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williamrowellwilliamrowell
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Standardized stat names, placing aggregator function on the right (e.g. read_count, depth_mean, etc).
1 parent eeb33f5 commit db3bb48

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Lines changed: 84 additions & 71 deletions

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‎docs/bam_statistics.md‎

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@@ -24,14 +24,14 @@ A histogram of read qualities, using only records marked `prim` or `unmapped`. T
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A histogram of mapping qualities and gap-compressed identities, respectively.
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## `stat_num_reads`, `stat_read_length_mean`, `stat_read_length_median`, `stat_read_length_n50`, `stat_read_quality_mean`, `stat_read_quality_median`
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## `stat_read_count`, `stat_read_length_mean`, `stat_read_length_median`, `stat_read_length_n50`, `stat_read_quality_mean`, `stat_read_quality_median`
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Statistics computed using only records marked `prim` or `unmapped`.
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## `stat_mapped_read_count`, `stat_mapped_percent`
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Count of primary alignments, and primary alignments as a percentage of total reads.
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## `stat_mean_gap_compressed_identity`
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## `stat_gap_compressed_identity_mean`, `stat_gap_compressed_identity_median`
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Mean gap-compressed identity of primary and supplementary alignments.
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Summary of gap-compressed identity for primary and supplementary alignments.

‎docs/family.md‎

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@@ -180,17 +180,18 @@ The `Sample` struct contains sample specific data and metadata. The struct has t
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| Array\[File\] | mosdepth_depth_distribution_plot | | |
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| Array\[File\] | mapq_distribution_plot | Distribution of mapping quality per alignment | |
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| Array\[File\] | mg_distribution_plot | Distribution of gap-compressed identity score per alignment | |
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| Array\[String\] | stat_num_reads | Number of reads | |
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| Array\[String\] | stat_read_count | Number of reads | |
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| Array\[String\] | stat_read_length_mean | Mean read length | |
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| Array\[String\] | stat_read_length_median | Median read length | |
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| Array\[String\] | stat_read_length_n50 | Read length N50 | |
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| Array\[String\] | stat_read_quality_mean | Mean read quality | |
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| Array\[String\] | stat_read_quality_median | Median read quality | |
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| Array\[String\] | stat_mapped_read_count | Count of reads mapped to reference | |
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| Array\[String\] | stat_mapped_percent | Percent of reads mapped to reference | |
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| Array\[String\] | stat_mean_gap_compressed_identity | Mean gap-compressed identity | |
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| Array\[String\] | stat_mapped_read_percent | Percent of reads mapped to reference | |
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| Array\[String\] | stat_gap_compressed_identity_mean | Mean gap-compressed identity | |
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| Array\[String\] | stat_gap_compressed_identity_median | Median gap-compressed identity | |
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| Array\[String\] | inferred_sex | Inferred sex | Sex is inferred based on relative depth of chrY alignments. |
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| Array\[String\] | stat_mean_depth | Mean depth | |
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| Array\[String\] | stat_depth_mean | Mean depth | |
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### Small Variants (<50 bp)
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‎docs/singleton.md‎

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@@ -136,17 +136,18 @@ flowchart TD
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| File | mosdepth_depth_distribution_plot | | |
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| File | mapq_distribution_plot | Distribution of mapping quality per alignment | |
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| File | mg_distribution_plot | Distribution of gap-compressed identity score per alignment | |
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| String | stat_num_reads | Number of reads | |
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| String | stat_read_count | Number of reads | |
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| String | stat_read_length_mean | Mean read length | |
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| String | stat_read_length_median | Median read length | |
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| String | stat_read_length_n50 | Read length N50 | |
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| String | stat_read_quality_mean | Mean read quality | |
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| String | stat_read_quality_median | Median read quality | |
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| String | stat_mapped_read_count | Count of reads mapped to reference | |
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| String | stat_mapped_percent | Percent of reads mapped to reference | |
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| String | stat_mean_gap_compressed_identity | Mean gap-compressed identity | |
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| String | stat_mapped_read_percent | Percent of reads mapped to reference | |
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| String | stat_gap_compressed_identity_mean | Mean gap-compressed identity | |
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| String | stat_gap_compressed_identity_median | Median gap-compressed identity | |
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| String | inferred_sex | Inferred sex | Sex is inferred based on relative depth of chrY alignments. |
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| String | stat_mean_depth | Mean depth | |
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| String | stat_depth_mean | Mean depth | |
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### Small Variants (<50 bp)
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‎wdl-ci.config.json‎

