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Merged
merged 7 commits into from
Dec 17, 2019
Merged

Minor Funcotator WDL updates. #6326

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37a42f6
Updated minor things in funcotator.wdl.
jonn-smith Dec 17, 2019
b1f949a
Minor update to README.md
jonn-smith Dec 17, 2019
71de24b
Minor updates.
jonn-smith Dec 17, 2019
d6682db
Addressing code review comments.
jonn-smith Dec 17, 2019
b5e32e2
Adding in default json for funcotator featured workspace.
jonn-smith Dec 17, 2019
499cf0e
Minor javascript update.
jonn-smith Dec 17, 2019
63a5135
Updates to featured workspace json.
jonn-smith Dec 17, 2019
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4 changes: 2 additions & 2 deletions scripts/funcotator_wdl/README.md
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Expand Up @@ -36,7 +36,7 @@ String output_file_name - Path to desired output file.

String output_format - Output file format (either VCF or MAF).

Boolean compress - Whether to compress the resulting output file.
Boolean compress - Whether to compress the resulting output file.

Boolean use_gnomad - If true, will enable the gnomAD data sources in the data source tar.gz, if they exist.

Expand Down Expand Up @@ -86,6 +86,6 @@ The follwing is an example of a JSON input file. It will not work as-is but is

## Further Information
- https://software.broadinstitute.org/gatk/documentation/article?id=11193
- https://software.broadinstitute.org/gatk/documentation/tooldocs/4.1.2.0/org_broadinstitute_hellbender_tools_funcotator_Funcotator.php
- https://software.broadinstitute.org/gatk/documentation/tooldocs/4.1.4.0/org_broadinstitute_hellbender_tools_funcotator_Funcotator.php


24 changes: 24 additions & 0 deletions scripts/funcotator_wdl/funcotator.json
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@@ -0,0 +1,24 @@
{
"Funcotator.gatk_docker": "broadinstitute/gatk:latest",

"Funcotator.ref_fasta": "gs://broad-references/hg38/v0/Homo_sapiens_assembly38.fasta",
"Funcotator.ref_fasta_index": "gs://broad-references/hg38/v0/Homo_sapiens_assembly38.fasta.fai",
"Funcotator.ref_dict": "gs://broad-references/hg38/v0/Homo_sapiens_assembly38.dict",

"Funcotator.reference_version": "hg38",
"Funcotator.output_format": "VCF",

"Funcotator.compress": "false",
"Funcotator.use_gnomad": "false",
"Funcotator.data_sources_tar_gz": "gs://broad-public-datasets/funcotator/funcotator_dataSources.v1.6.20190124s.tar.gz",

"Funcotator.interval_list": "gs://gatk-best-practices/funcotator/chr1_13313-187210.intervals.list",

"Funcotator.variant_vcf_to_funcotate": "gs://gatk-test-data/1kgp/downsampled_vcf_hg38/1kgp-50-exomes.vcf.gz",
"Funcotator.variant_vcf_to_funcotate_index": "gs://gatk-test-data/1kgp/downsampled_vcf_hg38/1kgp-50-exomes.vcf.gz.tbi",

"Funcotator.output_file_base_name": "1kgp-50-exomes.chr1_13313-187210.funcotated",

"Funcotator.Funcotate.sequencing_center": "\"1000 Genomes Project\"",
"Funcotator.Funcotate.sequence_source": "\"1000 Genomes Project\""
}
280 changes: 140 additions & 140 deletions scripts/funcotator_wdl/funcotator.wdl
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Expand Up @@ -87,169 +87,169 @@ workflow Funcotator {

task Funcotate {

# ==============
# Inputs
File ref_fasta
File ref_fasta_index
File ref_dict
# ==============
# Inputs
File ref_fasta
File ref_fasta_index
File ref_dict

File input_vcf
File input_vcf_idx
File input_vcf
File input_vcf_idx

String reference_version
String reference_version

String output_file_base_name
String output_format
String output_file_base_name
String output_format

