Merge remote-tracking branch 'origin/main' into kzm-metabuli-dev

Author: xonq

.dockstore.yml

@@ -340,3 +340,8 @@ workflows:
    primaryDescriptorPath: /workflows/utilities/data_import/wf_ont_barcode_concatenation.wdl
    testParameterFiles:
      - /tests/inputs/empty.json
+ - name: Microreact_Export_PHB
+   subclass: WDL
+   primaryDescriptorPath: /workflows/utilities/wf_microreact_export.wdl
+   testParameterFiles:
+     - /tests/inputs/empty.json

docs/assets/figures/Microreact_Export.png

@@ -219,6 +219,12 @@ usher_workflow	assembly_fasta	Array[File]	The assembly files for your samples in
 usher_workflow	organism	String	What organism to run UShER on; the following organism have default global phylogenies and reference files provided: sars-cov-2, mpox, RSV-A, RSV-B.		Required	Usher	general	
 usher_workflow	tree_name	String	The output prefix for the uncondensed tree output and the clades output.		Required	Usher	general	
 vadr_update	genome_fasta	File	Consensus genome assembly		Required	VADR_Update	general	
+wf_microreact_export	id_column	String	Column used as the unique identifier for Microreact		Required	Microreact_Export	general	
+wf_microreact_export	project_name	String	Name of the project to be uploaded to Microreact		Required	Microreact_Export	general	
+wf_microreact_export	set_id	String	ID column of the set being run		Required	Microreact_Export	general	
+wf_microreact_export	terra_project_name	String	Terra project location where metadata Terra table is housed		Required	Microreact_Export	general	
+wf_microreact_export	terra_table_name	String	Name of the Terra table used as the Microreact metadata table		Required	Microreact_Export	general	
+wf_microreact_export	terra_workspace_name	String	Terra workspace location where metadata Terra table is housed		Required	Microreact_Export	general	
 zip_column_content	files_to_zip	Array[File]	The column that has the files you want to zip.		Required	Zip_Column_Content	general	
 zip_column_content	zipped_file_name	String	The name you want your zipped file to have. The .zip file extension will be added to this name.		Required	Zip_Column_Content	general	
 abricate	cpu	Int	Number of CPUs to allocate to the task	2	Optional	TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT	runtime	
@@ -627,6 +633,10 @@ core_snp_sites	cpu	Int	Number of CPUs to allocate to the task	1	Optional	Core_Ge
 core_snp_sites	disk_size	Int	Amount of storage (in GB) to allocate to the task	100	Optional	Core_Gene_SNP	runtime	
 core_snp_sites	docker	String	Docker image to use for the task	us-docker.pkg.dev/general-theiagen/staphb/snp-sites:2.5.1	Optional	Core_Gene_SNP	docker	
 core_snp_sites	memory	Int	Amount of memory (in GB) to allocate to the task	2	Optional	Core_Gene_SNP	runtime	
+create_microreact_project	cpu	Int	Number of CPUs to allocate to the task	2	Optional	Microreact_Export	runtime	
+create_microreact_project	disk_size	Int	Amount of storage (in GB) to allocate to the task	10	Optional	Microreact_Export	runtime	
+create_microreact_project	docker	String	The Docker container to use for the task	us-docker.pkg.dev/general-theiagen/theiagen/microreact_export:1.0.0	Optional	Microreact_Export	docker	
+create_microreact_project	memory	Int	Amount of memory/RAM (in GB) to allocate to the task	4	Optional	Microreact_Export	runtime	
 create_table_from_array	cpu	Int	Number of CPUs to allocate to the task	1	Optional	Dorado_Basecalling	runtime	
 create_table_from_array	disk_size	Int	Amount of storage (in GB) to allocate to the task	25	Optional	Dorado_Basecalling	runtime	
 create_table_from_array	docker	String	The Docker container to use for the task	us-docker.pkg.dev/general-theiagen/theiagen/terra-tools:2023-06-21	Optional	Dorado_Basecalling	docker	