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@@ -377,7 +377,7 @@
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"png_validator"
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]
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},
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"stat_num_reads": {
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"stat_read_count": {
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"value": "27398",
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"test_tasks": [
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"compare_string"
@@ -419,13 +419,19 @@
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"compare_string"
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]
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},
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"stat_mapped_percent": {
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"stat_mapped_read_percent": {
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"value": "100.0",
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"test_tasks": [
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"compare_string"
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]
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},
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"stat_mean_gap_compressed_identity": {
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"stat_gap_compressed_identity_mean": {
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"value": "99.77",
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"test_tasks": [
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"compare_string"
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]
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},
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"stat_gap_compressed_identity_median": {
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"value": "99.77",
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"test_tasks": [
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"compare_string"
@@ -1225,7 +1231,7 @@
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"png_validator"
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]
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},
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"stat_mean_depth": {
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"stat_depth_mean": {
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"value": "0.07",
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"test_tasks": [
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"compare_string"
@@ -1274,7 +1280,7 @@
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"png_validator"
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]
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},
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"stat_mean_depth": {
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"stat_depth_mean": {
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"value": "0.07",
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"test_tasks": [
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"compare_string"

‎workflows/downstream/downstream.wdl‎

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@@ -216,21 +216,22 @@ workflow downstream {
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String stat_phase_block_ng50 = hiphase.stat_phase_block_ng50
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# bam stats
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File bam_statistics = bam_stats.bam_statistics
220-
File read_length_plot = bam_stats.read_length_plot
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File? read_quality_plot = bam_stats.read_quality_plot
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File mapq_distribution_plot = bam_stats.mapq_distribution_plot
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File mg_distribution_plot = bam_stats.mg_distribution_plot
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String stat_num_reads = bam_stats.stat_num_reads
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String stat_read_length_mean = bam_stats.stat_read_length_mean
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String stat_read_length_median = bam_stats.stat_read_length_median
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String stat_read_length_n50 = bam_stats.stat_read_length_n50
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String stat_read_quality_mean = bam_stats.stat_read_quality_mean
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String stat_read_quality_median = bam_stats.stat_read_quality_median
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String stat_mapped_read_count = bam_stats.stat_mapped_read_count
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String stat_mapped_percent = bam_stats.stat_mapped_percent
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String stat_mean_gap_compressed_identity = bam_stats.stat_mean_gap_compressed_identity
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File trgt_coverage_dropouts = coverage_dropouts.dropouts
219+
File bam_statistics = bam_stats.bam_statistics
220+
File read_length_plot = bam_stats.read_length_plot
221+
File? read_quality_plot = bam_stats.read_quality_plot
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File mapq_distribution_plot = bam_stats.mapq_distribution_plot
223+
File mg_distribution_plot = bam_stats.mg_distribution_plot
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String stat_read_count = bam_stats.stat_read_count
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String stat_read_length_mean = bam_stats.stat_read_length_mean
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String stat_read_length_median = bam_stats.stat_read_length_median
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String stat_read_length_n50 = bam_stats.stat_read_length_n50
228+
String stat_read_quality_mean = bam_stats.stat_read_quality_mean
229+
String stat_read_quality_median = bam_stats.stat_read_quality_median
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String stat_mapped_read_count = bam_stats.stat_mapped_read_count
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String stat_mapped_read_percent = bam_stats.stat_mapped_read_percent
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String stat_gap_compressed_identity_mean = bam_stats.stat_gap_compressed_identity_mean
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String stat_gap_compressed_identity_median = bam_stats.stat_gap_compressed_identity_median
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File trgt_coverage_dropouts = coverage_dropouts.dropouts
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# small variant stats
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File small_variant_stats = bcftools_stats_roh_small_variants.stats

‎workflows/family.wdl‎

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Original file line numberDiff line numberDiff line change
@@ -236,16 +236,17 @@ workflow humanwgs_family {
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Map[String, Array[String]] stats = {
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'sample_id': sample_id,
239-
'num_reads': downstream.stat_num_reads,
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'read_count': downstream.stat_read_count,
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'read_length_mean': downstream.stat_read_length_mean,
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'read_length_median': downstream.stat_read_length_median,
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'read_length_n50': downstream.stat_read_length_n50,
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'read_quality_mean': downstream.stat_read_quality_mean,
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'read_quality_median': downstream.stat_read_quality_median,
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'mapped_read_count': downstream.stat_mapped_read_count,
246-
'mapped_percent': downstream.stat_mapped_percent,
247-
'mean_gap_compressed_identity': downstream.stat_mean_gap_compressed_identity,
248-
'mean_depth': upstream.stat_mean_depth,
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'mapped_read_percent': downstream.stat_mapped_read_percent,
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'gap_compressed_identity_mean': downstream.stat_gap_compressed_identity_mean,
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'gap_compressed_identity_median': downstream.stat_gap_compressed_identity_median,
249+
'depth_mean': upstream.stat_depth_mean,
249250
'inferred_sex': upstream.inferred_sex,
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'stat_phased_basepairs': downstream.stat_phased_basepairs,
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'phase_block_ng50': downstream.stat_phase_block_ng50,
@@ -284,20 +285,21 @@ workflow humanwgs_family {
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File msg_file = consolidate_stats.messages
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# bam stats
287-
Array[File] bam_statistics = downstream.bam_statistics
288-
Array[File] read_length_plot = downstream.read_length_plot
289-
Array[File?] read_quality_plot = downstream.read_quality_plot
290-
Array[File] mapq_distribution_plot = downstream.mapq_distribution_plot
291-
Array[File] mg_distribution_plot = downstream.mg_distribution_plot
292-
Array[String] stat_num_reads = downstream.stat_num_reads
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Array[String] stat_read_length_mean = downstream.stat_read_length_mean
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Array[String] stat_read_length_median = downstream.stat_read_length_median
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Array[String] stat_read_length_n50 = downstream.stat_read_length_n50
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Array[String] stat_read_quality_mean = downstream.stat_read_quality_mean
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Array[String] stat_read_quality_median = downstream.stat_read_quality_median
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Array[String] stat_mapped_read_count = downstream.stat_mapped_read_count
299-
Array[String] stat_mapped_percent = downstream.stat_mapped_percent
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Array[String] stat_mean_gap_compressed_identity = downstream.stat_mean_gap_compressed_identity
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Array[File] bam_statistics = downstream.bam_statistics
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Array[File] read_length_plot = downstream.read_length_plot
290+
Array[File?] read_quality_plot = downstream.read_quality_plot
291+
Array[File] mapq_distribution_plot = downstream.mapq_distribution_plot
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Array[File] mg_distribution_plot = downstream.mg_distribution_plot
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Array[String] stat_read_count = downstream.stat_read_count
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Array[String] stat_read_length_mean = downstream.stat_read_length_mean
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Array[String] stat_read_length_median = downstream.stat_read_length_median
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Array[String] stat_read_length_n50 = downstream.stat_read_length_n50
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Array[String] stat_read_quality_mean = downstream.stat_read_quality_mean
298+
Array[String] stat_read_quality_median = downstream.stat_read_quality_median
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Array[String] stat_mapped_read_count = downstream.stat_mapped_read_count
300+
Array[String] stat_mapped_read_percent = downstream.stat_mapped_read_percent
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Array[String] stat_gap_compressed_identity_mean = downstream.stat_gap_compressed_identity_mean
302+
Array[String] stat_gap_compressed_identity_median = downstream.stat_gap_compressed_identity_median
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# merged, haplotagged alignments
303305
Array[File] merged_haplotagged_bam = downstream.merged_haplotagged_bam
@@ -308,7 +310,7 @@ workflow humanwgs_family {
308310
Array[File] mosdepth_region_bed = upstream.mosdepth_region_bed
309311
Array[File] mosdepth_region_bed_index = upstream.mosdepth_region_bed_index
310312
Array[File] mosdepth_depth_distribution_plot = upstream.mosdepth_depth_distribution_plot
311-
Array[String] stat_mean_depth = upstream.stat_mean_depth
313+
Array[String] stat_depth_mean = upstream.stat_depth_mean
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Array[String] inferred_sex = upstream.inferred_sex
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# phasing stats

‎workflows/singleton.wdl‎

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Original file line numberDiff line numberDiff line change
@@ -186,16 +186,17 @@ workflow humanwgs_singleton {
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Map[String, Array[String]] stats = {
188188
'sample_id': [sample_id],
189-
'num_reads': [downstream.stat_num_reads],
189+
'read_count': [downstream.stat_read_count],
190190
'read_length_mean': [downstream.stat_read_length_mean],
191191
'read_length_median': [downstream.stat_read_length_median],
192192
'read_length_n50': [downstream.stat_read_length_n50],
193193
'read_quality_mean': [downstream.stat_read_quality_mean],
194194
'read_quality_median': [downstream.stat_read_quality_median],
195195
'mapped_read_count': [downstream.stat_mapped_read_count],
196-
'mapped_percent': [downstream.stat_mapped_percent],
197-
'mean_gap_compressed_identity': [downstream.stat_mean_gap_compressed_identity],
198-
'mean_depth': [upstream.stat_mean_depth],
196+
'mapped_read_percent': [downstream.stat_mapped_read_percent],
197+
'gap_compressed_identity_mean': [downstream.stat_gap_compressed_identity_mean],
198+
'gap_compressed_identity_median': [downstream.stat_gap_compressed_identity_median],
199+
'depth_mean': [upstream.stat_depth_mean],
199200
'inferred_sex': [upstream.inferred_sex],
200201
'stat_phased_basepairs': [downstream.stat_phased_basepairs],
201202
'phase_block_ng50': [downstream.stat_phase_block_ng50],
@@ -233,20 +234,21 @@ workflow humanwgs_singleton {
233234
File msg_file = consolidate_stats.messages
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235236
# bam stats
236-
File bam_statistics = downstream.bam_statistics
237-
File read_length_plot = downstream.read_length_plot
238-
File? read_quality_plot = downstream.read_quality_plot
239-
File mapq_distribution_plot = downstream.mapq_distribution_plot
240-
File mg_distribution_plot = downstream.mg_distribution_plot
241-
String stat_num_reads = downstream.stat_num_reads
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String stat_read_length_mean = downstream.stat_read_length_mean
243-
String stat_read_length_median = downstream.stat_read_length_median
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String stat_read_length_n50 = downstream.stat_read_length_n50
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String stat_read_quality_mean = downstream.stat_read_quality_mean
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String stat_read_quality_median = downstream.stat_read_quality_median
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String stat_mapped_read_count = downstream.stat_mapped_read_count
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String stat_mapped_percent = downstream.stat_mapped_percent
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String stat_mean_gap_compressed_identity = downstream.stat_mean_gap_compressed_identity
237+
File bam_statistics = downstream.bam_statistics
238+
File read_length_plot = downstream.read_length_plot
239+
File? read_quality_plot = downstream.read_quality_plot
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File mapq_distribution_plot = downstream.mapq_distribution_plot
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File mg_distribution_plot = downstream.mg_distribution_plot
242+
String stat_read_count = downstream.stat_read_count
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String stat_read_length_mean = downstream.stat_read_length_mean
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String stat_read_length_median = downstream.stat_read_length_median
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String stat_read_length_n50 = downstream.stat_read_length_n50
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String stat_read_quality_mean = downstream.stat_read_quality_mean
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String stat_read_quality_median = downstream.stat_read_quality_median
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String stat_mapped_read_count = downstream.stat_mapped_read_count
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String stat_mapped_read_percent = downstream.stat_mapped_read_percent
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String stat_gap_compressed_identity_mean = downstream.stat_gap_compressed_identity_mean
251+
String stat_gap_compressed_identity_median = downstream.stat_gap_compressed_identity_median
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# merged, haplotagged alignments
252254
File merged_haplotagged_bam = downstream.merged_haplotagged_bam
@@ -257,7 +259,7 @@ workflow humanwgs_singleton {
257259
File mosdepth_region_bed = upstream.mosdepth_region_bed
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File mosdepth_region_bed_index = upstream.mosdepth_region_bed_index
259261
File mosdepth_depth_distribution_plot = upstream.mosdepth_depth_distribution_plot
260-
String stat_mean_depth = upstream.stat_mean_depth
262+
String stat_depth_mean = upstream.stat_depth_mean
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String inferred_sex = upstream.inferred_sex
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# phasing stats

‎workflows/upstream/upstream.wdl‎

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@@ -272,7 +272,7 @@ workflow upstream {
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File mosdepth_region_bed_index = mosdepth.region_bed_index
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File mosdepth_depth_distribution_plot = mosdepth.depth_distribution_plot
274274
String inferred_sex = mosdepth.inferred_sex
275-
String stat_mean_depth = mosdepth.stat_mean_depth
275+
String stat_depth_mean = mosdepth.stat_depth_mean
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277277
# per sample sv signatures
278278
File discover_tar = sawfish_discover.discover_tar

‎workflows/wdl-common‎

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