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added Fetch_SRA_to_BAM_BAM_only
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@lakras
lakras committed Jul 14, 2024
1 parent 4407ba1 commit 2c17fe2
Showing 1 changed file with 84 additions and 41 deletions.
125 changes: 84 additions & 41 deletions pipes/WDL/tasks/tasks_ncbi_tools.wdl
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Original file line number Diff line number Diff line change
Expand Up @@ -29,11 +29,10 @@ task Fetch_SRA_to_BAM {
CENTER=$(jq -r .EXPERIMENT_PACKAGE_SET.EXPERIMENT_PACKAGE.SUBMISSION.center_name SRA.json)
PLATFORM=$(jq -r '.EXPERIMENT_PACKAGE_SET.EXPERIMENT_PACKAGE.EXPERIMENT.PLATFORM | keys[] as $k | "\($k)"' SRA.json)
MODEL=$(jq -r ".EXPERIMENT_PACKAGE_SET.EXPERIMENT_PACKAGE.EXPERIMENT.PLATFORM.$PLATFORM.INSTRUMENT_MODEL" SRA.json)
SAMPLE=$(jq -r '.EXPERIMENT_PACKAGE_SET.EXPERIMENT_PACKAGE.SAMPLE.IDENTIFIERS.EXTERNAL_ID[]|select(.namespace == "BioSample")|.content' SRA.json)
SAMPLE=$(jq -r '.EXPERIMENT_PACKAGE_SET.EXPERIMENT_PACKAGE.SAMPLE.IDENTIFIERS.EXTERNAL_ID|select(.namespace == "BioSample")|.content' SRA.json)
LIBRARY=$(jq -r .EXPERIMENT_PACKAGE_SET.EXPERIMENT_PACKAGE.EXPERIMENT.alias SRA.json)
RUNDATE=$(jq -r '(.EXPERIMENT_PACKAGE_SET.EXPERIMENT_PACKAGE.RUN_SET | (if (.RUN|type) == "object" then (.RUN) else (.RUN[] | select(any(.; .accession == "~{SRA_ID}"))) end) | .SRAFiles) | if (.SRAFile|type) == "object" then .SRAFile.date else [.SRAFile[]|select(.supertype == "Original" or .supertype=="Primary ETL")][0].date end' SRA.json | cut -f 1 -d ' ')


if [[ -n "~{sample_name}" ]]; then
SAMPLE="~{sample_name}"
fi
Expand Down Expand Up @@ -72,7 +71,7 @@ task Fetch_SRA_to_BAM {
samtools view -c "~{SRA_ID}.bam" | tee OUT_NUM_READS

# pull other metadata from SRA -- allow for silent failures here!
touch OUT_MODEL OUT_COLLECTION_DATE OUT_STRAIN OUT_COLLECTED_BY OUT_GEO_LOC OUT_LIBRARY_STRATEGY
touch OUT_MODEL OUT_COLLECTION_DATE OUT_STRAIN OUT_COLLECTED_BY OUT_GEO_LOC
set +e
jq -r \
.EXPERIMENT_PACKAGE_SET.EXPERIMENT_PACKAGE.EXPERIMENT.PLATFORM."$PLATFORM".INSTRUMENT_MODEL \
Expand All @@ -93,44 +92,6 @@ task Fetch_SRA_to_BAM {
'.EXPERIMENT_PACKAGE_SET.EXPERIMENT_PACKAGE.EXPERIMENT.DESIGN.LIBRARY_DESCRIPTOR.LIBRARY_STRATEGY' \
SRA.json | tee OUT_LIBRARY_STRATEGY

# make sure the files exist
touch OUT_MODEL OUT_COLLECTION_DATE OUT_STRAIN OUT_COLLECTED_BY OUT_GEO_LOC OUT_LIBRARY_STRATEGY OUT_CENTER OUT_PLATFORM OUT_BIOSAMPLE OUT_LIBRARY OUT_RUNDATE

# set file contents to NA if they don't exist or are empty
if [ ! -s OUT_CENTER ]; then
echo "NA" > OUT_CENTER
fi
if [ ! -s OUT_PLATFORM ]; then
echo "NA" > OUT_PLATFORM
fi
if [ ! -s OUT_BIOSAMPLE ]; then
echo "NA" > OUT_BIOSAMPLE
fi
if [ ! -s OUT_LIBRARY ]; then
echo "NA" > OUT_LIBRARY
fi
if [ ! -s OUT_RUNDATE ]; then
echo "NA" > OUT_RUNDATE
fi
if [ ! -s OUT_MODEL ]; then
echo "NA" > OUT_MODEL
fi
if [ ! -s OUT_COLLECTION_DATE ]; then
echo "NA" > OUT_COLLECTION_DATE
fi
if [ ! -s OUT_STRAIN ]; then
echo "NA" > OUT_STRAIN
fi
if [ ! -s OUT_COLLECTED_BY ]; then
echo "NA" > OUT_COLLECTED_BY
fi
if [ ! -s OUT_GEO_LOC ]; then
echo "NA" > OUT_GEO_LOC
fi
if [ ! -s OUT_LIBRARY_STRATEGY ]; then
echo "NA" > OUT_LIBRARY_STRATEGY
fi