@@ -704,10 +714,10 @@ dorado_trim	cpu	Int	Number of CPUs to allocate to the task	4	Optional	Dorado_Bas
 dorado_trim	disk_size	Int	Amount of storage (in GB) to allocate to the task	100	Optional	Dorado_Basecalling	runtime	
 dorado_trim	docker	String	The Docker container to use for the task. This is not the most up-to-date image since there is a bug with this Dorado subcommand in v0.9.0	us-docker.pkg.dev/general-theiagen/staphb/dorado:0.8.3	Optional	Dorado_Basecalling	docker	
 dorado_trim	memory	Int	Amount of memory/RAM (in GB) to allocate to the task	16	Optional	Dorado_Basecalling	runtime	
-download_terra_table	cpu	Int	Number of CPUs to allocate to the task	1	Optional	CZGenEpi_Prep, Mercury_Prep_N_Batch, Terra_2_ENA	runtime	
-download_terra_table	disk_size	Int	Amount of storage (in GB) to allocate to the task	10	Optional	CZGenEpi_Prep, Mercury_Prep_N_Batch, Terra_2_ENA	runtime	
-download_terra_table	docker	String	The Docker container to use for the task	us-docker.pkg.dev/general-theiagen/theiagen/terra-tools:2023-06-21	Optional	CZGenEpi_Prep, Mercury_Prep_N_Batch, Terra_2_ENA	docker	
-download_terra_table	memory	Int	Amount of memory/RAM (in GB) to allocate to the task	2	Optional	CZGenEpi_Prep, Mercury_Prep_N_Batch, Terra_2_ENA	runtime	
+download_terra_table	cpu	Int	Number of CPUs to allocate to the task	1	Optional	CZGenEpi_Prep, Mercury_Prep_N_Batch, Microreact_Export, Terra_2_ENA	runtime	
+download_terra_table	disk_size	Int	Amount of storage (in GB) to allocate to the task	10	Optional	CZGenEpi_Prep, Mercury_Prep_N_Batch, Microreact_Export, Terra_2_ENA	runtime	
+download_terra_table	docker	String	The Docker container to use for the task	us-docker.pkg.dev/general-theiagen/theiagen/terra-tools:2023-06-21	Optional	CZGenEpi_Prep, Mercury_Prep_N_Batch, Microreact_Export, Terra_2_ENA	docker	
+download_terra_table	memory	Int	Amount of memory/RAM (in GB) to allocate to the task	2	Optional	CZGenEpi_Prep, Mercury_Prep_N_Batch, Microreact_Export, Terra_2_ENA	runtime	
 est_genome_length	cpu	Int	Number of CPUs to allocate to the task	1	Optional	TheiaViral_Illumina_PE, TheiaViral_ONT	runtime	
 est_genome_length	disk_size	Int	Amount of storage (in GB) to allocate to the task	50	Optional	TheiaViral_Illumina_PE, TheiaViral_ONT	runtime	
 est_genome_length	docker	String	Docker image to use for the task	us-docker.pkg.dev/general-theiagen/theiagen/ncbi-datasets:18.9.0-python-jq	Optional	TheiaViral_Illumina_PE, TheiaViral_ONT	docker	
@@ -1168,7 +1178,7 @@ ksnp4_task	disk_size	Int	Amount of storage (in GB) to allocate to the task	100	O
 ksnp4_task	docker_image	String	The Docker container to use for the task	us-docker.pkg.dev/general-theiagen/staphb/ksnp4:4.1	Optional	kSNP4	docker	
 ksnp4_task	kmer_size	Int	The length of kmer containing the SNP you want ksnp4 to use	19	Optional	kSNP4	general	
 ksnp4_task	ksnp4_args	String	Additional arguments you want kSNP4 to use; e.g., "-ML" or "-NJ"		Optional	kSNP4	general	
-ksnp4_task	memory	Int	Amount of memory/RAM (in GB) to allocate to the task	4	Optional	kSNP4	runtime	
+ksnp4_task	memory	Int	Amount of memory/RAM (in GB) to allocate to the task	16	Optional	kSNP4	runtime	
 ksnp4_task	previous_ksnp4_snps	File	File with existing SNPs for the current run to be appended to.		Optional	kSNP4	general	
 ksnp4_workflow	cluster_name_updated	String	Internal component, do not modify	cluster_name where ' ' is substituted with '_'	Optional	kSNP4	general	
 ksnp4_workflow	data_summary_column_names	String	A comma-separated list of the column names from the sample-level data table for generating a data summary (presence/absence .csv matrix); e.g., "amrfinderplus_amr_genes,amrfinderplus_virulence_genes"		Optional	kSNP4	general	
@@ -1531,8 +1541,8 @@ merlin_magic	stxtyper_cpu	Int	Internal component, do not modify	1	Optional	Theia
