From 599e8aa9a9d2416591f7f121fb0b7108e8cc2414 Mon Sep 17 00:00:00 2001 From: William Rowell Date: Mon, 9 Dec 2024 12:44:56 -0800 Subject: [PATCH] Support for BAMs that lack basemods. --- docs/family.md | 18 ++++++++--------- docs/singleton.md | 18 ++++++++--------- wdl-ci.config.json | 30 +++++++++++++++++++++++++++++ workflows/downstream/downstream.wdl | 18 ++++++++--------- workflows/family.wdl | 18 ++++++++--------- workflows/singleton.wdl | 18 ++++++++--------- workflows/wdl-common | 2 +- 7 files changed, 76 insertions(+), 46 deletions(-) diff --git a/docs/family.md b/docs/family.md index 273f9e84..d334c9ad 100644 --- a/docs/family.md +++ b/docs/family.md @@ -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 | | diff --git a/docs/singleton.md b/docs/singleton.md index 6878ff97..7f571fc0 100644 --- a/docs/singleton.md +++ b/docs/singleton.md @@ -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 | | diff --git a/wdl-ci.config.json b/wdl-ci.config.json index adc43376..91fd4d1d 100644 --- a/wdl-ci.config.json +++ b/wdl-ci.config.json @@ -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" + ] + } + } } ] } diff --git a/workflows/downstream/downstream.wdl b/workflows/downstream/downstream.wdl index 031ca870..70b6aeb4 100644 --- a/workflows/downstream/downstream.wdl +++ b/workflows/downstream/downstream.wdl @@ -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 diff --git a/workflows/family.wdl b/workflows/family.wdl index 7c86be9d..7fb3ef0a 100644 --- a/workflows/family.wdl +++ b/workflows/family.wdl @@ -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 diff --git a/workflows/singleton.wdl b/workflows/singleton.wdl index ae3cdb83..170b8ff5 100644 --- a/workflows/singleton.wdl +++ b/workflows/singleton.wdl @@ -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 diff --git a/workflows/wdl-common b/workflows/wdl-common index 60e9eb5c..931dca92 160000 --- a/workflows/wdl-common +++ b/workflows/wdl-common @@ -1 +1 @@ -Subproject commit 60e9eb5c798b6d35dc26fe8561423cf1dab193bd +Subproject commit 931dca928596c19707ede000608435ab90597ee8