set -e
python3 << CODE
import json
Expand Down Expand Up @@ -194,6 +155,88 @@ task Fetch_SRA_to_BAM {
}
}

task Fetch_SRA_to_BAM_BAM_only {

input {
String SRA_ID

String? sample_name
String? email_address
String? ncbi_api_key
Int? machine_mem_gb
String docker = "quay.io/broadinstitute/ncbi-tools:2.10.7.10"
}
Int disk_size = 750
meta {
description: "This searches NCBI SRA for accessions using the Entrez interface and returns read sets as unaligned BAM files. This has been tested with both SRA and ENA accessions. This queries the NCBI production database, and as such, the output of this task is non-deterministic given the same input."
volatile: true
}
command <<<
set -e
~{if defined(ncbi_api_key) then "export NCBI_API_KEY=~{ncbi_api_key}}" else ""}

# fetch SRA metadata on this record
esearch ~{if defined(email_address) then "-email ~{email_address}" else ""} -db sra -query "~{SRA_ID}" | efetch -db sra ~{if defined(email_address) then "-email ~{email_address}" else ""} -mode json -json > SRA.json

cp SRA.json "~{SRA_ID}.json"

# pull reads from SRA and make a fully annotated BAM -- must succeed
# CENTER=$(jq -r .EXPERIMENT_PACKAGE_SET.EXPERIMENT_PACKAGE.SUBMISSION.center_name SRA.json)
# PLATFORM=$(jq -r '.EXPERIMENT_PACKAGE_SET.EXPERIMENT_PACKAGE.EXPERIMENT.PLATFORM | keys[] as $k | "\($k)"' SRA.json)
# MODEL=$(jq -r ".EXPERIMENT_PACKAGE_SET.EXPERIMENT_PACKAGE.EXPERIMENT.PLATFORM.$PLATFORM.INSTRUMENT_MODEL" SRA.json)
# SAMPLE=$(jq -r '.EXPERIMENT_PACKAGE_SET.EXPERIMENT_PACKAGE.SAMPLE.IDENTIFIERS.EXTERNAL_ID|select(.namespace == "BioSample")|.content' SRA.json)
# LIBRARY=$(jq -r .EXPERIMENT_PACKAGE_SET.EXPERIMENT_PACKAGE.EXPERIMENT.alias SRA.json)
# RUNDATE=$(jq -r '(.EXPERIMENT_PACKAGE_SET.EXPERIMENT_PACKAGE.RUN_SET | (if (.RUN|type) == "object" then (.RUN) else (.RUN[] | select(any(.; .accession == "~{SRA_ID}"))) end) | .SRAFiles) | if (.SRAFile|type) == "object" then .SRAFile.date else [.SRAFile[]|select(.supertype == "Original" or .supertype=="Primary ETL")][0].date end' SRA.json | cut -f 1 -d ' ')

# if [[ -n "~{sample_name}" ]]; then
# SAMPLE="~{sample_name}"
# fi

# if [ "$PLATFORM" = "OXFORD_NANOPORE" ]; then
# # per the SAM/BAM specification
# SAM_PLATFORM="ONT"
# else
# SAM_PLATFORM="$PLATFORM"
# fi

sam-dump --unaligned --header "~{SRA_ID}" \
| samtools view -bhS - \
> temp.bam
picard AddOrReplaceReadGroups \
I=temp.bam \
O="~{SRA_ID}.bam" \
RGID=1 \
# RGLB="$LIBRARY" \
RGSM="$SAMPLE" \
# RGPL="$SAM_PLATFORM" \
# RGPU="$LIBRARY" \
# RGPM="$MODEL" \
# RGDT="$RUNDATE" \
# RGCN="$CENTER" \
VALIDATION_STRINGENCY=SILENT
rm temp.bam
samtools view -H "~{SRA_ID}.bam"

# emit read count
samtools view -c "~{SRA_ID}.bam" | tee OUT_NUM_READS
>>>

output {
File reads_ubam = "~{SRA_ID}.bam"
Int num_reads = read_int("OUT_NUM_READS")
}

runtime {
cpu: 2
memory: select_first([machine_mem_gb, 6]) + " GB"
disks: "local-disk " + disk_size + " LOCAL"
disk: disk_size + " GB" # TES
dx_instance_type: "mem2_ssd1_v2_x2"
docker: docker
maxRetries: 2
}
}

task fetch_genbank_metadata {
input {
String genbank_accession
Expand Down

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