Boolean compress
Boolean use_gnomad
Boolean compress
Boolean use_gnomad

# This should be updated when a new version of the data sources is released
# TODO: Make this dynamically chosen in the command.
File? data_sources_tar_gz = "gs://broad-public-datasets/funcotator/funcotator_dataSources.v1.6.20190124s.tar.gz"
# This should be updated when a new version of the data sources is released
# TODO: Make this dynamically chosen in the command.
File? data_sources_tar_gz = "gs://broad-public-datasets/funcotator/funcotator_dataSources.v1.6.20190124s.tar.gz"

String? control_id
String? case_id
String? sequencing_center
String? sequence_source
String? transcript_selection_mode
File? transcript_selection_list
Array[String]? annotation_defaults
Array[String]? annotation_overrides
Array[String]? funcotator_excluded_fields
Boolean? filter_funcotations
File? interval_list
String? control_id
String? case_id
String? sequencing_center
String? sequence_source
String? transcript_selection_mode
File? transcript_selection_list
Array[String]? annotation_defaults
Array[String]? annotation_overrides
Array[String]? funcotator_excluded_fields
Boolean? filter_funcotations
File? interval_list

String? extra_args
String? extra_args

# ==============
# Process input args:
# ==============
# Process input args:

String output_maf = output_file_base_name + ".maf"
String output_maf_index = output_maf + ".idx"
String output_maf = output_file_base_name + ".maf"
String output_maf_index = output_maf + ".idx"

String output_vcf = output_file_base_name + if compress then ".vcf.gz" else ".vcf"
String output_vcf_idx = output_vcf + if compress then ".tbi" else ".idx"
String output_vcf = output_file_base_name + if compress then ".vcf.gz" else ".vcf"
String output_vcf_idx = output_vcf + if compress then ".tbi" else ".idx"

String output_file = if output_format == "MAF" then output_maf else output_vcf
String output_file_index = if output_format == "MAF" then output_maf_index else output_vcf_idx
String output_file = if output_format == "MAF" then output_maf else output_vcf
String output_file_index = if output_format == "MAF" then output_maf_index else output_vcf_idx

String transcript_selection_arg = if defined(transcript_selection_list) then " --transcript-list " else ""
String annotation_def_arg = if defined(annotation_defaults) then " --annotation-default " else ""
String annotation_over_arg = if defined(annotation_overrides) then " --annotation-override " else ""
String filter_funcotations_args = if defined(filter_funcotations) && (filter_funcotations) then " --remove-filtered-variants " else ""
String excluded_fields_args = if defined(funcotator_excluded_fields) then " --exclude-field " else ""
String transcript_selection_arg = if defined(transcript_selection_list) then " --transcript-list " else ""
String annotation_def_arg = if defined(annotation_defaults) then " --annotation-default " else ""
String annotation_over_arg = if defined(annotation_overrides) then " --annotation-override " else ""
String filter_funcotations_args = if defined(filter_funcotations) && (filter_funcotations) then " --remove-filtered-variants " else ""
String excluded_fields_args = if defined(funcotator_excluded_fields) then " --exclude-field " else ""

String interval_list_arg = if defined(interval_list) then " -L " else ""
String interval_list_arg = if defined(interval_list) then " -L " else ""

String extra_args_arg = select_first([extra_args, ""])
String extra_args_arg = select_first([extra_args, ""])

# ==============
# Runtime options:
String gatk_docker
# ==============
# Runtime options:
String gatk_docker

File? gatk_override
Int? mem
Int? preemptible_attempts
Int? max_retries
Int? disk_space_gb
Int? cpu
File? gatk_override
Int? mem
Int? preemptible_attempts
Int? max_retries
Int? disk_space_gb
Int? cpu

