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bugfix output location of fasta in download_annotations; pass NCBI API key to tasks: download_fasta, download_annotations #481

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bugfix output location of fasta in download_annotations; pass NCBI API key to tasks: download_fasta, download_annotations #481

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014f69f
bugfix output location of fasta in download_annotations; pass NCBI AP…
tomkinsc Aug 10, 2023
81c17a5
write combined fasta as temp file, then move to final output path in …
tomkinsc Aug 10, 2023
fe0e860
s/apiKey/apiKeyNCBI/
tomkinsc Aug 10, 2023
5de5cef
Merge branch 'master' into ct-bugfix-ncbi-fasta-fetch
tomkinsc Dec 15, 2023
02f4b83
Merge branch 'master' into ct-bugfix-ncbi-fasta-fetch
tomkinsc Jan 5, 2024
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30 changes: 25 additions & 5 deletions pipes/WDL/tasks/tasks_ncbi.wdl
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Original file line number Diff line number Diff line change
Expand Up @@ -5,21 +5,31 @@ task download_fasta {
String out_prefix
Array[String]+ accessions
String emailAddress
String apiKeyNCBI

String docker = "quay.io/broadinstitute/viral-phylo:2.1.20.2"
}

parameter_meta {
out_prefix: { description: "basename of the output fasta file. Will contain multiple sequences if multiple accessions are specified" }
accessions: { description: "accessions of sequences to download" }
apiKeyNCBI: { description: "NCBI API key for more frequent requests; see: https://support.nlm.nih.gov/knowledgebase/article/KA-05317/en-us" }
}

command {
ncbi.py --version | tee VERSION
mkdir -p combined
ncbi.py fetch_fastas \
--combinedFilePrefix "tmp.${out_prefix}" \
~{'--api_key ' + apiKeyNCBI} \
${emailAddress} \
. \
${sep=' ' accessions} \
--combinedFilePrefix ${out_prefix} \
${sep=' ' accessions}
mv "tmp.${out_prefix}.fasta" "combined/${out_prefix}.fasta"
}

output {
File sequences_fasta = "${out_prefix}.fasta"
File sequences_fasta = "combined/${out_prefix}.fasta"
String viralngs_version = read_string("VERSION")
}

Expand All @@ -36,27 +46,37 @@ task download_annotations {
input {
Array[String]+ accessions
String emailAddress
String apiKeyNCBI
String combined_out_prefix

String docker = "quay.io/broadinstitute/viral-phylo:2.1.20.2"
}

parameter_meta {
combined_out_prefix: { description: "basename of the output fasta file. Will contain multiple sequences if multiple accessions are specified" }
accessions: { description: "accessions for which sequences and feature tables will be downloaded" }
apiKeyNCBI: { description: "NCBI API key for more frequent requests; see: https://support.nlm.nih.gov/knowledgebase/article/KA-05317/en-us" }
}

command <<<
set -ex -o pipefail
ncbi.py --version | tee VERSION
ncbi.py fetch_feature_tables \
~{'--api_key ' + apiKeyNCBI} \
~{emailAddress} \
./ \
~{sep=' ' accessions} \
--loglevel DEBUG
mkdir -p combined
ncbi.py fetch_fastas \
--combinedFilePrefix "temp.~{combined_out_prefix}" \
~{'--api_key ' + apiKeyNCBI} \
--forceOverwrite \
~{emailAddress} \
./ \
~{sep=' ' accessions} \
--combinedFilePrefix "combined/~{combined_out_prefix}" \
--forceOverwrite \
--loglevel DEBUG
mv "temp.~{combined_out_prefix}.fasta" "combined/~{combined_out_prefix}.fasta"
>>>

output {
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