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update filenames #60

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merged 13 commits into from
Mar 23, 2024
Merged

update filenames #60

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a114f3c
use function to generate filenames
alkaZeltser Mar 20, 2024
847aa17
update test cases
alkaZeltser Mar 20, 2024
c654349
typo fixes
alkaZeltser Mar 21, 2024
8f08318
update HsMetrics extension
alkaZeltser Mar 21, 2024
ba73a5c
update changelog
alkaZeltser Mar 22, 2024
08a9d29
update readme
alkaZeltser Mar 22, 2024
6e046d8
update diagram labels
alkaZeltser Mar 22, 2024
ebec90b
remove old drawio diagram
alkaZeltser Mar 22, 2024
f20c651
Update SVG images for PlantUML diagrams
alkaZeltser Mar 22, 2024
cfb56ed
fix asterisks in puml labels
alkaZeltser Mar 22, 2024
fc56327
Merge branch 'nzeltser-update-filenames' of github.com:uclahs-cds/pip…
alkaZeltser Mar 22, 2024
e5185f3
Update SVG images for PlantUML diagrams
alkaZeltser Mar 22, 2024
571eb2a
Empty commit
yashpatel6 Mar 22, 2024
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13 changes: 12 additions & 1 deletion module/depth_to_bed.nf
View file
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Original file line number Diff line number Diff line change
@@ -1,3 +1,4 @@
include { generate_standard_filename } from '../external/pipeline-Nextflow-module/modules/common/generate_standardized_filename/main.nf'
/*
* Module/process description here
*
Expand Down Expand Up @@ -32,12 +33,22 @@ process convert_depth_to_bed {
path ".command.*"

script:

output_filename = generate_standard_filename(
"SAMtools-${params.samtools_version}",
params.dataset_id,
params.sample_id,
[
'additional_information': "${tag}-depth-per-base.bed"
]
)

"""
set -euo pipefail

cat ${input_tsv} | \
awk 'BEGIN {OFS="\t"} {chr = \$1; start=\$2-1; stop=\$2; depth=\$3; print chr,start,stop,depth}' \
| sort -k1,1 -k2,2n \
> ${params.sample_id}.${tag}_depth-per-base.bed
> ${output_filename}
"""
}
38 changes: 34 additions & 4 deletions module/filter_off_target_depth.nf
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Original file line number Diff line number Diff line change
@@ -1,4 +1,4 @@

include { generate_standard_filename } from '../external/pipeline-Nextflow-module/modules/common/generate_standardized_filename/main.nf'
/*
* Filter for sites with read depth above a minimum threshold.
* Important for excluding near-target regions from off-target calculations.
Expand Down Expand Up @@ -28,14 +28,24 @@ process run_depth_filter {
path ".command.*"

script:

output_filename = generate_standard_filename(
"SAMtools-${params.samtools_version}",
params.dataset_id,
params.sample_id,
[
'additional_information': "depth-filtered.bed"
]
)

"""
set -euo pipefail

awk \
-v min_depth="${params.min_read_depth}" \
'\$4 >= min_depth' \
${input} \
> ${params.sample_id}.depth-filtered.bed
> ${output_filename}
"""
}

Expand Down Expand Up @@ -73,6 +83,16 @@ process run_slop_BEDtools {
path ".command.*"

script:

output_filename = generate_standard_filename(
"BEDtools-${params.bedtools_version}",
params.dataset_id,
params.sample_id,
[
'additional_information': "${tag}_slop-${slop}.bed"
]
)

"""
set -euo pipefail

Expand All @@ -81,7 +101,7 @@ process run_slop_BEDtools {
-i ${target_bed} \
-g ${genome_sizes} \
-b ${slop} \
> ${params.sample_id}.${tag}_slop-${slop}.bed
> ${output_filename}
"""
}

Expand Down Expand Up @@ -113,6 +133,16 @@ process run_intersect_BEDtools {
path ".command.*"

script:

output_filename = generate_standard_filename(
"BEDtools-${params.bedtools_version}",
params.dataset_id,
params.sample_id,
[
'additional_information': "off-target-dbSNP_depth-per-base.bed"
]
)

