diff --git a/.github/workflows/pipeline_db.yaml b/.github/workflows/pipeline_db.yaml
index 834c4de1b..51e31481b 100644
--- a/.github/workflows/pipeline_db.yaml
+++ b/.github/workflows/pipeline_db.yaml
@@ -9,10 +9,6 @@ env:
     CONDA_ENVS_PATH: "/home/runner/miniconda/envs:/usr/share/miniconda/envs"
     CONDA_PKGS_DIRS: "/home/runner/miniconda/pkgs"
     GH_RESOURCES:    "--max_memory 6.GB --max_cpus 2"
-    SQLITE_CONFIG:   "/home/runner/.nextflow/assets/ktmeaton/plague-phylogeography/config/ncbimeta.yaml"
-    SQLITE_TABLE:    "BioSample"
-    SQLITE_BACKUP:   "/home/runner/.nextflow/assets/ktmeaton/plague-phylogeography/results/ncbimeta_db/update/latest/yersinia_pestis_db_BioSample.tsv"
-    SQLITE_TEST_DB: "/home/runner/work/plague-phylogeography/plague-phylogeography/test/ncbimeta_db/update/latest/output/database/yersinia_pestis_db.sqlite"
 #------------------------------------------------------------------------------#
 # Workflow conditions
 on:
@@ -74,18 +70,21 @@ jobs:
         shell: bash -l {0}
         run: scripts/install.sh ${{github.repository}} ${{ github.sha }}
       #------------------------------------------------------------------------#
-      #  Create the database
+      #  Create the example database
       - name: pipeline db create
         shell: bash -l {0}
         run: |
           conda activate ${PHYLO_CONDA_ENV}
           nextflow run -r ${{ github.sha }} ${{github.repository}} \
-            --ncbimeta_create ${SQLITE_CONFIG} \
+            --ncbimeta_create example/ncbimeta_test.yaml \
             --ncbimeta_api_param "--force-pause-seconds 0 --email ${{secrets.EMAIL}} --api ${{secrets.NCBI_API}}" \
+            --ncbimeta_output_dir test \
+            --ncbimeta_sqlite_db test.sqlite \
             --skip_sqlite_import \
             --skip_reference_download \
             --skip_outgroup_download \
-            --outdir test
+            --outdir test \
+            ${GH_RESOURCES}
           conda deactivate
       #------------------------------------------------------------------------#
       #  Update the database
@@ -94,13 +93,16 @@ jobs:
         run: |
           conda activate ${PHYLO_CONDA_ENV}
           nextflow run -r ${{ github.sha }} ${{github.repository}} \
-           --ncbimeta_update ${SQLITE_CONFIG} \
-           --ncbimeta_annot ${SQLITE_BACKUP} \
-           --ncbimeta_annot_table ${SQLITE_TABLE} \
-           --sqlite ${SQLITE_TEST_DB} \
-           --skip_sqlite_import \
-           --skip_reference_download \
-           --skip_outgroup_download \
-           --outdir test \
-           -resume
+            --ncbimeta_update example/ncbimeta_test.yaml \
+            --ncbimeta_sqlite_db test.sqlite \
+            --ncbimeta_output_dir test \
+            --ncbimeta_annot example/ncbimeta_test_annot.txt \
+            --ncbimeta_annot_table BioSample \
+            --sqlite test.sqlite \
+            --skip_sqlite_import \
+            --skip_reference_download \
+            --skip_outgroup_download \
+            --outdir test \
+            -resume \
+            ${GH_RESOURCES}
           conda deactivate
diff --git a/custom/GCA_009669545.1_ASM966954v1_genomic.fna b/example/GCA_009669545.1_ASM966954v1_genomic.fna
similarity index 100%
rename from custom/GCA_009669545.1_ASM966954v1_genomic.fna
rename to example/GCA_009669545.1_ASM966954v1_genomic.fna
diff --git a/custom/GCA_009669555.1_ASM966955v1_genomic.fna b/example/GCA_009669555.1_ASM966955v1_genomic.fna
similarity index 100%
rename from custom/GCA_009669555.1_ASM966955v1_genomic.fna
