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Next minor release. #174

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Next minor release. #174

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4f8d071
Support for BAMs that lack basemods.
williamrowell Dec 9, 2024
85472e8
update wdl-ci config file after successful tests
github-actions[bot] Dec 9, 2024
342d259
Support input without rq values.
williamrowell Dec 9, 2024
8445aed
update wdl-ci config file after successful tests
github-actions[bot] Dec 10, 2024
ecdbf3e
Added merge_bam_stats test for sample with no rq.
williamrowell Dec 10, 2024
381313b
update wdl-ci config file after successful tests
github-actions[bot] Dec 10, 2024
71a1115
Updated to TRGT v1.4.1.
williamrowell Nov 27, 2024
a0504ae
Address trgt OOM errors when using catalogs with very low complexity …
williamrowell Dec 13, 2024
b7934ed
update wdl-ci config file after successful tests
github-actions[bot] Dec 17, 2024
c3734ab
Merge pull request #173 from PacificBiosciences/feature/trgt-v1.4.1
williamrowell Dec 17, 2024
108657f
Update to pbmm2 v1.16.99 prerelease.
williamrowell Dec 18, 2024
d959399
update wdl-ci config file after successful tests
github-actions[bot] Dec 18, 2024
79e2640
Merge pull request #177 from PacificBiosciences/fix/pbmm2-1.16.99
williamrowell Dec 20, 2024
a6a0565
Filter `NO_READS` no-call lines from StarPhase input to PharmCAT.
williamrowell Dec 18, 2024
0e6292a
update wdl-ci config file after successful tests
github-actions[bot] Dec 18, 2024
21ab0ef
Only attempt to run PharmCAT if at least one PharmCAT region has dept…
williamrowell Dec 18, 2024
d291a4d
update wdl-ci config file after successful tests
github-actions[bot] Dec 18, 2024
8e62d96
Added test for exclusion of NO_READS.
williamrowell Dec 18, 2024
1b76849
update wdl-ci config file after successful tests
github-actions[bot] Dec 18, 2024
34466b0
update wdl-ci config file after successful tests
github-actions[bot] Dec 18, 2024
9c55fc5
Merge pull request #176 from PacificBiosciences/fix/remove_starphase_…
williamrowell Dec 20, 2024
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20 changes: 10 additions & 10 deletions docs/family.md
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Original file line number Diff line number Diff line change
Expand Up @@ -119,7 +119,7 @@ The `Sample` struct contains sample specific data and metadata. The struct has t
| File | stats_file | Table of summary statistics | |
| Array\[File\] | bam_stats | BAM stats | Per-read length and read-quality |
| Array\[File\] | read_length_plot | Read length plot | |
| Array\[File\] | read_quality_plot | Read quality plot | |
| Array\[File?\] | read_quality_plot | Read quality plot | |
| Array\[File\] | merged_haplotagged_bam | Merged, haplotagged alignments | Includes unmapped reads |
| Array\[File\] | merged_haplotagged_bam_index | | |
| Array\[File\] | mosdepth_summary | Summary of aligned read depth. | |
Expand Down 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 | |
Expand Down
20 changes: 10 additions & 10 deletions docs/singleton.md
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Expand Up @@ -84,7 +84,7 @@ flowchart TD
| File | stats_file | Table of summary statistics | |
| File | bam_stats | BAM stats | Per-read length and read-quality |
| File | read_length_plot | Read length plot | |
| File | read_quality_plot | Read quality plot | |
| File? | read_quality_plot | Read quality plot | |
| File | merged_haplotagged_bam | Merged, haplotagged alignments | Includes unmapped reads |
| File | merged_haplotagged_bam_index | | |
| File | mosdepth_summary | Summary of aligned read depth. | |
Expand Down 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 | |
Expand Down
122 changes: 119 additions & 3 deletions wdl-ci.config.json
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Original file line number Diff line number Diff line change
Expand Up @@ -586,7 +586,7 @@
"tasks": {
"cpg_pileup": {
"key": "cpg_pileup",
"digest": "noq7e5yf5h6s2sf7lzolbgigqec4izmg",
"digest": "km7kr546iovkhccy3yb2ovvvdmmnmet7",
"tests": [
{
"inputs": {
Expand Down 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": "${default_runtime_attributes}"
},
"output_tests": {
"stat_hap1_cpg_count": {
"value": "0",
"test_tasks": [
"compare_string"
]
},
"stat_hap2_cpg_count": {
"value": "0",
"test_tasks": [
"compare_string"
]
},
"stat_combined_cpg_count": {
"value": "0",
"test_tasks": [
"compare_string"
]
}
}
}
]
}
Expand Down Expand Up @@ -934,7 +964,7 @@
"tasks": {
"merge_bam_stats": {
"key": "merge_bam_stats",
"digest": "k2zoxoqmson4rr7meogbb675w3bnj2gt",
"digest": "mjd6zpbxtabbulmq3kwhcx4cnubxaf74",
"tests": [
{
"inputs": {
Expand Down Expand Up @@ -1068,6 +1098,64 @@
]
}
}
},
{
