blast-blastn.diff

Changes in component 'nf-core/blast/blastn'
'modules/nf-core/blast/blastn/meta.yml' is unchanged
Changes in 'blast/blastn/main.nf':
--- modules/nf-core/blast/blastn/main.nf
+++ modules/nf-core/blast/blastn/main.nf
@@ -1,6 +1,5 @@
 process BLAST_BLASTN {
     tag "$meta.id"
-    label 'process_medium'
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
@@ -9,7 +8,7 @@
 
     input:
     tuple val(meta) , path(fasta)
-    tuple val(meta2), path(db)
+    tuple val(meta2), path(db, stageAs: "BLASTN_DB_DIR")
     path taxidlist
     val taxids
     val negative_tax
@@ -32,6 +31,7 @@
     if (taxidlist_cmd.any() && taxids_cmd.any()) {
         log.error("ERROR: taxidlist and taxids can not be used at the same time, choose only one argument to use for tax id filtering.")
     }
+    def db_name = meta2.db_name ?: ''
 
     """
     if [ "${is_compressed}" == "true" ]; then
@@ -40,21 +40,48 @@
 
     export BLASTDB=${db}
 
-    DB=`find -L ./ -name "*.nal" | sed 's/\\.nal\$//'`
-    if [ -z "\$DB" ]; then
-        DB=`find -L ./ -name "*.nin" | sed 's/\\.nin\$//'`
+    if [ "${db_name}" == "" ]; then
+        DB=`find -L ./ -name "*.nal" | sed 's/\\.nal\$//'`
+        if [ -z "\$DB" ]; then
+            DB=`find -L ./ -name "*.nin" | sed 's/\\.nin\$//'`
+        fi
+    else
+        DB="${db}/${db_name}"
     fi
     echo Using \$DB
 
-    blastn \\
+    if [ -n "${taxidlist_cmd}${taxids_cmd}" ]; then
+        # Symlink the tax* files (needed for -taxid options to work)
+        for file in taxdb.btd taxdb.bti taxonomy4blast.sqlite3; do
+            if [ ! -f ${db}/\$file ]; then
+                echo "Error: \$file not found in ${db}"
+                exit 1
+            fi
+            ln -s ${db}/\$file .
+        done
+    fi
+
+    timeout 11.9h blastn \\
         -num_threads ${task.cpus} \\
         -db \$DB \\
         -query ${fasta_name} \\
         ${taxidlist_cmd} \\
         ${taxids_cmd} \\
         ${args} \\
-        -out ${prefix}.txt
+        -out ${prefix}.txt \\
+        2> >( tee "${prefix}.error.log" >&2 ) || true
 
+    # Fallback if blastn fails or times out — make sure output exists
+    if [[ ! -s "${prefix}.txt" ]]
+    then
+        echo "blastn failed or timed out — creating empty output"
+        touch "${prefix}.txt"
+    fi
+
+    if [[ -s "${prefix}.error.log" ]]
+    then
+        grep -qF 'BLAST Database error: Taxonomy ID(s) not found.Taxonomy ID(s) not found' "${prefix}.error.log"
+    fi
     """
 
     stub:

'modules/nf-core/blast/blastn/environment.yml' is unchanged
'modules/nf-core/blast/blastn/tests/main.nf.test' is unchanged
'modules/nf-core/blast/blastn/tests/nextflow.config' is unchanged
'modules/nf-core/blast/blastn/tests/main.nf.test.snap' is unchanged
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