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add additional optional metadata fields
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@kevinlibuit
kevinlibuit committed Feb 12, 2021
1 parent f75b7ea commit 2f1ecc5
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Showing 3 changed files with 31 additions and 13 deletions.
11 changes: 7 additions & 4 deletions tasks/task_ont_pub_repo_submission.wdl
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Original file line number Diff line number Diff line change
Expand Up @@ -57,7 +57,6 @@ task gisaid {
File sequence
String iso_host
String iso_country
String? specimen_type

String gisaid_submitter
String iso_state
Expand All @@ -74,6 +73,10 @@ task gisaid {
String gender="unknown"
String patient_age="unknown"
String patient_status="unknown"
String specimen_source=""
String outbreak=""
String last_vaccinated=""
String treatment=""

String docker_image = "staphb/seqyclean:1.10.09"
Int mem_size_gb = 3
Expand All @@ -93,7 +96,7 @@ task gisaid {

echo Submitter,FASTA filename,Virus name,Type,Passage details/history,Collection date,Location,Additional location information,Host,Additional host information,Gender,Patient age,Patient status,Specimen source,Outbreak,Last vaccinated,Treatment,Sequencing technology,Assembly method,Coverage,Originating lab,Address,Sample ID given by the sample provider,Submitting lab,Address,Sample ID given by the submitting laboratory,Authors Comment,Comment Icon >> ${submission_id}.gisaidMeta.csv

echo "\"${gisaid_submitter}\",\"gisaid_upload.fasta\",\"hCoV-19/${iso_country}/${submission_id}/$year\",\"betacoronavirus\",\"${passage_details}\",\"${collection_date}\",\"${iso_continent} \ ${iso_country} \ ${iso_state}\",,\"${iso_host}\",,\"${gender}\",\"${patient_age}\",\"${patient_status}\",\"${specimen_type}\",,,,\"${seq_platform}\",\"${artic_pipeline_version}\",,\"${originating_lab}\",\"${origLab_address}\",,\"${submitting_lab}\",\"${subLab_address}\",,\"${Authors}\"" >> ${submission_id}.gisaidMeta.csv
echo "\"${gisaid_submitter}\",\"gisaid_upload.fasta\",\"hCoV-19/${iso_country}/${submission_id}/$year\",\"betacoronavirus\",\"${passage_details}\",\"${collection_date}\",\"${iso_continent} \ ${iso_country} \ ${iso_state}\",,\"${iso_host}\",,\"${gender}\",\"${patient_age}\",\"${patient_status}\",\"${specimen_source}\",\"${outbreak}\",\"${last_vaccinated}\",\"${treatment}\",\"${seq_platform}\",\"${artic_pipeline_version}\",,\"${originating_lab}\",\"${origLab_address}\",,\"${submitting_lab}\",\"${subLab_address}\",,\"${Authors}\"" >> ${submission_id}.gisaidMeta.csv

}

Expand Down Expand Up @@ -122,7 +125,7 @@ task genbank {
String iso_org
String iso_host
String iso_country
String specimen_type
String specimen_source
String BioProject

String docker_image = "staphb/seqyclean:1.10.09"
Expand All @@ -141,7 +144,7 @@ task genbank {

echo Sequence_ID,Organism,collection-date,country,host,isolate,isolation-source,BioProject,notes > ${submission_id}.genbankMeta.csv

echo "\"${submission_id}\",\"Severe acute respiratory syndrome coronavirus 2\",\"${collection_date}\",\"${iso_country}\",\"${iso_host}\",\"${iso_org}/${iso_host}/${iso_country}/${submission_id}/$year\",\"${specimen_type}\",\"${BioProject}\"," >> ${submission_id}.genbankMeta.csv
echo "\"${submission_id}\",\"Severe acute respiratory syndrome coronavirus 2\",\"${collection_date}\",\"${iso_country}\",\"${iso_host}\",\"${iso_org}/${iso_host}/${iso_country}/${submission_id}/$year\",\"${specimen_source}\",\"${BioProject}\"," >> ${submission_id}.genbankMeta.csv