"inputs": {
"sample_id": "HG002",
"bam_stats": [
"${resources_file_path}/pbmm2_align_wgs/vega_10k_no_rq/HG002.vega_10k.no_rq.hifi_reads.read_length_and_quality.tsv.gz"
],
"runtime_attributes": "${default_runtime_attributes}"
},
"output_tests": {
"read_length_and_quality": {
"value": "${resources_file_path}/merge_bam_stats/no_rq/HG002.read_length_and_quality.tsv.gz",
"test_tasks": [
"compare_file_basename",
"check_tab_delimited",
"count_columns",
"check_gzip"
]
},
"read_length_plot": {
"value": "${resources_file_path}/merge_bam_stats/no_rq/HG002.read_length_histogram.png",
"test_tasks": [
"calculate_md5sum",
"compare_file_basename",
"png_validator"
]
},
"stat_num_reads": {
"value": "10000",
"test_tasks": [
"compare_string"
]
},
"stat_read_length_mean": {
"value": "21837.4",
"test_tasks": [
"compare_string"
]
},
"stat_read_length_median": {
"value": "21385.0",
"test_tasks": [
"compare_string"
]
},
"stat_read_quality_mean": {
"value": "nan",
"test_tasks": [
"compare_string"
]
},
"stat_read_quality_median": {
"value": "nan",
"test_tasks": [
"compare_string"
]
}
}
}
]
}
Expand Down Expand Up @@ -1238,7 +1326,7 @@
"tasks": {
"pbmm2_align_wgs": {
"key": "pbmm2_align_wgs",
"digest": "r2mrlrcc34hmpeetxabc7ujwfb2zzykq",
"digest": "jnyotwps3swl7ulnqunr5ktstoxdbvs3",
"tests": [
{
"inputs": {
Expand Down Expand Up @@ -1352,6 +1440,34 @@
]
}
}
},
{
"inputs": {
"sample_id": "HG002",
"bam": "${resources_file_path}/inputs/vega_10k.no_rq.hifi_reads.bam",
"ref_fasta": "${ref_fasta}",
"ref_index": "${ref_index}",
"ref_name": "${ref_name}",
"runtime_attributes": "${default_runtime_attributes}"
},
"output_tests": {
"aligned_bam": {
"value": "${resources_file_path}/pbmm2_align_wgs/vega_10k_no_rq/HG002.vega_10k.no_rq.hifi_reads.GRCh38.aligned.bam",
"test_tasks": [
"compare_file_basename",
"samtools_quickcheck"
]
},
"bam_stats": {
"value": "${resources_file_path}/pbmm2_align_wgs/vega_10k_no_rq/HG002.vega_10k.no_rq.hifi_reads.read_length_and_quality.tsv.gz",
"test_tasks": [
"compare_file_basename",
"check_tab_delimited",
"count_columns",
"check_gzip"
]
}
}
}
]
}
Expand Down
18 changes: 9 additions & 9 deletions workflows/downstream/downstream.wdl
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Original file line number Diff line number Diff line change
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
Expand Down
20 changes: 10 additions & 10 deletions workflows/family.wdl
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Original file line number Diff line number Diff line change
Expand Up @@ -273,7 +273,7 @@ workflow humanwgs_family {
# bam stats
Array[File] bam_stats = upstream.read_length_and_quality
Array[File] read_length_plot = upstream.read_length_plot
Array[File] read_quality_plot = upstream.read_quality_plot
Array[File?] read_quality_plot = upstream.read_quality_plot
Array[String] stat_num_reads = upstream.stat_num_reads
Array[String] stat_read_length_mean = upstream.stat_read_length_mean
Array[String] stat_read_length_median = upstream.stat_read_length_median
Expand Down 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
Expand Down
20 changes: 10 additions & 10 deletions workflows/singleton.wdl
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Original file line number Diff line number Diff line change
Expand Up @@ -213,7 +213,7 @@ workflow humanwgs_singleton {
# bam stats
File bam_stats = upstream.read_length_and_quality
File read_length_plot = upstream.read_length_plot
File read_quality_plot = upstream.read_quality_plot
File? read_quality_plot = upstream.read_quality_plot
String stat_num_reads = upstream.stat_num_reads
String stat_read_length_mean = upstream.stat_read_length_mean
String stat_read_length_median = upstream.stat_read_length_median
Expand Down 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
Expand Down
2 changes: 1 addition & 1 deletion workflows/upstream/upstream.wdl
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Original file line number Diff line number Diff line change
Expand Up @@ -219,7 +219,7 @@ workflow upstream {
# bam stats
File read_length_and_quality = merge_bam_stats.read_length_and_quality
File read_length_plot = merge_bam_stats.read_length_plot
File read_quality_plot = merge_bam_stats.read_quality_plot
File? read_quality_plot = merge_bam_stats.read_quality_plot
String stat_num_reads = merge_bam_stats.stat_num_reads
String stat_read_length_mean = merge_bam_stats.stat_read_length_mean
String stat_read_length_median = merge_bam_stats.stat_read_length_median
Expand Down
2 changes: 1 addition & 1 deletion workflows/wdl-common
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Submodule wdl-common updated 3 files
+22 −29 wdl/tasks/cpg_pileup.wdl
+25 −24 wdl/tasks/merge_bam_stats.wdl
+8 −5 wdl/tasks/pbmm2.wdl