rename to example/GCA_009669555.1_ASM966955v1_genomic.fna
diff --git a/custom/GCA_009669565.1_ASM966956v1_genomic.fna b/example/GCA_009669565.1_ASM966956v1_genomic.fna
similarity index 100%
rename from custom/GCA_009669565.1_ASM966956v1_genomic.fna
rename to example/GCA_009669565.1_ASM966956v1_genomic.fna
diff --git a/custom/SAMN02442718/paired/SRR1048902_1.fastq.gz b/example/SAMN02442718/paired/SRR1048902_1.fastq.gz
similarity index 100%
rename from custom/SAMN02442718/paired/SRR1048902_1.fastq.gz
rename to example/SAMN02442718/paired/SRR1048902_1.fastq.gz
diff --git a/custom/SAMN02442718/paired/SRR1048902_2.fastq.gz b/example/SAMN02442718/paired/SRR1048902_2.fastq.gz
similarity index 100%
rename from custom/SAMN02442718/paired/SRR1048902_2.fastq.gz
rename to example/SAMN02442718/paired/SRR1048902_2.fastq.gz
diff --git a/custom/SAMN02442721/paired/SRR1048905_1.fastq.gz b/example/SAMN02442721/paired/SRR1048905_1.fastq.gz
similarity index 100%
rename from custom/SAMN02442721/paired/SRR1048905_1.fastq.gz
rename to example/SAMN02442721/paired/SRR1048905_1.fastq.gz
diff --git a/custom/SAMN02442721/paired/SRR1048905_2.fastq.gz b/example/SAMN02442721/paired/SRR1048905_2.fastq.gz
similarity index 100%
rename from custom/SAMN02442721/paired/SRR1048905_2.fastq.gz
rename to example/SAMN02442721/paired/SRR1048905_2.fastq.gz
diff --git a/custom/local_data_eager.tsv b/example/local_data_eager.tsv
similarity index 100%
rename from custom/local_data_eager.tsv
rename to example/local_data_eager.tsv
diff --git a/example/ncbimeta_test.yaml b/example/ncbimeta_test.yaml
new file mode 100644
index 000000000..ea1582088
--- /dev/null
+++ b/example/ncbimeta_test.yaml
@@ -0,0 +1,247 @@
+# User Configuration Variables
+OUTPUT_DIR : test
+EMAIL : myusername@domain.com
+API_KEY :
+FORCE_PAUSE_SECONDS : 1
+DATABASE : test.sqlite
+
+# NCBI Tables to Query
+TABLES :
+  - Assembly
+  - BioSample
+  - BioProject
+  - SRA
+  - Nucleotide
+  - Pubmed
+
+# Query Terms to Use
+SEARCH_TERMS :
+  - Assembly : (SAMN12991206[BioSample])
+  - BioProject : (PRJNA269675[BioProject IDs and Accessions])
+  - BioSample: (SAMN12991206[Accession])
+  - SRA : (SAMN12991206[BioSample])
+  - Nucleotide : (SAMN12991206[BioSample])
+  - Pubmed : (26634751[uid])
+
+# Columns of the database (ie. metadata fields to retrieve)
+TABLE_COLUMNS :
+
+  - Assembly :
+    - AssemblyAccession : AssemblyAccession
+    - AssemblyBioSampleAccession : BioSampleAccn
+    - AssemblyBioSampleID : BioSampleId
+    - AssemblyGenbankBioprojectAccession : GB_BioProjects, BioprojectAccn
+    - AssemblyGenbankID : GbUid
+    - AssemblyRefseqBioprojectAccession : RS_BioProjects, BioprojectAccn
+    - AssemblyRefSeqCategory : RefSeq_category
+    - AssemblyRefSeqID : RsUid
+    - AssemblyWGSAccession : WGS
+    - AssemblyInfraspecies : InfraspeciesList, Sub_value
+    - AssemblyIsolate : Isolate
+    - AssemblyOrganism : Organism
+    - AssemblySpeciesTaxonomicID : SpeciesTaxid
+    - AssemblySpeciesName : SpeciesName
+    - AssemblyTaxonomicID : Taxid
+    - AssemblyName : AssemblyName
+    - AssemblyStatus : AssemblyStatus
+    - AssemblyType : AssemblyType
+    - AssemblyCoverage : Coverage
+    - AssemblyChromosomes : Meta, Stat, category, chromosome_count
+    - AssemblyContigCount: Meta, Stat, category, contig_count
+    - AssemblyContigN50 : Meta, Stat, category, contig_n50
+    - AssemblyContigL50 : Meta, Stat, category, contig_l50
+    - AssemblyNonChromosomalReplicons : Meta, Stat, category, non_chromosome_replicon_count
+    - AssemblyReplicons : Meta, Stat, category, replicon_count
+    - AssemblyScaffolds : Meta, Stat, category, scaffold_count
+    - AssemblyScaffoldN50 : Meta, Stat, category, scaffold_n50
+    - AssemblyScaffoldL50 : Meta, Stat, category, scaffold_l50
+    - AssemblyTotalLength : Meta, Stat, category, total_length
+    - AssemblyUngappedLength : Meta, Stat, category, ungapped_length
+    - AssemblySubmitterOrganization : SubmitterOrganization
+    - AssemblySubmissionDate : SubmissionDate
+    - AssemblyReleaseDate : SeqReleaseDate
+    - AssemblyFTPAssemblyReport : FtpPath_Assembly_rpt
+    - AssemblyFTPGenbank : FtpPath_GenBank
+    - AssemblyFTPRefSeq : FtpPath_RefSeq
+    - AssemblyFTPStatsReport : FtpPath_Stats_rpt
+    - AssemblyComment : NullValue
+
+  - BioSample :
+    - BioSampleAccession: BioSample, accession
+    - BioSampleAccessionSecondary: NullValue
+    - BioSampleBioProjectAccession: XPATH, //Links/Link[@target='bioproject']/@label
+    - BioSampleSRAAccession: Id, db, SRA
+    - BioSampleTitle: Title
+    - BioSampleName: Id, db_label, Sample name
+    - BioSampleType: Attribute, harmonized_name, sample_type
+    - BioSamplePackage: Package
+    - BioSampleInfraspecies: Infraspecies
+    - BioSampleOrganism: Description, OrganismName
+    - BioSampleOrganismAlt: Description, Organism, taxonomy_name
+    - BioSampleSubSpecies: Attribute, harmonized_name, sub_species
+    - BioSampleStrain: Attribute, harmonized_name, strain
+    - BioSampleTaxonomyID: Organism, taxonomy_id
+    - BioSampleBiovar: Attribute, harmonized_name, biovar
+    - BioSampleSerovar: Attribute, harmonized_name, serovar
+    - BioSampleCollectionDate: Attribute, harmonized_name, collection_date
+    - BioSampleGeographicLocation: Attribute, harmonized_name, geo_loc_name
+    - BioSampleHost: Attribute, harmonized_name, host
+    - BioSampleHostDisease : Attribute, harmonized_name, host_disease
+    - BioSampleHostHealthState : Attribute, harmonized_name, host_health_state
+    - BioSampleIsolateNameAlias: Attribute, harmonized_name, isolate_name_alias
+    - BioSampleIsolationSource: Attribute, harmonized_name, isolation_source
+    - BioSampleLat : Attribute, attribute_name, Latitude
+    - BioSampleLatLon : Attribute, harmonized_name, lat_lon
+    - BioSampleLon : Attribute, attribute_name, Longitude
+    - BioSampleSubmissionDate: BioSample, submission_date
+    - BioSampleModificationDate: BioSample, last_update
+    - BioSamplePublicationDate: BioSample, publication_date
+    - BioSampleOrganization: Owner, Name
+    - BioSampleComment : NullValue
+
+  - BioProject :
+    - BioProjectAccession : ArchiveID, accession
+    - BioProjectDataType : ProjectDataTypeSet, DataType
+    - BioProjectDescription : ProjectDescr, Description
+    - BioProjectMethodType : Method, method_type
+    - BioProjectName : ProjectDescr, Name
+    - BioProjectTargetCapture : Target, capture
+    - BioProjectTargetMaterial : Target, material
+    - BioProjectTargetScope : Target, sample_scope
+    - BioProjectTitle : XPATH, //ProjectDescr/Title/text()
+    - BioProjectOrganismLabel : ProjectTypeSubmission, Label
+    - BioProjectOrganismStrain : ProjectTypeSubmission, Strain
+    - BioProjectOrganismTaxID : ProjectTypeSubmission, Organism, taxID
+    - BioProjectSpeciesTaxID : ProjectTypeSubmission, Organism, species
+    - BioProjectSupergroup : ProjectTypeSubmission, Supergroup
+    - BioProjectRegistrationDate : Submission, submitted
+    - BioProjectReleaseDate: ProjectReleaseDate
+    - BioProjectModificationDate: Submission, last_update
+    - BioProjectRelevanceMedical : Relevance, Medical
+    - BioProjectSubmitterOrganization : Organization, Name
+    - BioProjectPublished: Publication, status
+    - BioProjectDatePublished: Publication, date
+    - BioProjectPublicationID: Publication, id
+    - BioProjectPublicationDB: Publication, DbType
+    - BioProjectComment : NullValue
+
+  - Nucleotide :
+    - NucleotideAccession : GBSeq_primary-accession
+    - NucleotideAccessionVersion : GBSeq_accession-version
+    - NucleotideBioSampleAccession: XPATH, //GBXref[GBXref_dbname/text() = 'BioSample']/GBXref_id
+    - NucleotideBioProjectAccession : GBSeq_project
+    - NucleotideOrganism : GBSeq_organism
+    - NucleotideTaxonomy : GBSeq_taxonomy
+    - NucleotideDefinition : GBSeq_definition
+    - NucleotideDivision : GBSeq_division
+    - NucleotideReferenceJournal: GBSeq_references, GBReference_journal
+    - NucleotideReferenceTitle : GBSeq_references, GBReference_title
+    - NucleotideReferenceAuthors : GBSeq_references, GBReference_authors, GBAuthor
+    - NucleotideLength : GBSeq_length
+    - NucleotideMoleculeType : GBSeq_moltype
+    - NucleotideSeqDataName : GBSeq_alt-seq, GBAltSeqData_name
+    - NucleotideSource : GBSeq_source
+    - NucleotideStrandedness : GBSeq_strandedness
+    - NucleotideTopology : GBSeq_topology
+    - NucleotideCreateDate : GBSeq_create-date
+    - NucleotideUpdateDate : GBSeq_update-date
+    - NucleotideGenBankComment : GBSeq_comment
+    - NucleotideAnnotationDate: Annotation Date
+    - NucleotideAnnotationMethod: Annotation Method
+    - NucleotideAnnotationPipeline: Annotation Pipeline
+    - NucleotideAnnotationProvider: Annotation Provider
+    - NucleotideAnnotationSoftwarerevision: Annotation Software revision
+    - NucleotideAssemblyDate: Assembly Date
+    - NucleotideAssemblyMethod: Assembly Method
+    - NucleotideAssemblyName: Assembly Name
+    - NucleotideCDS: CDS
+    - NucleotideCDSTotal: CDS (total)
+    - NucleotideCDSCoding: CDS (coding)
+    - NucleotideCDSProtein: CDS (with protein)
+    - NucleotideCDSWithoutProtein: CDS (without protein)
+    - NucleotideCRISPRArrays: CRISPR Arrays
+    - NucleotideExpectedFinalVersion: Expected Final Version
+    - NucleotideFeaturesAnnotated: Features Annotated
+    - NucleotideGenes: Genes
+    - NucleotideGenesTotal: Genes (total)
+    - NucleotideGenesCoding: Genes (coding)
+    - NucleotideGenesRNA: Genes (RNA)
+    - NucleotideGenomeCoverage: Genome Coverage
+    - NucleotideGenomeRepresentation: Genome Representation
+    - NucleotidencRNAs: ncRNAs
+    - NucleotidePseudoGenes: Pseudo Genes
+    - NucleotidePseudoGenesTotal: Pseudo Genes (total)
+    - NucleotidePseudoGenesAmbResidues: Pseudo Genes (ambiguous residues)
+    - NucleotidePseudoGenesFrameshifted: Pseudo Genes (frameshifted)
+    - NucleotidePseudoGenesIncomplete: Pseudo Genes (incomplete)
+    - NucleotidePseudoGenesInternalStop: Pseudo Genes (internal stop)
+    - NucleotidePseudoGenesMultipleProblems: Pseudo Genes (multiple problems)
+    - NucleotiderRNAs: rRNAs
+    - NucleotiderRNAsComplete: complete rRNAs
+    - NucleotiderRNAsPartial: partial rRNAs
+    - NucleotideSequencingTechnology: Sequencing Technology
+    - NucleotideRNAs: tRNAs
+    - NucleotideComment : NullValue
+
+  - SRA :
+    - SRABioProjectAccession : STUDY, EXTERNAL_ID, namespace, BioProject
+    - SRABioSampleAccession : RUN_SET, RUN, Pool, EXTERNAL_ID, namespace, BioSample
+    - SRASampleAccession : SAMPLE_DESCRIPTOR, accession
+    - SRASampleName : SAMPLE, alias
+    - SRAExperimentAccession : EXPERIMENT, accession
+    - SRAExperimentName : EXPERIMENT, alias
+    - SRARunAccession : RUN, accession
+    - SRARunName : RUN, alias
+    - SRAIsPublic : RUN, is_public
+    - SRAStaticDataAvailable : RUN, static_data_available
+    - SRAStudyAcc : STUDY, accession
+    - SRAStudyName : STUDY_TITLE
+    - SRAStudyAbstract: STUDY_ABSTRACT
+    - SRAOrganismName : SAMPLE_NAME, SCIENTIFIC_NAME
+    - SRAOrganismTaxID : SAMPLE, TAXON_ID
+    - SRAClusterName : RUN, cluster_name
+    - SRAPlatform : PLATFORM
+    - SRAInstrumentModel : PLATFORM, INSTRUMENT_MODEL
+    - SRALibraryName : LIBRARY_NAME
+    - SRALibraryLayout : LIBRARY_LAYOUT
+    - SRALibrarySelection : LIBRARY_SELECTION
+    - SRALibrarySource : LIBRARY_SOURCE
+    - SRALibraryStrategy : LIBRARY_STRATEGY
+    - SRATotalBases : RUN_SET, RUN, total_bases
+    - SRATotalSize : RUN_SET, RUN, size
+    - SRATotalSpots : RUN_SET, RUN, total_spots
+    - SRAFileUrl : SRAFile, url
+    - SRAFileName : SRAFile, filename
+    - SRAFileSize : SRAFile, size
+    - SRAFileType : SRAFile, semantic_name
+    - SRARunPublishDate : RUN_SET, RUN, published
+    - SRACenterName : SUBMISSION, center_name
+    - SRAContactEmail : Organization, Contact, email
+    - SRALabName : SUBMISSION, lab_name
+    - SRASubmitterAccession : SUBMISSION, accession
+    - SRAComment : NullValue
+
+  - Pubmed :
+    - PubmedPublishYear : PubDate, Year
+    - PubmedPubishMonth : PubDate, Month
+    - PubmedPublishDay : PubDate, Day
+    - PubmedEPublishDate : EPubDate
+    - PubmedPublishModel : Article, PubModel
+    - PubmedType : PublicationType
+    - PubmedJournalTitle : Journal, Title
+    - PubmedJournalAbbrev : Journal, ISOAbbreviation
+    - PubmedJournalISSN : Journal, ISSN
+    - PubmedArticleTitle : ArticleTitle
+    - PubmedAbstract : AbstractText
+    - PubmedVolume : Volume
+    - PubmedIssue : Issue
+    - PubmedPages : MedlinePgn
+    - PubmedDOI : ELocationID, EIdType, doi
+    - PubmedAuthorsLastName : AuthorList, LastName
+    - PubmedAuthorsForeName : AuthorList, ForeName
+    - PubmedAuthorsAffiliation : AuthorList, Affiliation
+    - PubmedLanguage : Language
+    - PubmedCitations : Reference, Citation
+    - PubmedRecordStatus : MedlineCitation, Status
+    - PubmedPubStatus : PublicationStatus
+    - PubmedComment : NullValue
diff --git a/example/ncbimeta_test_annot.txt b/example/ncbimeta_test_annot.txt
new file mode 100644
index 000000000..3dcd12696
--- /dev/null
+++ b/example/ncbimeta_test_annot.txt
@@ -0,0 +1,3 @@
+BioSampleAccession	BioSampleHostDisease	BioSampleCollectionDate
+SAMN12991206	Plague	1984
+MissingAccession123	MissingDisease	MissingDate
diff --git a/main.nf b/main.nf
index 816aa8c91..6146269ed 100644
--- a/main.nf
+++ b/main.nf
@@ -207,7 +207,6 @@ if (!params.skip_ncbimeta_db_create && params.ncbimeta_create){
     tag "$ncbimeta_yaml"
     publishDir "${outdir}/ncbimeta_db/create", mode: 'copy'
     publishDir "${outdir}/ncbimeta_db/update/latest", mode: 'copy'
-    echo true
 
     ch_ncbimeta_yaml_create = Channel.fromPath(params.ncbimeta_create, checkIfExists: true)
                          .ifEmpty { exit 1, "NCBImeta config file not found: ${params.ncbimeta-create}" }
@@ -233,6 +232,9 @@ if (!params.skip_ncbimeta_db_create && params.ncbimeta_create){
 
 if(!params.skip_ncbimeta_db_update && params.ncbimeta_update){
 
+  ncbimeta_sqlite_db_latest = "${params.outdir}/ncbimeta_db/update/latest/${params.ncbimeta_output_dir}/database/${params.ncbimeta_sqlite_db}"
+  println "${ncbimeta_sqlite_db_latest}"
+
   process ncbimeta_db_update{
     /*
     Run NCBImeta queries to update, annotate, and join a previously created database.