 merlin_magic	stxtyper_cpu	Int	Number of CPUs to allocate to the task	1	Optional	TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT	runtime	
 merlin_magic	stxtyper_disk_size	Int	Internal component, do not modify	50	Optional	TheiaEuk_Illumina_PE, TheiaEuk_ONT	general	
 merlin_magic	stxtyper_disk_size	Int	Amount of storage (in GB) to allocate to the task	50	Optional	TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT	runtime	
-merlin_magic	stxtyper_docker_image	String	Internal component, do not modify	us-docker.pkg.dev/general-theiagen/staphb/stxtyper:1.0.42	Optional	TheiaEuk_Illumina_PE, TheiaEuk_ONT	general	
-merlin_magic	stxtyper_docker_image	String	The Docker container to use for the task	us-docker.pkg.dev/general-theiagen/staphb/stxtyper:1.0.42	Optional	TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT	docker	
+merlin_magic	stxtyper_docker_image	String	Internal component, do not modify	us-docker.pkg.dev/general-theiagen/staphb/stxtyper:1.0.45	Optional	TheiaEuk_Illumina_PE, TheiaEuk_ONT	general	
+merlin_magic	stxtyper_docker_image	String	The Docker container to use for the task	us-docker.pkg.dev/general-theiagen/staphb/stxtyper:1.0.45	Optional	TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT	docker	
 merlin_magic	stxtyper_enable_debug	Boolean	Internal component, do not modify	False	Optional	TheiaEuk_Illumina_PE, TheiaEuk_ONT	general	
 merlin_magic	stxtyper_enable_debug	Boolean	When enabled, additional messages are printed and files in $TMPDIR are not removed after running	False	Optional	TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT	general	
 merlin_magic	stxtyper_memory	Int	Internal component, do not modify	4	Optional	TheiaEuk_Illumina_PE, TheiaEuk_ONT	general	
@@ -2772,6 +2782,16 @@ vadr_update	vadr_opts	String	Options for the v-annotate.pl VADR script	--noseqna
 vadr_update	vadr_skip_length	Int	Minimum assembly length (unambiguous) to run VADR	10000	Optional	VADR_Update	general	True
 version_capture	docker	String	The Docker container to use for the task	us-docker.pkg.dev/general-theiagen/theiagen/alpine-plus-bash:3.20.0	Optional	AMRFinderPlus, AMR_Search, Assembly_Fetch, Augur, Augur_Prep, BaseSpace_Fetch, CZGenEpi_Prep, Cauris_CladeTyper, Clair3_Variants_ONT, Concatenate_Column_Content, Concatenate_Illumina_Lanes, Core_Gene_SNP, Dorado_Basecalling, Fetch_SRR_Accession, Find_Shared_Variants, Freyja_Dashboard, Freyja_FASTQ, Freyja_Plot, Gambit_Query, Kraken_ONT, Kraken_PE, Kraken_SE, Lyve_SET, MashTree_FASTA, Mercury_Prep_N_Batch, Metabuli, NCBI_Scrub_PE, NCBI_Scrub_SE, Nextclade_Batch, Pangolin_Update, PhyloCompare, RASUSA, Rename_FASTQ, SRA_Fetch, Snippy_Streamline, Snippy_Streamline_FASTA, Snippy_Tree, Snippy_Variants, TBProfiler_tNGS, Terra_2_ENA, Terra_2_GISAID, Terra_2_NCBI, TheiaCoV_ClearLabs, TheiaCoV_FASTA, TheiaCoV_FASTA_Batch, TheiaCoV_Illumina_PE, TheiaCoV_Illumina_SE, TheiaCoV_ONT, TheiaEuk_Illumina_PE, TheiaEuk_ONT, TheiaMeta_Illumina_PE, TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT, TheiaValidate, TheiaViral_Illumina_PE, TheiaViral_ONT, TheiaViral_Panel, Transfer_Column_Content, Usher, VADR_Update, Zip_Column_Content, kSNP3, kSNP4	docker	
 version_capture	timezone	String	Set the time zone to get an accurate date of analysis (uses UTC by default)		Optional	AMRFinderPlus, AMR_Search, Assembly_Fetch, Augur, Augur_Prep, BaseSpace_Fetch, CZGenEpi_Prep, Cauris_CladeTyper, Clair3_Variants_ONT, Concatenate_Column_Content, Concatenate_Illumina_Lanes, Core_Gene_SNP, Dorado_Basecalling, Fetch_SRR_Accession, Find_Shared_Variants, Freyja_Dashboard, Freyja_FASTQ, Freyja_Plot, Gambit_Query, Kraken_ONT, Kraken_PE, Kraken_SE, Lyve_SET, MashTree_FASTA, Mercury_Prep_N_Batch, Metabuli, NCBI_Scrub_PE, NCBI_Scrub_SE, Nextclade_Batch, Pangolin_Update, PhyloCompare, RASUSA, Rename_FASTQ, SRA_Fetch, Snippy_Streamline, Snippy_Streamline_FASTA, Snippy_Tree, Snippy_Variants, TBProfiler_tNGS, Terra_2_ENA, Terra_2_GISAID, Terra_2_NCBI, TheiaCoV_ClearLabs, TheiaCoV_FASTA, TheiaCoV_FASTA_Batch, TheiaCoV_Illumina_PE, TheiaCoV_Illumina_SE, TheiaCoV_ONT, TheiaEuk_Illumina_PE, TheiaEuk_ONT, TheiaMeta_Illumina_PE, TheiaProk_FASTA, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT, TheiaValidate, TheiaViral_Illumina_PE, TheiaViral_ONT, TheiaViral_Panel, Transfer_Column_Content, Usher, VADR_Update, Zip_Column_Content, kSNP3, kSNP4	general	