"""
set -euo pipefail

Expand All @@ -121,6 +151,6 @@ process run_intersect_BEDtools {
-a ${off_target_bed} \
-b ${target_bed} \
-v \
> ${params.sample_id}.off-target-dbSNP_depth-per-base.bed
> ${output_filename}
"""
}
11 changes: 10 additions & 1 deletion module/get_depth_samtools.nf
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Original file line number Diff line number Diff line change
@@ -1,3 +1,4 @@
include { generate_standard_filename } from '../external/pipeline-Nextflow-module/modules/common/generate_standardized_filename/main.nf'
/*
* Module/process description here
*
Expand Down Expand Up @@ -28,6 +29,14 @@ process run_depth_SAMtools {
path ".command.*"

script:
output_filename = generate_standard_filename(
"SAMtools-${params.samtools_version}",
params.dataset_id,
params.sample_id,
[
'additional_information': "${tag}-depth-per-base.tsv"
]
)
"""
set -euo pipefail

Expand All @@ -38,7 +47,7 @@ process run_depth_SAMtools {
-aa \
--min-BQ ${params.min_base_quality} \
--min-MQ ${params.min_mapping_quality} \
-o ${params.sample_id}.${tag}.depth_per_base.tsv \
-o ${output_filename} \
${params.samtools_depth_extra_args}
"""
}
13 changes: 12 additions & 1 deletion module/merge_bedfiles_bedtools.nf
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Original file line number Diff line number Diff line change
@@ -1,3 +1,4 @@
include { generate_standard_filename } from '../external/pipeline-Nextflow-module/modules/common/generate_standardized_filename/main.nf'
/*
* Module/process description here
*
Expand Down Expand Up @@ -26,13 +27,23 @@ process merge_bedfiles_BEDtools {
path ".command.*"

script:

output_filename = generate_standard_filename(
"BEDtools-${params.bedtools_version}",
params.dataset_id,
params.sample_id,
[
'additional_information': "target-with-enriched-off-target-intervals.bed"
]
)

"""
set -euo pipefail

cat ${target_bed} ${off_target_bed} | \
sort -k1,1 -k2,2n | \
awk '{OFS = "\t"}{print \$1, \$2, \$3}' | \
bedtools merge \
> ${params.sample_id}.target_with_enriched_off-target_intervals.bed
> ${output_filename}
"""
}
13 changes: 12 additions & 1 deletion module/merge_intervals_bedtools.nf
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Original file line number Diff line number Diff line change
@@ -1,3 +1,4 @@
include { generate_standard_filename } from '../external/pipeline-Nextflow-module/modules/common/generate_standardized_filename/main.nf'
/*
* Module/process description here
*
Expand Down Expand Up @@ -25,6 +26,16 @@ process run_merge_BEDtools {
path ".command.*"

script:

output_filename = generate_standard_filename(
"BEDtools-${params.bedtools_version}",
params.dataset_id,
params.sample_id,
[
'additional_information': "collapsed-coverage.bed"
]
)

"""
set -euo pipefail

Expand All @@ -33,6 +44,6 @@ process run_merge_BEDtools {
-i ${input_depth_bed} \
-c 4 \
-o ${params.merge_operation} \
> ${params.sample_id}.collapsed_coverage.bed
> ${output_filename}
"""
}
27 changes: 25 additions & 2 deletions module/run_HS_metrics.nf
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Original file line number Diff line number Diff line change
@@ -1,3 +1,4 @@
include { generate_standard_filename } from '../external/pipeline-Nextflow-module/modules/common/generate_standardized_filename/main.nf'
/*
* Module/process description here
*
Expand Down Expand Up @@ -34,14 +35,26 @@ process run_BedToIntervalList_picard {
path ".command.*"

script:

output_filename_base = generate_standard_filename(
"Picard-${params.picard_version}",
params.dataset_id,
params.sample_id,
[
'additional_information': "${tag}"
]
)

output_filename = "${output_filename_base}.interval_list"