@@ -263,23 +265,27 @@ if(!params.skip_ncbimeta_db_update && params.ncbimeta_update){
                          .ifEmpty { exit 1, "NCBImeta config file not found: ${params.ncbimeta_update}" }
 
     // If create and update not in same run (not fully reproducing finished pipeline)
+"${params.outdir}/ncbimeta_db/update/latest/${params.ncbimeta_output_dir}/database/${params.ncbimeta_sqlite_db}"
     if (!params.ncbimeta_create){
-        ch_ncbimeta_sqlite_update = Channel.fromPath(params.ncbimeta_sqlite_db_latest, checkIfExists: true)
-                                .ifEmpty { exit 1, "NCBImeta SQLite database not found: ${params.ncbimeta_sqlite_db_latest}" }
+        ch_ncbimeta_sqlite_update = Channel.fromPath("${ncbimeta_sqlite_db_latest}", checkIfExists: true)
+                                .ifEmpty { exit 1, "NCBImeta SQLite database not found: ${ncbimeta_sqlite_db_latest}" }
     }
 
     // If an annotation file has been supplied, the annotation script will be run
     if (params.ncbimeta_annot){
-    Channel
-      .fromPath(params.ncbimeta_annot, checkIfExists: true)
-      .ifEmpty { exit 1, "NCBImeta annotation file not found: ${params.ncbimeta_annot}" }
-      .collectFile(name: 'dummy_annot.txt', newLine: true, storeDir: "${workDir}")
+    ch_ncbimeta_annot = Channel
+                          .fromPath(params.ncbimeta_annot, checkIfExists: true)
+                          .ifEmpty { exit 1, "NCBImeta annotation file not found: ${params.ncbimeta_annot}" }
+    }
+    else{
+      ch_ncbimeta_annot = Channel.empty()
     }
 
     // IO and conditional behavior
     input:
     file ncbimeta_yaml from ch_ncbimeta_yaml_update
     file ncbimeta_sqlite from ch_ncbimeta_sqlite_update
+    file ncbimeta_annot from ch_ncbimeta_annot
     output:
     file "${params.ncbimeta_output_dir}/database/${params.ncbimeta_sqlite_db}" into ch_ncbimeta_sqlite_import
     file ncbimeta_yaml
@@ -299,10 +305,8 @@ if(!params.skip_ncbimeta_db_update && params.ncbimeta_update){
     # Execute NCBImeta
     NCBImeta.py --config ${ncbimeta_yaml}
     # If annotation file supplied, run the annotation script
-    if [[ ${params.ncbimeta_annot} != "false" ]]; then
-      ANNOT_FILE=`basename ${params.ncbimeta_annot}`
-      mv ${workDir}/dummy_annot.txt `pwd`/\$ANNOT_FILE;
-      NCBImetaAnnotateReplace.py --table ${params.ncbimeta_annot_table} --annot ${params.ncbimeta_annot} --database ${params.ncbimeta_output_dir}/database/${params.ncbimeta_sqlite_db}
+    if [[ "${params.ncbimeta_annot}" != "false" ]]; then
+      NCBImetaAnnotateReplace.py --table ${params.ncbimeta_annot_table} --annot ${ncbimeta_annot} --database ${params.ncbimeta_output_dir}/database/${params.ncbimeta_sqlite_db}
     fi
     # Drop old or outdated join tables
     sqlite3 ${params.ncbimeta_output_dir}/database/${params.ncbimeta_sqlite_db} "DROP TABLE IF EXISTS MasterFirst"
@@ -837,7 +841,6 @@ process eager{
   // Other variables and config
   tag "$biosample_val"
   publishDir "${outdir}/eager", mode: 'copy'
-  echo true
 
   // If a custom tsv was supplied
   if (params.eager_tsv){
diff --git a/nextflow.config b/nextflow.config
index 96a2488c5..6844bb91b 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -81,7 +81,6 @@ params{
   ncbimeta_output_dir = "output"
   ncbimeta_api_param = false
   ncbimeta_sqlite_db = "yersinia_pestis_db.sqlite"
-  ncbimeta_sqlite_db_latest = "${params.outdir}/ncbimeta_db/update/latest/${params.ncbimeta_output_dir}/database/${params.ncbimeta_sqlite_db}"
 
   // NCBImetaAnnotate parameters
   ncbimeta_annot_table = "BioSample"