+wf_microreact_export	access_token	String	Users token used to upload projects to their Microreact account		Optional	Microreact_Export	general	
+wf_microreact_export	date_column	String	Column within the input Terra table to be used as the date designation		Optional	Microreact_Export	general	
+wf_microreact_export	download_table	Boolean	When true, will download th specified Terra table	True	Optional	Microreact_Export	general	
+wf_microreact_export	matrix_files	Array[File]	A list of matrix files a user would like to upload to the Microreact project. Can be written as [this.matrix1, this.matrix2, etc].		Optional	Microreact_Export	general	
+wf_microreact_export	metadata_columns	Array[String]	A list of column names from the input Terra table that the user would like to be included in their Microreact metadata table		Optional	Microreact_Export	general	
+wf_microreact_export	metadata_file	File	To be used if a separate metadata TSV is required other than downloading a Terra table		Optional	Microreact_Export	general	
+wf_microreact_export	project_url	String	URL used to update a microreact project. Can be found as the code within the webpage URL. "microreact.org/project/<project_url>-<title>""		Optional	Microreact_Export	general	
+wf_microreact_export	remove_file_columns	Boolean	When true, this will remove all columns that contain file opjects to prevent the pushing of Google cloud addresses to the metadata table	True	Optional	Microreact_Export	general	
+wf_microreact_export	restricted_access	Boolean	Sets the access level of the project to restricted when true. Only those specifically added will be able to access.	True	Optional	Microreact_Export	general	
+wf_microreact_export	tree_files	Array[File]	A list of tree files a user would like to upload to the Microreact project. Can be written as [this.tree1, this.tree2, etc].		Optional	Microreact_Export	general	
 wg_reorder_matrix	cpu	Int	Number of CPUs to allocate to the task	1	Optional	Snippy_Tree	runtime	
 wg_reorder_matrix	disk_size	Int	Amount of storage (in GB) to allocate to the task	100	Optional	Snippy_Tree	runtime	
 wg_reorder_matrix	docker	String	The Docker container to use for the task	us-docker.pkg.dev/general-theiagen/staphb/mykrobe:0.12.1	Optional	Snippy_Tree	docker	

docs/assets/tables/all_inputs.tsv

@@ -685,6 +685,8 @@ metaspades_version	String	The version of metaspades	TheiaMeta_Illumina_PE
 metaviralspades_docker	String	Docker image used for MetaviralSPAdes	TheiaViral_Illumina_PE
 metaviralspades_status	String	Status of MetaviralSPAdes assembly	TheiaViral_Illumina_PE
 metaviralspades_version	String	Version of MetaviralSPAdes used	TheiaViral_Illumina_PE
+microreact_api_response	File	Result of the Microreact API request	Microreact_Export
+microreact_input	File	A project file in JSON format that can be used for manual upload to Microreact	Microreact_Export
 midas_docker	String	MIDAS docker image used	TheiaProk_Illumina_PE, TheiaProk_Illumina_SE
 midas_primary_genus	String	The primary genus detected by MIDAS	TheiaMeta_Illumina_PE, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE
 midas_report	File	TSV report of full MIDAS results	TheiaMeta_Illumina_PE, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE