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Resolve intervals when needed #73

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merged 8 commits into from
May 29, 2024
Merged

Resolve intervals when needed #73

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739ec89
Resolve intervals as needed
yashpatel6 May 28, 2024
04e6f81
Update CHANGELOG
yashpatel6 May 29, 2024
8cf396d
Bump version
yashpatel6 May 29, 2024
a2212ed
Update in DOC
yashpatel6 May 29, 2024
e62f762
Mask version numbers in tests
nwiltsie May 29, 2024
fdf4731
Ensure intervals directory is mounted on docker for RTC
yashpatel6 May 29, 2024
05b2763
Merge branch 'yashpatel-resolve-intervals' of github.com:uclahs-cds/p…
yashpatel6 May 29, 2024
1001624
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yashpatel6 May 29, 2024
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5 changes: 5 additions & 0 deletions CHANGELOG.md
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Expand Up @@ -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

---

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2 changes: 1 addition & 1 deletion module/base-recalibration.nf
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Expand Up @@ -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 ]
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4 changes: 2 additions & 2 deletions module/summary-qc.nf
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Expand Up @@ -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,
Expand Down Expand Up @@ -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,
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2 changes: 1 addition & 1 deletion nextflow.config
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Expand Up @@ -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'
}
20 changes: 14 additions & 6 deletions test/configtest-F16.json
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Expand Up @@ -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)",
Expand All @@ -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",
Expand Down Expand Up @@ -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,
Expand All @@ -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",
Expand Down Expand Up @@ -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"
}
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20 changes: 14 additions & 6 deletions test/configtest-F32.json
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Original file line number Diff line number Diff line change
Expand Up @@ -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)",
Expand All @@ -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",
Expand Down Expand Up @@ -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,
Expand All @@ -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",
Expand Down Expand Up @@ -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"
}
Expand Down