From 568cdb686c8e73aa7afb18a498943cf22bcfe7a0 Mon Sep 17 00:00:00 2001 From: Christopher Tomkins-Tinch Date: Tue, 13 Apr 2021 20:31:16 -0400 Subject: [PATCH] include generate_author_sbt in sarscov2_illumina_full wdl workflow --- .../WDL/workflows/sarscov2_illumina_full.wdl | 22 ++++++++++++++++++- 1 file changed, 21 insertions(+), 1 deletion(-) diff --git a/pipes/WDL/workflows/sarscov2_illumina_full.wdl b/pipes/WDL/workflows/sarscov2_illumina_full.wdl index c649bec3a..b40bcb4aa 100644 --- a/pipes/WDL/workflows/sarscov2_illumina_full.wdl +++ b/pipes/WDL/workflows/sarscov2_illumina_full.wdl @@ -34,7 +34,16 @@ workflow sarscov2_illumina_full { description: "A post-submission attributes file from NCBI BioSample, which is available at https://submit.ncbi.nlm.nih.gov/subs/ and clicking on 'Download attributes file with BioSample accessions'. The 'sample_name' column must match the external_ids used in sample_rename_map (or internal ids if sample_rename_map is omitted).", patterns: ["*.txt", "*.tsv"] } - + author_list: { + description: "A string containing a space-delimited list with of author surnames separated by first name and (optional) middle initial. Ex. 'Lastname,Firstname, Last-hypenated,First,M., Last,F.'" + } + author_sbt_defaults_yaml: { + description: "A YAML file with default values to use for the submitter, submitter affiliation, and author affiliation. Optionally including authors at the start and end of the author_list. Example: gs://pathogen-public-dbs/other-related/default_sbt_values.yaml", + patterns: ["*.yaml","*.yml"] + } + author_sbt_j2_template: { + description: "A jinja2-format template for the sbt file expected by NCBI. Example: gs://pathogen-public-dbs/other-related/author_template.sbt.j2" + } } input { @@ -42,6 +51,10 @@ workflow sarscov2_illumina_full { File reference_fasta String amplicon_bed_prefix + String? author_list # of the form "Lastname,A.B., Lastname,C.,"; optional alternative to names in author_sbt_defaults_yaml + File author_sbt_defaults_yaml # defaults to fill in for author_sbt file (including both author and non-author fields) + File author_sbt_j2_template + Array[File] biosample_attributes String instrument_model String sra_title @@ -272,10 +285,17 @@ workflow sarscov2_illumina_full { sequences = passing_genomes.combined, keep_list = [biosample_to_genbank.sample_ids] } + call ncbi.generate_author_sbt_file as generate_author_sbt { + input: + author_list = author_list, + defaults_yaml = author_sbt_defaults_yaml, + j2_template = author_sbt_j2_template + } call ncbi.package_genbank_ftp_submission { input: sequences_fasta = submit_genomes.filtered_fasta, source_modifier_table = biosample_to_genbank.genbank_source_modifier_table, + author_template_sbt = generate_author_sbt.sbt_file, structured_comment_table = structured_comments.structured_comment_table, submission_name = flowcell_id, submission_uid = flowcell_id