg_hap2_bed
File? cpg_hap2_bed_index = downstream.cpg_hap2_bed_index
File? cpg_combined_bw = downstream.cpg_combined_bw
File? cpg_hap1_bw = downstream.cpg_hap1_bw
File? cpg_hap2_bw = downstream.cpg_hap2_bw
String stat_cpg_hap1_count = downstream.stat_hap1_cpg_count
String stat_cpg_hap2_count = downstream.stat_hap2_cpg_count
String stat_cpg_combined_count = downstream.stat_combined_cpg_count
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2 changes: 1 addition & 1 deletion workflows/wdl-common
Submodule wdl-common updated 1 files
+17 −24 wdl/tasks/cpg_pileup.wdl

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