Resolve intervals when needed (#73)

* Resolve intervals as needed * Update CHANGELOG * Bump version * Update in DOC * Mask version numbers in tests * Ensure intervals directory is mounted on docker for RTC * Add slash --------- Co-authored-by: Nicholas Wiltsie <[email protected]>
uclahs-cds · May 29, 2024 · 3ee8f38 · 3ee8f38
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -9,8 +9,13 @@ This project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.htm
 
 ## [Unreleased]
 
+---
+
+## [1.0.1] - 2024-05-29
 ### [Changed]
 - Update Nextflow configuration test workflows
+### [Fixed]
+- Resolve interval path for original given intervals to ensure the index file for intervals is found when present
 
 ---
 

diff --git a/module/base-recalibration.nf b/module/base-recalibration.nf
@@ -65,7 +65,7 @@ process run_BaseRecalibrator_GATK {
 
     script:
     all_ir_bams = indelrealigned_bams.collect{ "--input '${it}'" }.join(' ')
-    targeted_options = params.is_targeted ? "--intervals ${intervals} --interval-padding 100" : ""
+    targeted_options = params.is_targeted ? "--intervals \"\$(realpath ${intervals})\" --interval-padding 100" : ""
     """
     set -euo pipefail
     if [ ! -f ${sample_id}_recalibration_table.grp ]

diff --git a/module/indel-realignment.nf b/module/indel-realignment.nf
@@ -41,6 +41,7 @@ process run_RealignerTargetCreator_GATK {
     path(bundle_mills_and_1000g_gold_standards_vcf_gz_tbi)
     path(bundle_known_indels_vcf_gz)
     path(bundle_known_indels_vcf_gz_tbi)
+    path(original_intervals)
     tuple path(bam), path(bam_index), val(interval_id), path(interval)
 
     output:
@@ -174,6 +175,7 @@ workflow realign_indels {
         "${params.bundle_mills_and_1000g_gold_standard_indels_vcf_gz}.tbi",
         params.bundle_known_indels_vcf_gz,
         "${params.bundle_known_indels_vcf_gz}.tbi",
+        "${params.getOrDefault('intervals', null) ?: params.work_dir + '/NO_FILE.bed'}",
         input_ch_rtc
         )
 

diff --git a/module/summary-qc.nf b/module/summary-qc.nf
@@ -42,7 +42,7 @@ process run_GetPileupSummaries_GATK {
     tuple val(sample_id), path("*getpileupsummaries.table"), emit: pileupsummaries
 
     script:
-    interval_options = all_intervals.collect{ "--intervals '$it'" }.join(' ')
+    interval_options = all_intervals.collect{ "--intervals \"\$(realpath ${it})\"" }.join(' ')
     output_filename = generate_standard_filename(
         "GATK-${params.gatk_version}",
         params.dataset_id,
@@ -168,7 +168,7 @@ process run_DepthOfCoverage_GATK {
     params.is_DOC_run
 
     script:
-    interval_options = all_intervals.collect{ "--intervals '$it'" }.join(' ')
+    interval_options = all_intervals.collect{ "--intervals \"\$(realpath ${it})\"" }.join(' ')
     output_filename = generate_standard_filename(
         "GATK-${params.gatk_version}",
         params.dataset_id,

diff --git a/nextflow.config b/nextflow.config
@@ -3,5 +3,5 @@ manifest {
     name = 'recalibrate-BAM'
     author = 'Yash Patel, Nicholas Wiltsie'
     description = 'Nextflow pipeline to perform Indel Realignment and Base Quality Score Recalibration'
-    version = '1.0.0'
+    version = '1.0.1'
 }
diff --git a/test/configtest-F16.json b/test/configtest-F16.json
@@ -28,6 +28,14 @@
     "timeline.file",
     "trace.file"
   ],
+  "version_fields": [
+    "manifest.version",
+    "params.log_output_dir",
+    "params.output_dir_base",
+    "report.file",
+    "trace.file",
+    "timeline.file"
+  ],
   "expected_result": {
     "docker": {
       "all_group_ids": "$(for i in `id --real --groups`; do echo -n \"--group-add=$i \"; done)",
@@ -39,7 +47,7 @@
       "author": "Yash Patel, Nicholas Wiltsie",
       "description": "Nextflow pipeline to perform Indel Realignment and Base Quality Score Recalibration",
       "name": "recalibrate-BAM",
-      "version": "1.0.0"
+      "version": "VER.SI.ON"
     },
     "params": {
       "aligner": "BWA-MEM2-2.2.1",
@@ -74,7 +82,7 @@
       "is_DOC_run": false,
       "is_emit_original_quals": true,
       "is_targeted": false,
-      "log_output_dir": "/tmp/outputs/recalibrate-BAM-1.0.0/TWGSAMIN000001/log-recalibrate-BAM-1.0.0-19970704T165655Z",
+      "log_output_dir": "/tmp/outputs/recalibrate-BAM-VER.SI.ON/TWGSAMIN000001/log-recalibrate-BAM-VER.SI.ON-19970704T165655Z",
       "max_cpus": "16",
       "max_memory": "31 GB",
       "metapipeline_delete_input_bams": false,
@@ -85,7 +93,7 @@
       "min_cpus": "1",
       "min_memory": "1 MB",
       "output_dir": "/tmp/outputs",
-      "output_dir_base": "/tmp/outputs/recalibrate-BAM-1.0.0/TWGSAMIN000001/GATK-4.2.4.1",
+      "output_dir_base": "/tmp/outputs/recalibrate-BAM-VER.SI.ON/TWGSAMIN000001/GATK-4.2.4.1",
       "parallelize_by_chromosome": true,
       "patient_id": "TWGSAMIN000001",
       "picard_version": "2.26.10",
@@ -414,15 +422,15 @@
     },
     "report": {
       "enabled": true,
-      "file": "/tmp/outputs/recalibrate-BAM-1.0.0/TWGSAMIN000001/log-recalibrate-BAM-1.0.0-19970704T165655Z/nextflow-log/report.html"
+      "file": "/tmp/outputs/recalibrate-BAM-VER.SI.ON/TWGSAMIN000001/log-recalibrate-BAM-VER.SI.ON-19970704T165655Z/nextflow-log/report.html"
     },
     "timeline": {
       "enabled": true,
-      "file": "/tmp/outputs/recalibrate-BAM-1.0.0/TWGSAMIN000001/log-recalibrate-BAM-1.0.0-19970704T165655Z/nextflow-log/timeline.html"
+      "file": "/tmp/outputs/recalibrate-BAM-VER.SI.ON/TWGSAMIN000001/log-recalibrate-BAM-VER.SI.ON-19970704T165655Z/nextflow-log/timeline.html"
     },
     "trace": {
       "enabled": true,
-      "file": "/tmp/outputs/recalibrate-BAM-1.0.0/TWGSAMIN000001/log-recalibrate-BAM-1.0.0-19970704T165655Z/nextflow-log/trace.txt"
+      "file": "/tmp/outputs/recalibrate-BAM-VER.SI.ON/TWGSAMIN000001/log-recalibrate-BAM-VER.SI.ON-19970704T165655Z/nextflow-log/trace.txt"
     },
     "workDir": "/scratch/851543"
   }

