From c6c84f55a173b9d32e49c52e952d0153ded2b2c7 Mon Sep 17 00:00:00 2001 From: EC2 Default User Date: Tue, 19 Nov 2024 20:11:46 +0000 Subject: [PATCH] need to confirm that this image is the issue --- configs/containers.config | 7 ++--- modules/local/downloadVirusHostDB/main.nf | 2 +- tests/nextflow.config | 14 ++++------ workflows/index.nf | 34 +++++++++++------------ 4 files changed, 25 insertions(+), 32 deletions(-) diff --git a/configs/containers.config b/configs/containers.config index 2cb821c..b5d2991 100644 --- a/configs/containers.config +++ b/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 diff --git a/modules/local/downloadVirusHostDB/main.nf b/modules/local/downloadVirusHostDB/main.nf index 16cc74e..0b21b70 100644 --- a/modules/local/downloadVirusHostDB/main.nf +++ b/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 ''' } diff --git a/tests/nextflow.config b/tests/nextflow.config index bfa6695..4817fd6 100644 --- a/tests/nextflow.config +++ b/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 diff --git a/workflows/index.nf b/workflows/index.nf index faa32b4..04b1394 100644 --- a/workflows/index.nf +++ b/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" }