"""
set -euo pipefail

java \"-Xmx${(task.memory - params.gatk_command_mem_diff).getMega()}m\" \
-jar /usr/local/share/picard-slim-${params.picard_version}-0/picard.jar \
BedToIntervalList \
--INPUT $input_bed \
--OUTPUT ${params.sample_id}.${tag}.interval_list \
--OUTPUT ${output_filename} \
--SEQUENCE_DICTIONARY $reference_dict \
--SORT false
"""
Expand Down Expand Up @@ -70,6 +83,16 @@ process run_CollectHsMetrics_picard {
path ".command.*"

script:

output_filename = generate_standard_filename(
"Picard-${params.picard_version}",
params.dataset_id,
params.sample_id,
[
'additional_information': "HsMetrics.txt"
]
)

"""
set -euo pipefail

Expand All @@ -79,7 +102,7 @@ process run_CollectHsMetrics_picard {
--BAIT_INTERVALS $bait_interval_list \
--INPUT $input_bam \
--TARGET_INTERVALS $target_interval_list \
--OUTPUT ${params.sample_id}.HsMetrics.txt \
--OUTPUT ${output_filename} \
--COVERAGE_CAP ${params.coverage_cap} \
${params.picard_CollectHsMetrics_extra_args} \
--NEAR_DISTANCE ${params.near_distance} \
Expand Down
15 changes: 3 additions & 12 deletions nftest.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -12,21 +12,12 @@ cases:
skip: false
verbose: true
asserts:
- actual: calculate-targeted-coverage-*/TWGSAMIN000001-T002-S02-F/SAMtools-*/output/TWGSAMIN000001-T002-S02-F.collapsed_coverage.bed
- actual: calculate-targeted-coverage-*/TWGSAMIN000001-T002-S02-F/SAMtools-*/output/BEDtools-*_TWGSAMIN000001_TWGSAMIN000001-T002-S02-F_collapsed-coverage.bed
expect: /hot/software/pipeline/pipeline-calculate-targeted-coverage/Nextflow/development/output/TWGSAMIN000001-T002-S02-F.collapsed_coverage.bed
method: md5
- actual: calculate-targeted-coverage-*/TWGSAMIN000001-T002-S02-F/SAMtools-*/output/TWGSAMIN000001-T002-S02-F.collapsed_coverage.bed.sha512
expect: /hot/software/pipeline/pipeline-calculate-targeted-coverage/Nextflow/development/output/TWGSAMIN000001-T002-S02-F.collapsed_coverage.bed.sha512
method: md5
- actual: calculate-targeted-coverage-*/TWGSAMIN000001-T002-S02-F/SAMtools-*/output/TWGSAMIN000001-T002-S02-F.off-target-dbSNP_depth-per-base.bed
- actual: calculate-targeted-coverage-*/TWGSAMIN000001-T002-S02-F/SAMtools-*/output/BEDtools-*_TWGSAMIN000001_TWGSAMIN000001-T002-S02-F_off-target-dbSNP-depth-per-base.bed
expect: /hot/software/pipeline/pipeline-calculate-targeted-coverage/Nextflow/development/output/TWGSAMIN000001-T002-S02-F.off-target-dbSNP_depth-per-base.bed
method: md5
- actual: calculate-targeted-coverage-*/TWGSAMIN000001-T002-S02-F/SAMtools-*/output/TWGSAMIN000001-T002-S02-F.off-target-dbSNP_depth-per-base.bed.sha512
expect: /hot/software/pipeline/pipeline-calculate-targeted-coverage/Nextflow/development/output/TWGSAMIN000001-T002-S02-F.off-target-dbSNP_depth-per-base.bed.sha512
method: md5
- actual: calculate-targeted-coverage-*/TWGSAMIN000001-T002-S02-F/SAMtools-*/output/TWGSAMIN000001-T002-S02-F.target_with_enriched_off-target_intervals.bed
- actual: calculate-targeted-coverage-*/TWGSAMIN000001-T002-S02-F/SAMtools-*/output/BEDtools-*_TWGSAMIN000001_TWGSAMIN000001-T002-S02-F_target-with-enriched-off-target-intervals.bed
expect: /hot/software/pipeline/pipeline-calculate-targeted-coverage/Nextflow/development/output/TWGSAMIN000001-T002-S02-F.target_with_enriched_off-target_intervals.bed
method: md5
- actual: calculate-targeted-coverage-*/TWGSAMIN000001-T002-S02-F/SAMtools-*/output/TWGSAMIN000001-T002-S02-F.target_with_enriched_off-target_intervals.bed.sha512
expect: /hot/software/pipeline/pipeline-calculate-targeted-coverage/Nextflow/development/output/TWGSAMIN000001-T002-S02-F.target_with_enriched_off-target_intervals.bed.sha512
method: md5
2 changes: 1 addition & 1 deletion test/configtest-F16.json
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Original file line number Diff line number Diff line change
@@ -1,450 +1,450 @@
{
"nextflow_version": "23.10.0",
"config": [
"test/nftest.config"
],
"params_file": "test/single.yaml",
"cpus": 16,
"memory_gb": 31,
"nf_params": {
"output_dir": "/tmp/nf-config-test-outputs"