Boolean use_ssd = false
Boolean use_ssd = false

# Mem is in units of GB but our command and memory runtime values are in MB
Int default_ram_mb = 1024 * 3
Int machine_mem = if defined(mem) then mem *1024 else default_ram_mb
Int command_mem = machine_mem - 1024
# Mem is in units of GB but our command and memory runtime values are in MB
Int default_ram_mb = 1024 * 3
Int machine_mem = if defined(mem) then mem *1024 else default_ram_mb
Int command_mem = machine_mem - 1024

# Calculate disk size:
Float ref_size_gb = size(ref_fasta, "GiB") + size(ref_fasta_index, "GiB") + size(ref_dict, "GiB")
Float vcf_size_gb = size(input_vcf, "GiB") + size(input_vcf_idx, "GiB")
Float ds_size_gb = size(data_sources_tar_gz, "GiB")
# Calculate disk size:
Float ref_size_gb = size(ref_fasta, "GiB") + size(ref_fasta_index, "GiB") + size(ref_dict, "GiB")
Float vcf_size_gb = size(input_vcf, "GiB") + size(input_vcf_idx, "GiB")
Float ds_size_gb = size(data_sources_tar_gz, "GiB")

Int default_disk_space_gb = ceil( ref_size_gb + (ds_size_gb * 2) + (vcf_size_gb * 10) ) + 20
Int default_disk_space_gb = ceil( ref_size_gb + (ds_size_gb * 2) + (vcf_size_gb * 10) ) + 20

# Silly hack to allow us to use the dollar sign in the command section:
String dollar = "$"
# Silly hack to allow us to use the dollar sign in the command section:
String dollar = "$"

command <<<
set -e
export GATK_LOCAL_JAR=${default="/root/gatk.jar" gatk_override}
command <<<
set -e
export GATK_LOCAL_JAR=${default="/root/gatk.jar" gatk_override}

# =======================================
# Hack to validate our WDL inputs:
#
# NOTE: This happens here so that we don't waste time copying down the data sources if there's an error.
# =======================================
# Hack to validate our WDL inputs:
#
# NOTE: This happens here so that we don't waste time copying down the data sources if there's an error.

if [[ "${output_format}" != "MAF" ]] && [[ "${output_format}" != "VCF" ]] ; then
if [[ "${output_format}" != "MAF" ]] && [[ "${output_format}" != "VCF" ]] ; then
echo "ERROR: Output format must be MAF or VCF."
fi

# =======================================
# Handle our data sources:

# Extract the tar.gz:
echo "Extracting data sources tar/gzip file..."
mkdir datasources_dir
tar zxvf ${data_sources_tar_gz} -C datasources_dir --strip-components 1
DATA_SOURCES_FOLDER="$PWD/datasources_dir"

# Handle gnomAD:
if ${use_gnomad} ; then
echo "Enabling gnomAD..."
for potential_gnomad_gz in gnomAD_exome.tar.gz gnomAD_genome.tar.gz ; do
if [[ -f ${dollar}{DATA_SOURCES_FOLDER}/${dollar}{potential_gnomad_gz} ]] ; then
cd ${dollar}{DATA_SOURCES_FOLDER}
tar -zvxf ${dollar}{potential_gnomad_gz}
cd -
else
echo "ERROR: Cannot find gnomAD folder: ${dollar}{potential_gnomad_gz}" 1>&2
false
fi
done
fi

# =======================================
# Run Funcotator:
gatk --java-options "-Xmx${command_mem}m" Funcotator \
--data-sources-path $DATA_SOURCES_FOLDER \
--ref-version ${reference_version} \
--output-file-format ${output_format} \
-R ${ref_fasta} \
-V ${input_vcf} \
-O ${output_file} \
${interval_list_arg} ${default="" interval_list} \
--annotation-default normal_barcode:${default="Unknown" control_id} \
--annotation-default tumor_barcode:${default="Unknown" case_id} \
--annotation-default Center:${default="Unknown" sequencing_center} \
--annotation-default source:${default="Unknown" sequence_source} \
${"--transcript-selection-mode " + transcript_selection_mode} \
${transcript_selection_arg}${default="" sep=" --transcript-list " transcript_selection_list} \
${annotation_def_arg}${default="" sep=" --annotation-default " annotation_defaults} \
${annotation_over_arg}${default="" sep=" --annotation-override " annotation_overrides} \
${excluded_fields_args}${default="" sep=" --exclude-field " funcotator_excluded_fields} \
${filter_funcotations_args} \
${extra_args_arg}

# =======================================
# Make sure we have a placeholder index for MAF files so this workflow doesn't fail:
if [[ "${output_format}" == "MAF" ]] ; then
fi

# =======================================
# Handle our data sources:

# Extract the tar.gz:
echo "Extracting data sources tar/gzip file..."
mkdir datasources_dir
tar zxvf ${data_sources_tar_gz} -C datasources_dir --strip-components 1
DATA_SOURCES_FOLDER="$PWD/datasources_dir"

# Handle gnomAD:
if ${use_gnomad} ; then
echo "Enabling gnomAD..."
for potential_gnomad_gz in gnomAD_exome.tar.gz gnomAD_genome.tar.gz ; do
if [[ -f ${dollar}{DATA_SOURCES_FOLDER}/${dollar}{potential_gnomad_gz} ]] ; then
cd ${dollar}{DATA_SOURCES_FOLDER}
tar -zvxf ${dollar}{potential_gnomad_gz}
cd -
else
echo "ERROR: Cannot find gnomAD folder: ${dollar}{potential_gnomad_gz}" 1>&2
false
fi
done
fi

# =======================================
# Run Funcotator:
gatk --java-options "-Xmx${command_mem}m" Funcotator \
--data-sources-path $DATA_SOURCES_FOLDER \
--ref-version ${reference_version} \
--output-file-format ${output_format} \
-R ${ref_fasta} \
-V ${input_vcf} \
-O ${output_file} \
${interval_list_arg} ${default="" interval_list} \
--annotation-default normal_barcode:${default="Unknown" control_id} \
--annotation-default tumor_barcode:${default="Unknown" case_id} \
--annotation-default Center:${default="Unknown" sequencing_center} \
--annotation-default source:${default="Unknown" sequence_source} \
${"--transcript-selection-mode " + transcript_selection_mode} \
${transcript_selection_arg}${default="" sep=" --transcript-list " transcript_selection_list} \
${annotation_def_arg}${default="" sep=" --annotation-default " annotation_defaults} \
${annotation_over_arg}${default="" sep=" --annotation-override " annotation_overrides} \
${excluded_fields_args}${default="" sep=" --exclude-field " funcotator_excluded_fields} \
${filter_funcotations_args} \
${extra_args_arg}

# =======================================
# Make sure we have a placeholder index for MAF files so this workflow doesn't fail:
if [[ "${output_format}" == "MAF" ]] ; then
touch ${output_maf_index}
fi
>>>

runtime {
docker: gatk_docker
bootDiskSizeGb: 20
memory: machine_mem + " MB"
disks: "local-disk " + select_first([disk_space_gb, default_disk_space_gb]) + if use_ssd then " SSD" else " HDD"
preemptible: select_first([preemptible_attempts, 3])
maxRetries: select_first([max_retries, 0])
cpu: select_first([cpu, 1])
}

output {
File funcotated_output_file = "${output_file}"
File funcotated_output_file_index = "${output_file_index}"
}
}
fi
>>>

runtime {
docker: gatk_docker
bootDiskSizeGb: 20
memory: machine_mem + " MB"
disks: "local-disk " + select_first([disk_space_gb, default_disk_space_gb]) + if use_ssd then " SSD" else " HDD"
preemptible: select_first([preemptible_attempts, 3])
maxRetries: select_first([max_retries, 0])
cpu: select_first([cpu, 1])
}

output {
File funcotated_output_file = "${output_file}"
File funcotated_output_file_index = "${output_file_index}"
}
}