fix accessions for assemblies

bactopia · Jul 1, 2023 · c37e4ef · c37e4ef
1 parent dff203d
commit c37e4ef
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Showing 4 changed files with 8 additions and 7 deletions.
diff --git a/lib/nf/bactopia.nf b/lib/nf/bactopia.nf
@@ -195,6 +195,7 @@ def process_accession(accession, genome_size, species) {
     def meta = [:]
     meta.genome_size = genome_size
     meta.species = species
+
     if (accession.length() > 0) {
         if (accession.startsWith('GCF') || accession.startsWith('GCA')) {
             meta.id = accession.split(/\./)[0]

diff --git a/lib/nf/bactopia_tools.nf b/lib/nf/bactopia_tools.nf
@@ -132,7 +132,7 @@ def _collect_inputs(sample, dir, extension) {
     PATHS.gff = "annotator"
     PATHS.meta = "gather"
 
-    base_dir = "${dir}/${sample}/bactopia/main/"
+    base_dir = "${dir}/${sample}/main/"
     se = "${base_dir}/${PATHS['fastq']}/${sample}.fastq.gz"
     ont = "${base_dir}/${PATHS['fastq']}/.ont"
     pe1 = "${base_dir}/${PATHS['fastq']}/${sample}_R1.fastq.gz"

diff --git a/lib/nf/functions.nf b/lib/nf/functions.nf
@@ -412,15 +412,15 @@ def saveFiles(Map args) {
                 // outdir/<SAMPLE_NAME>/{main|tools}
                 if (goto_base) {
                     // my-sample/assembly-error.txt
-                    final_output = "${args.prefix}/bactopia/${final_output}"
+                    final_output = "${args.prefix}/${final_output}"
                 } else {
                     // my-sample/bactopia-main/assembler
                     if (process_name == "bakta" || process_name == "prokka") {
                         // my-sample/bactopia-main/<process_name>/<output>
-                        final_output = "${args.prefix}/bactopia/${args.opts.btype}/annotator/${final_output}"
+                        final_output = "${args.prefix}/${args.opts.btype}/annotator/${final_output}"
                     } else {
                         // my-sample/bactopia-main/<output>
-                        final_output = "${args.prefix}/bactopia/${args.opts.btype}/${final_output}"
+                        final_output = "${args.prefix}/${args.opts.btype}/${final_output}"
                     }
                 }
             } else {

diff --git a/modules/local/bactopia/gather/main.nf b/modules/local/bactopia/gather/main.nf
@@ -4,7 +4,7 @@ RESOURCES      = get_resources(workflow.profile, params.max_memory, params.max_c
 options        = initOptions(params.options ? params.options : [:], 'gather')
 options.ignore = [".fastq.gz", ".fna.gz"]
 options.btype  = options.btype ?: "main"
-conda_tools    = "bioconda::bactopia-gather=1.0.2"
+conda_tools    = "bioconda::bactopia-gather=1.0.3"
 conda_name     = conda_tools.replace("=", "-").replace(":", "-").replace(" ", "-")
 conda_env      = file("${params.condadir}/${conda_name}").exists() ? "${params.condadir}/${conda_name}" : conda_tools
 
@@ -16,8 +16,8 @@ process GATHER {
 
     conda (params.enable_conda ? conda_env : null)
     container "${ workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/bactopia-gather:1.0.2--hdfd78af_0' :
-        'quay.io/biocontainers/bactopia-gather:1.0.2--hdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/bactopia-gather:1.0.3--hdfd78af_0' :
+        'quay.io/biocontainers/bactopia-gather:1.0.3--hdfd78af_0' }"
 
     input:
     tuple val(meta), path(r1, stageAs: '*???-r1'), path(r2, stageAs: '*???-r2'), path(extra)