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<     "nextflow_version": "23.10.0",
<     "config": [
<         "test/nftest.config"
<     ],
<     "params_file": "test/single.yaml",
<     "cpus": 16,
<     "memory_gb": 31,
<     "nf_params": {
<         "output_dir": "/tmp/nf-config-test-outputs"
---
>   "nextflow_version": "23.10.0",
>   "config": [
>     "test/nftest.config"
>   ],
>   "params_file": "test/single.yaml",
>   "cpus": 16,
>   "memory_gb": 31,
>   "nf_params": {
>     "output_dir": "/tmp/nf-config-test-outputs"
>   },
>   "envvars": {
>     "SLURM_JOB_ID": "4674821"
>   },
>   "mocks": {
>     "check_path": ""
>   },
>   "dated_fields": [
>     "params.log_output_dir",
>     "report.file",
>     "timeline.file",
>     "trace.file",
>     "params.date"
>   ],
>   "expected_result": {
>     "docker": {
>       "all_group_ids": "$(for i in `id --real --groups`; do echo -n \"--group-add=$i \"; done)",
>       "enabled": true,
>       "runOptions": "-u $(id -u):$(id -g) $(for i in `id --real --groups`; do echo -n \"--group-add=$i \"; done)",
>       "uid_and_gid": "-u $(id -u):$(id -g)"
},
"envvars": {
"SLURM_JOB_ID": "4674821"

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<     "envvars": {
<         "SLURM_JOB_ID": "4674821"
---
>     "manifest": {
>       "author": "Nicole Zeltser",
>       "description": "Nextflow pipeline for calculating read-depth related statistics for targeted sequencing experiments",
>       "name": "calculate-targeted-coverage",
>       "version": "1.0.0-rc.2"
},
"mocks": {
"check_path": ""

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<     "mocks": {
<         "check_path": ""
---
>     "params": {
>       "bait_bed": "",
>       "bait_interval_list": "",
>       "bedr_version": "1.1.0",
>       "bedtools_version": "2.29.2",
>       "blcds_registered_dataset": false,
>       "collect_metrics": true,
>       "coverage_cap": "3000",
>       "dataset_id": "TWGSAMIN000001",
>       "dataset_registry_prefix": "/hot/data",
>       "date": "19970704T165655Z",
>       "dbSNP_slop": "150",
>       "docker_container_registry": "ghcr.io/uclahs-cds",
>       "docker_image_bedops": "ghcr.io/uclahs-cds/bedr:1.1.0",
>       "docker_image_bedtools": "ghcr.io/uclahs-cds/bedtools:2.29.2",
>       "docker_image_picard": "ghcr.io/uclahs-cds/picard:3.0.0",
>       "docker_image_samtools": "ghcr.io/uclahs-cds/samtools:1.16.1",
>       "docker_image_validate": "ghcr.io/uclahs-cds/pipeval:4.0.0-rc.2",
>       "gatk_command_mem_diff": "2 GB",
>       "genome_sizes": "/hot/ref/reference/GRCh38-BI-20160721/Homo_sapiens_assembly38.fasta.fai",
>       "input": {
>         "bam": "/hot/resource/SMC-HET/tumours/A-mini/bams/n1/output/S2.T-n1.bam"
>       },
>       "log_output_dir": "/tmp/nf-config-test-outputs/calculate-targeted-coverage-1.0.0-rc.2/TWGSAMIN000001-T002-S02-F/log-calculate-targeted-coverage-1.0.0-rc.2-19970704T165655Z",
>       "max_cpus": "16",
>       "max_memory": "31 GB",
>       "merge_operation": "collapse",
>       "min_base_quality": "20",
>       "min_cpus": "1",
>       "min_mapping_quality": "20",
>       "min_memory": "1 MB",
>       "min_read_depth": "30",
>       "near_distance": "250",
>       "off_target_depth": true,
>       "off_target_slop": "500",
>       "output_dir": "/tmp/nf-config-test-outputs",
>       "output_dir_base": "/tmp/nf-config-test-outputs/calculate-targeted-coverage-1.0.0-rc.2/TWGSAMIN000001-T002-S02-F",
>       "output_enriched_target_file": true,
>       "patient": "null",
>       "picard_CollectHsMetrics_extra_args": "",
>       "picard_version": "3.0.0",
>       "pipeval_version": "4.0.0-rc.2",
>       "reference_dbSNP": "/hot/ref/database/dbSNP-155/thinned/GRCh38/dbSNP-155_thinned_hg38.vcf.gz",
>       "reference_dict": "/hot/ref/reference/GRCh38-BI-20160721/Homo_sapiens_assembly38.dict",
>       "sample": "null",
>       "sample_id": "TWGSAMIN000001-T002-S02-F",
>       "samtools_depth_extra_args": "",
>       "samtools_version": "1.16.1",
>       "save_all_dbSNP": false,
>       "save_intermediate_files": false,
>       "save_interval_list": false,
>       "save_raw_target_bed": false,
>       "target_bed": "/hot/software/pipeline/pipeline-calculate-targeted-coverage/Nextflow/development/input/GRch38-small.bed",
>       "target_depth": true,
>       "target_interval_list": "",
>       "ucla_cds": true,
>       "work_dir": "/scratch/4674821",
>       "workflow_output_dir": "/tmp/nf-config-test-outputs/calculate-targeted-coverage-1.0.0-rc.2/TWGSAMIN000001-T002-S02-F/SAMtools-1.16.1"
},
"dated_fields": [
"params.log_output_dir",
"report.file",
"timeline.file",
"trace.file",
"params.date"
],
"expected_result": {
"docker": {
"all_group_ids": "$(for i in `id --real --groups`; do echo -n \"--group-add=$i \"; done)",
"enabled": true,
"runOptions": "-u $(id -u):$(id -g) $(for i in `id --real --groups`; do echo -n \"--group-add=$i \"; done)",
"uid_and_gid": "-u $(id -u):$(id -g)"
},
"manifest": {
"author": "Nicole Zeltser",
"description": "Nextflow pipeline for calculating read-depth related statistics for targeted sequencing experiments",
"name": "calculate-targeted-coverage",
"version": "1.0.0-rc.2"
},
"params": {
"bait_bed": "",
"bait_interval_list": "",
"bedr_version": "1.1.0",
"bedtools_version": "2.29.2",
"blcds_registered_dataset": false,
"collect_metrics": true,
"coverage_cap": "3000",
"dataset_id": "TWGSAMIN000001-T002-S02-F",
"dataset_id": "TWGSAMIN000001",
"dataset_registry_prefix": "/hot/data",
"date": "19970704T165655Z",
"dbSNP_slop": "150",
"docker_container_registry": "ghcr.io/uclahs-cds",
"docker_image_bedops": "ghcr.io/uclahs-cds/bedr:1.1.0",
"docker_image_bedtools": "ghcr.io/uclahs-cds/bedtools:2.29.2",
"docker_image_picard": "ghcr.io/uclahs-cds/picard:3.0.0",
"docker_image_samtools": "ghcr.io/uclahs-cds/samtools:1.16.1",
"docker_image_validate": "ghcr.io/uclahs-cds/pipeval:4.0.0-rc.2",
"gatk_command_mem_diff": "2 GB",
"genome_sizes": "/hot/ref/reference/GRCh38-BI-20160721/Homo_sapiens_assembly38.fasta.fai",
"input": {
"bam": "/hot/resource/SMC-HET/tumours/A-mini/bams/n1/output/S2.T-n1.bam"
},
"log_output_dir": "/tmp/nf-config-test-outputs/calculate-targeted-coverage-1.0.0-rc.2/TWGSAMIN000001-T002-S02-F/log-calculate-targeted-coverage-1.0.0-rc.2-19970704T165655Z",
"max_cpus": "16",
"max_memory": "31 GB",
"merge_operation": "collapse",
"min_base_quality": "20",
"min_cpus": "1",
"min_mapping_quality": "20",
"min_memory": "1 MB",
"min_read_depth": "30",
"near_distance": "250",
"off_target_depth": true,
"off_target_slop": "500",
"output_dir": "/tmp/nf-config-test-outputs",
"output_dir_base": "/tmp/nf-config-test-outputs/calculate-targeted-coverage-1.0.0-rc.2/TWGSAMIN000001-T002-S02-F",
"output_enriched_target_file": true,
"patient": "null",
"picard_CollectHsMetrics_extra_args": "",
"picard_version": "3.0.0",
"pipeval_version": "4.0.0-rc.2",
"reference_dbSNP": "/hot/ref/database/dbSNP-155/thinned/GRCh38/dbSNP-155_thinned_hg38.vcf.gz",
"reference_dict": "/hot/ref/reference/GRCh38-BI-20160721/Homo_sapiens_assembly38.dict",
"sample": "null",
"sample_id": "TWGSAMIN000001-T002-S02-F",
"samtools_depth_extra_args": "",
"samtools_version": "1.16.1",
"save_all_dbSNP": false,
"save_intermediate_files": false,
"save_interval_list": false,
"save_raw_target_bed": false,
"target_bed": "/hot/software/pipeline/pipeline-calculate-targeted-coverage/Nextflow/development/input/GRch38-small.bed",
"target_depth": true,
"target_interval_list": "",
"ucla_cds": true,
"work_dir": "/scratch/4674821",
"workflow_output_dir": "/tmp/nf-config-test-outputs/calculate-targeted-coverage-1.0.0-rc.2/TWGSAMIN000001-T002-S02-F/SAMtools-1.16.1"
},
"params_schema": {
"bait_bed": {
"allow_empty": true,
"help": "Target intervals to process for DNA panel/targeted sequencing samples; leave empty for WGS",
"required": true,
"type": "String"
},
"bait_interval_list": {
"allow_empty": true,
"help": "Target intervals to process for DNA panel/targeted sequencing samples; leave empty for WGS",
"required": true,
"type": "String"
},
"collect_metrics": {
"default": true,
"help": "Whether to run picard CollectHsMetrics",
"required": true,
"type": "Bool"
},
"dataset_id": {
"help": "Dataset ID",
"required": true,
"type": "String"
},
"genome_sizes": {
"help": "Absolute path to table of chromosome lengths, can be fasta index",
"mode": "r",
"required": true,
"type": "Path"
},
"input": {
"elements": {
"bam": {
"help": "Input BAM for coverage analysis",
"mode": "r",
"required": true,
"type": "Path"
}
},
"help": "Input samples",
"required": true,
"type": "InputNamespace"
},
"off_target_depth": {
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},
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},
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"allow_empty": true,
"help": "Target intervals to process for DNA panel/targeted sequencing samples; leave empty for WGS",
"required": true,
"type": "String"

