need to confirm that this image is the issue

configs/containers.config

@@ -1,11 +1,8 @@
 // Specify Docker containers for workflow processes
 process {
-//    withLabel: base {
-//        container = "eclipse/alpine_jdk8:latest"
-//        // NB: As of 2024-07-01, no more specific tag available
-//    }
     withLabel: base {
-        container = "ubuntu:latest"
+        container = "eclipse/alpine_jdk8:latest"
+        // NB: As of 2024-07-01, no more specific tag available
     }
     withLabel: MultiQC {
         // NB: As of 2024-07-01, newer versions currently cause errors

modules/local/downloadVirusHostDB/main.nf

@@ -8,6 +8,6 @@ process DOWNLOAD_VIRUS_HOST_DB {
         path("virus-host-db.tsv")
     shell:
         '''
-        curl -sS --retry 3 !{virus_host_db_url} > virus-host-db.tsv
+        curl -sS !{virus_host_db_url} > virus-host-db.tsv
         '''
 }

tests/nextflow.config

@@ -11,18 +11,14 @@ params {
     base_dir = "./" // Parent for working and output directories (can be S3)
 
     // Cow & E. coli
-    genome_urls = "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=nucleotide&id=NC_037352.1&rettype=fasta https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=nucleotide&id=NZ_CP128970.1&rettype=fasta"
+    genome_urls = "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=nucleotide&id=NZ_CP128970.1&rettype=fasta"
 
     // URLs for downloading reference genomes etc
     taxonomy_url = "https://ftp.ncbi.nlm.nih.gov/pub/taxonomy/taxdump_archive/taxdmp_2024-06-01.zip"
     virus_host_db_url = "https://www.genome.jp/ftp/db/virushostdb/virushostdb.tsv"
-    human_url = "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=nucleotide&id=NC_000022.11&rettype=fasta"
 
-    // Cow - https://www.ncbi.nlm.nih.gov/datasets/genome/GCF_002263795.3/, 
-    // Pig - https://www.ncbi.nlm.nih.gov/datasets/genome/GCF_000003025.6/
-    // Carp - https://www.ncbi.nlm.nih.gov/datasets/genome/GCF_000951615.1/
-    // Mouse - https://www.ncbi.nlm.nih.gov/datasets/genome/GCF_000001635.27/
-    // E. coli - https://www.ncbi.nlm.nih.gov/datasets/genome/GCF_030389925.1/
+    // This is actually ecoli
+    human_url = "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=nucleotide&id=NZ_CP128970.1&rettype=fasta"
 
     ssu_url = "https://www.arb-silva.de/fileadmin/silva_databases/release_138.1/Exports/SILVA_138.1_SSURef_NR99_tax_silva.fasta.gz"
     lsu_url = "https://www.arb-silva.de/fileadmin/silva_databases/release_138.1/Exports/SILVA_138.1_LSURef_NR99_tax_silva.fasta.gz"
@@ -40,7 +36,7 @@ params {
     // Other input values
     virus_taxid = "10239"
     viral_taxids_exclude = "2731619 2732413 2732411" // Exclude Caudoviricetes, Malgrantaviricetes, Faserviricetes
-    host_taxa_screen = "vertebrate human" // Host taxa to screen for when building reference virus DB
+    host_taxa_screen = "human" // Host taxa to screen for when building reference virus DB
 
     // Initializing run params to avoid warnings
     kraken_memory = ""
@@ -80,4 +76,4 @@ process {
 }
 
 // What I need to do because I got error for touch .command.trace
-docker.fixOwnership = true
+// docker.fixOwnership = true

workflows/index.nf

@@ -29,16 +29,16 @@ workflow INDEX {
     // Build viral taxonomy and infection DB
     MAKE_VIRUS_TAXONOMY_DB(params.taxonomy_url, params.virus_host_db_url, params.host_taxon_db, params.virus_taxid, params.viral_taxids_exclude)
     // Get reference DB of viral genomes of interest
-    MAKE_VIRUS_GENOME_DB(params.ncbi_viral_params, MAKE_VIRUS_TAXONOMY_DB.out.db, params.genome_patterns_exclude, params.host_taxa_screen)
+//    MAKE_VIRUS_GENOME_DB(params.ncbi_viral_params, MAKE_VIRUS_TAXONOMY_DB.out.db, params.genome_patterns_exclude, params.host_taxa_screen)
     // Build viral alignment index
-    MAKE_VIRUS_INDEX(MAKE_VIRUS_GENOME_DB.out.fasta)
+//    MAKE_VIRUS_INDEX(MAKE_VIRUS_GENOME_DB.out.fasta)
     // Build other alignment indices
-    MAKE_HUMAN_INDEX(params.human_url)
-    MAKE_CONTAMINANT_INDEX(params.genome_urls, params.contaminants)
+//    MAKE_HUMAN_INDEX(params.human_url)
+//    MAKE_CONTAMINANT_INDEX(params.genome_urls, params.contaminants)
     // Other index files
-    JOIN_RIBO_REF(params.ssu_url, params.lsu_url)
-    DOWNLOAD_BLAST_DB(params.blast_db_name)
-    EXTRACT_KRAKEN_DB(params.kraken_db, "kraken_db", true)
+//    JOIN_RIBO_REF(params.ssu_url, params.lsu_url)
+//    DOWNLOAD_BLAST_DB(params.blast_db_name)
+//    EXTRACT_KRAKEN_DB(params.kraken_db, "kraken_db", true)
     // Publish results
     params_str = JsonOutput.prettyPrint(JsonOutput.toJson(params))
     params_ch = Channel.of(params_str).collectFile(name: "index-params.json")
@@ -54,16 +54,16 @@ workflow INDEX {
         MAKE_VIRUS_TAXONOMY_DB.out.nodes >> "results"
         MAKE_VIRUS_TAXONOMY_DB.out.names >> "results"
         // Virus genome database
-        MAKE_VIRUS_GENOME_DB.out.fasta >> "results"
-        MAKE_VIRUS_GENOME_DB.out.metadata >> "results"
+//        MAKE_VIRUS_GENOME_DB.out.fasta >> "results"
+//        MAKE_VIRUS_GENOME_DB.out.metadata >> "results"
         // Alignment indexes
-        MAKE_HUMAN_INDEX.out.bbm >> "results"
-        MAKE_HUMAN_INDEX.out.bt2 >> "results"
-        MAKE_CONTAMINANT_INDEX.out.bbm >> "results"
-        MAKE_CONTAMINANT_INDEX.out.bt2 >> "results"
-        MAKE_VIRUS_INDEX.out.bt2 >> "results"
+//        MAKE_HUMAN_INDEX.out.bbm >> "results"
+//        MAKE_HUMAN_INDEX.out.bt2 >> "results"
+//        MAKE_CONTAMINANT_INDEX.out.bbm >> "results"
+//        MAKE_CONTAMINANT_INDEX.out.bt2 >> "results"
+//        MAKE_VIRUS_INDEX.out.bt2 >> "results"
         // Other reference files & directories
-        JOIN_RIBO_REF.out.ribo_ref >> "results"
-        DOWNLOAD_BLAST_DB.out.db >> "results"
-        EXTRACT_KRAKEN_DB.out >> "results"
+//        JOIN_RIBO_REF.out.ribo_ref >> "results"
+//        DOWNLOAD_BLAST_DB.out.db >> "results"
+//        EXTRACT_KRAKEN_DB.out >> "results"
 }