diff --git a/test/configtest-F32.json b/test/configtest-F32.json
@@ -28,6 +28,14 @@
     "timeline.file",
     "trace.file"
   ],
+  "version_fields": [
+    "manifest.version",
+    "params.log_output_dir",
+    "params.output_dir_base",
+    "report.file",
+    "trace.file",
+    "timeline.file"
+  ],
   "expected_result": {
     "docker": {
       "all_group_ids": "$(for i in `id --real --groups`; do echo -n \"--group-add=$i \"; done)",
@@ -39,7 +47,7 @@
       "author": "Yash Patel, Nicholas Wiltsie",
       "description": "Nextflow pipeline to perform Indel Realignment and Base Quality Score Recalibration",
       "name": "recalibrate-BAM",
-      "version": "1.0.0"
+      "version": "VER.SI.ON"
     },
     "params": {
       "aligner": "BWA-MEM2-2.2.1",
@@ -74,7 +82,7 @@
       "is_DOC_run": false,
       "is_emit_original_quals": true,
       "is_targeted": false,
-      "log_output_dir": "/tmp/outputs/recalibrate-BAM-1.0.0/TWGSAMIN000001/log-recalibrate-BAM-1.0.0-19970704T165655Z",
+      "log_output_dir": "/tmp/outputs/recalibrate-BAM-VER.SI.ON/TWGSAMIN000001/log-recalibrate-BAM-VER.SI.ON-19970704T165655Z",
       "max_cpus": "32",
       "max_memory": "64 GB",
       "metapipeline_delete_input_bams": false,
@@ -85,7 +93,7 @@
       "min_cpus": "1",
       "min_memory": "1 MB",
       "output_dir": "/tmp/outputs",
-      "output_dir_base": "/tmp/outputs/recalibrate-BAM-1.0.0/TWGSAMIN000001/GATK-4.2.4.1",
+      "output_dir_base": "/tmp/outputs/recalibrate-BAM-VER.SI.ON/TWGSAMIN000001/GATK-4.2.4.1",
       "parallelize_by_chromosome": true,
       "patient_id": "TWGSAMIN000001",
       "picard_version": "2.26.10",
@@ -414,15 +422,15 @@
     },
     "report": {
       "enabled": true,
-      "file": "/tmp/outputs/recalibrate-BAM-1.0.0/TWGSAMIN000001/log-recalibrate-BAM-1.0.0-19970704T165655Z/nextflow-log/report.html"
+      "file": "/tmp/outputs/recalibrate-BAM-VER.SI.ON/TWGSAMIN000001/log-recalibrate-BAM-VER.SI.ON-19970704T165655Z/nextflow-log/report.html"
     },
     "timeline": {
       "enabled": true,
-      "file": "/tmp/outputs/recalibrate-BAM-1.0.0/TWGSAMIN000001/log-recalibrate-BAM-1.0.0-19970704T165655Z/nextflow-log/timeline.html"
+      "file": "/tmp/outputs/recalibrate-BAM-VER.SI.ON/TWGSAMIN000001/log-recalibrate-BAM-VER.SI.ON-19970704T165655Z/nextflow-log/timeline.html"
     },
     "trace": {
       "enabled": true,
-      "file": "/tmp/outputs/recalibrate-BAM-1.0.0/TWGSAMIN000001/log-recalibrate-BAM-1.0.0-19970704T165655Z/nextflow-log/trace.txt"
+      "file": "/tmp/outputs/recalibrate-BAM-VER.SI.ON/TWGSAMIN000001/log-recalibrate-BAM-VER.SI.ON-19970704T165655Z/nextflow-log/trace.txt"
     },
     "workDir": "/scratch/851543"
   }