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<     "dated_fields": [
<         "params.log_output_dir",
<         "report.file",
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<         "author": "Nicole Zeltser",
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<         "bedr_version": "1.1.0",
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<         "coverage_cap": "3000",
<         "dataset_id": "TWGSAMIN000001",
<         "dataset_registry_prefix": "/hot/data",
<         "date": "19970704T165655Z",
<         "dbSNP_slop": "150",
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<         "docker_image_picard": "ghcr.io/uclahs-cds/picard:3.0.0",
<         "docker_image_samtools": "ghcr.io/uclahs-cds/samtools:1.16.1",
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<         "genome_sizes": "/hot/ref/reference/GRCh38-BI-20160721/Homo_sapiens_assembly38.fasta.fai",
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<         "max_cpus": "16",
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},
"target_depth": {
"default": false,
"help": "Whether or not to output a new target file containing high-coverage off-target dbSNP loci",
"required": true,
"type": "Bool"

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<         "target_depth": {
<           "default": false,
<           "help": "Whether or not to output a new target file containing high-coverage off-target dbSNP loci",
<           "required": true,
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---
>         "help": "Input samples",
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>       },
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},
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"allow_empty": true,
"help": "Target intervals to process for DNA panel/targeted sequencing samples; leave empty for WGS",
"required": true,
"type": "String"

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<         "target_interval_list": {
<           "allow_empty": true,
<           "help": "Target intervals to process for DNA panel/targeted sequencing samples; leave empty for WGS",
<           "required": true,
<           "type": "String"
---
>         "memory": {
>           "1": "31 GB",
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>           "3": "31 GB",
>           "closure": "closure()"
}
},
"process": {
"cache": true,
"containerOptions": {
"1": "--cpu-shares 1024 --cpus $task.cpus",
"2": "--cpu-shares 1024 --cpus $task.cpus",
"3": "--cpu-shares 1024 --cpus $task.cpus",
"closure": "--cpu-shares 1024 --cpus $task.cpus"
},

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<       "process": {
<         "cache": true,
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<           "1": "--cpu-shares 1024 --cpus $task.cpus",
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<         },
---
>       "withLabel:process_low": {
"cpus": {
"1": "1",
"2": "2",
"3": "3",

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<           "1": "1",
<           "2": "2",
<           "3": "3",
---
>           "1": "2",
>           "2": "4",
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"closure": "closure()"
},
"echo": true,
"errorStrategy": {
"1": "finish",
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"3": "finish",
"closure": "finish"
},
"executor": "local",
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"memory": "31 GB",
"withLabel:process_high": {
"cpus": {
"1": "12",
"2": "16",
"3": "16",
"closure": "closure()"
},
"memory": {
"1": "31 GB",
"2": "31 GB",
"3": "31 GB",
"closure": "closure()"
}
},
"withLabel:process_low": {
"cpus": {
"1": "2",
"2": "4",
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"closure": "closure()"
},
"memory": {
"1": "3 GB",
"2": "6 GB",
"3": "9 GB",
"closure": "closure()"
}
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"cpus": {
"1": "6",
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"closure": "closure()"
},
"memory": {
"1": "31 GB",
"2": "31 GB",
"3": "31 GB",
"closure": "closure()"
}
},
"withName:convert_depth_to_bed": {
"cpus": "1",
"memory": "1 GB"
},
"withName:merge_bedfiles_BEDtools": {
"cpus": "1",
"memory": "1 GB"
},
"withName:run_BedToIntervalList_picard": {
"cpus": "1",
"memory": "3 GB"
},
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"cpus": "1",
"memory": "25 GB"
},
"withName:run_depth_SAMtools": {
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},
"withName:run_depth_filter": {
"cpus": "1",
"memory": "1 GB"
},
"withName:run_intersect_BEDtools": {
"cpus": "1",
"memory": "1 GB"
},
"withName:run_merge_BEDtools": {
"cpus": "1",
"memory": "1 GB"
},
"withName:run_slop_BEDtools": {
"cpus": "1",
"memory": "1 GB"

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<         "echo": true,
<         "errorStrategy": {
<           "1": "finish",
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---
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}
},
"report": {
"enabled": true,
"file": "/tmp/nf-config-test-outputs/calculate-targeted-coverage-1.0.0-rc.2/TWGSAMIN000001-T002-S02-F/log-calculate-targeted-coverage-1.0.0-rc.2-19970704T165655Z/nextflow-log/report.html"
},
"timeline": {
"enabled": true,
"file": "/tmp/nf-config-test-outputs/calculate-targeted-coverage-1.0.0-rc.2/TWGSAMIN000001-T002-S02-F/log-calculate-targeted-coverage-1.0.0-rc.2-19970704T165655Z/nextflow-log/timeline.html"
},
"trace": {
"enabled": true,
"file": "/tmp/nf-config-test-outputs/calculate-targeted-coverage-1.0.0-rc.2/TWGSAMIN000001-T002-S02-F/log-calculate-targeted-coverage-1.0.0-rc.2-19970704T165655Z/nextflow-log/trace.txt"
},
"tz": "sun.util.calendar.ZoneInfo[id=\"UTC\",offset=0,dstSavings=0,useDaylight=false,transitions=0,lastRule=null]",
"workDir": "/scratch/4674821",
"yaml": {
"bait_bed": {
"allow_empty": true,
"help": "Target intervals to process for DNA panel/targeted sequencing samples; leave empty for WGS",
"required": true,
"type": "String"
},
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"allow_empty": true,
"help": "Target intervals to process for DNA panel/targeted sequencing samples; leave empty for WGS",
"required": true,
"type": "String"
},
"collect_metrics": {
"default": true,
"help": "Whether to run picard CollectHsMetrics",
"required": true,
"type": "Bool"
},
"dataset_id": {
"help": "Dataset ID",
"required": true,
"type": "String"
},
"genome_sizes": {
"help": "Absolute path to table of chromosome lengths, can be fasta index",
"mode": "r",
"required": true,
"type": "Path"
},
"input": {
"elements": {
"bam": {
"help": "Input BAM for coverage analysis",
"mode": "r",
"required": true,
"type": "Path"
}
},
"help": "Input samples",
"required": true,
"type": "InputNamespace"
},
"off_target_depth": {
"default": true,
"help": "Whether to calculate depth at off-target dbSNP loci",
"required": true,
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},
"output_dir": {
"help": "Absolute path to output directory",
"mode": "w",
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},
"output_enriched_target_file": {
"default": true,
"help": "Whether or not to output a new target file containing high-coverage off-target dbSNP loci",
"required": true,
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},
"picard_CollectHsMetrics_extra_args": {
"allow_empty": true,
"help": "Extra arguments for CollectHsMetrics",
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},
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"help": "Absolute path to thinned dbSNP VCF",
"mode": "r",
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},
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},
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},
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},
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"help": "Whether or not to output a new target file containing high-coverage off-target dbSNP loci",
"required": true,
"type": "Bool"

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<       "report": {
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<           "type": "InputNamespace"
<         },
<         "off_target_depth": {
<           "default": true,
<           "help": "Whether to calculate depth at off-target dbSNP loci",
<           "required": true,
<           "type": "Bool"
<         },
<         "output_dir": {
<           "help": "Absolute path to output directory",
<           "mode": "w",
<           "required": true,
<           "type": "Path"
<         },
<         "output_enriched_target_file": {
<           "default": true,
<           "help": "Whether or not to output a new target file containing high-coverage off-target dbSNP loci",
<           "required": true,
<           "type": "Bool"
<         },
<         "picard_CollectHsMetrics_extra_args": {
<           "allow_empty": true,
<           "help": "Extra arguments for CollectHsMetrics",
<           "required": true,
<           "type": "String"
<         },
<         "reference_dbSNP": {
<           "help": "Absolute path to thinned dbSNP VCF",
<           "mode": "r",
<           "required": true,
<           "type": "Path"
<         },
<         "reference_dict": {
<           "help": "Absolute path to reference genome dictionary",
<           "mode": "r",
<           "required": true,
<           "type": "Path"
<         },
<         "sample_id": {
<           "help": "Sample ID",
<           "required": true,
<           "type": "String"
<         },
<         "samtools_depth_extra_args": {
<           "allow_empty": true,
<           "help": "Extra arguments for samtools depth",
<           "required": true,
<           "type": "String"
<         },
<         "save_intermediate_files": {
<           "default": false,
<           "help": "Whether to save intermediate files",
<           "required": true,
<           "type": "B
},
"target_interval_list": {
"allow_empty": true,
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2 changes: 1 addition & 1 deletion test/nftest.config
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Original file line number Diff line number Diff line change
Expand Up @@ -9,7 +9,7 @@ includeConfig "${projectDir}/nextflow.config"
// Inputs/parameters of the pipeline
params {
// sample inputs
dataset_id = 'TWGSAMIN000001-T002-S02-F'
dataset_id = 'TWGSAMIN000001'
blcds_registered_dataset = false // if you want the output to be registered

// reference files
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