}

Expand Down
19 changes: 14 additions & 5 deletions workflows/wf_clearlabs_viral_refbased_assembly.wdl
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Original file line number Diff line number Diff line change
Expand Up @@ -34,14 +34,17 @@ workflow viral_refbased_assembly {
String organism = "Severe acute respiratory syndrome coronavirus 2"
String iso_org = "SARS-CoV-2"
String iso_host = "Human"
String specimen_type = ""
String assembly_or_consensus = "consensus"
String seq_platform = "Nanopore via Clear Labs Dx WGS SARS-CoV-2"

String passage_details="Original"
String gender="unknown"
String patient_age="unknown"
String patient_status="unknown"
String specimen_source=""
String outbreak=""
String last_vaccinated=""
String treatment=""

}

Expand Down Expand Up @@ -106,7 +109,6 @@ workflow viral_refbased_assembly {
iso_org = iso_org,
iso_host = iso_host,
iso_country = iso_country,
specimen_type = specimen_type,
assembly_or_consensus = assembly_or_consensus,

gisaid_submitter = gisaid_submitter,
Expand All @@ -124,7 +126,11 @@ workflow viral_refbased_assembly {
passage_details = passage_details,
gender = gender,
patient_age = patient_age,
patient_status = patient_status
patient_status = patient_status,
specimen_source = specimen_source,
outbreak = outbreak,
last_vaccinated = last_vaccinated,
treatment = treatment
}
}
if (! vadr.vadr_result) {
Expand All @@ -140,7 +146,6 @@ workflow viral_refbased_assembly {
iso_org = iso_org,
iso_host = iso_host,
iso_country = iso_country,
specimen_type = specimen_type,
assembly_or_consensus = assembly_or_consensus,

gisaid_submitter = gisaid_submitter,
Expand All @@ -158,7 +163,11 @@ workflow viral_refbased_assembly {
passage_details = passage_details,
gender = gender,
patient_age = patient_age,
patient_status = patient_status
patient_status = patient_status,
specimen_source = specimen_source,
outbreak = outbreak,
last_vaccinated = last_vaccinated,
treatment = treatment
}
}

Expand Down
14 changes: 10 additions & 4 deletions workflows/wf_ont_sc2_pubRepo_submission.wdl
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Original file line number Diff line number Diff line change
Expand Up @@ -15,7 +15,6 @@ workflow SC2_submission_files {
String iso_org = "SARS-CoV-2"
String iso_host = "Human"
String iso_country = "USA"
String specimen_type = ""
String assembly_or_consensus = "consensus"

String gisaid_submitter
Expand All @@ -34,6 +33,10 @@ workflow SC2_submission_files {
String gender="unknown"
String patient_age="unknown"
String patient_status="unknown"
String specimen_source=""
String outbreak=""
String last_vaccinated=""
String treatment=""

# Optional inputs/user-defined thresholds for generating submission files
Float coverage = 100.00
Expand Down Expand Up @@ -69,7 +72,6 @@ workflow SC2_submission_files {
sequence = sequence,
iso_host = iso_host,
iso_country = iso_country,
specimen_type = specimen_type,
gisaid_submitter = gisaid_submitter,
iso_state = gisaid_submitter,
iso_continent = iso_continent,
Expand All @@ -84,7 +86,11 @@ workflow SC2_submission_files {
passage_details = passage_details,
gender = gender,
patient_age = patient_age,
patient_status = patient_status
patient_status = patient_status,
specimen_source = specimen_source,
outbreak = outbreak,
last_vaccinated = last_vaccinated,
treatment = treatment



Expand All @@ -101,7 +107,7 @@ workflow SC2_submission_files {
iso_org = iso_org,
iso_host = iso_host,
iso_country = iso_country,
specimen_type = specimen_type,
specimen_source = specimen_source,
BioProject = BioProject
}
}
Expand Down

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