chore: update krakenuniq

modules.json

@@ -99,7 +99,7 @@
                     },
                     "krakenuniq/preloadedkrakenuniq": {
                         "branch": "master",
-                        "git_sha": "13b9d4854593c03e5e25e8a8f47462542c2c0dd4"
+                        "git_sha": "05649975c6611c6e007537a7984e186e12ae03af"
                     },
                     "krona/ktimporttaxonomy": {
                         "branch": "master",

modules/nf-core/krakenuniq/preloadedkrakenuniq/main.nf

@@ -1,4 +1,5 @@
 process KRAKENUNIQ_PRELOADEDKRAKENUNIQ {
+    tag "$meta.id"
     label 'process_high'
 
     conda (params.enable_conda ? "bioconda::krakenuniq=1.0.0" : null)
@@ -29,25 +30,31 @@ process KRAKENUNIQ_PRELOADEDKRAKENUNIQ {
     def args = task.ext.args ?: ''
     def args2 = task.ext.args ?: ''
 
-    def paired       = meta.single_end ? "" : "--paired"
+    def classified   = meta.single_end ? '"\${PREFIX}.classified.fastq"'   : '"\${PREFIX}.classified#.fastq"'
-    def classified   = meta.single_end ? '"\$PREFIX".classified.fastq'   : '"\$PREFIX".classified#.fastq'
+    def unclassified = meta.single_end ? '"\${PREFIX}.unclassified.fastq"' : '"\${PREFIX}.unclassified#.fastq"'
-    def unclassified = meta.single_end ? '"\$PREFIX".unclassified.fastq' : '"\$PREFIX".unclassified#.fastq'
+    def classified_option = save_output_fastqs ? "--classified-out ${classified}" : ''
-    def classified_option = save_output_fastqs ? "--classified-out ${classified}" : ""
+    def unclassified_option = save_output_fastqs ? "--unclassified-out ${unclassified}" : ''
-    def unclassified_option = save_output_fastqs ? "--unclassified-out ${unclassified}" : ""
+    def output_option = save_output ? '--output "\${PREFIX}.krakenuniq.classified.txt"' : ''
-    def output_option = save_output ? '--output "\$PREFIX".krakenuniq.classified.txt' : ""
+    def report = report_file ? '--report-file "\${PREFIX}.krakenuniq.report.txt"' : ''
-    def report = report_file ? '--report-file "\$PREFIX".krakenuniq.report.txt' : ""
+    def compress_reads_command = save_output_fastqs ? 'gzip --no-name *.fastq' : ''
-    def compress_reads_command = save_output_fastqs ? "gzip --no-name *.fastq" : ""
+    if (meta.single_end) {
-
         """
         krakenuniq \\
-        $args \\
             --db $db \\
-        --preload $ram_chunk_size \\
+            --preload \\
-        --threads $task.cpus
+            --preload-size $ram_chunk_size \\
+            --threads $task.cpus \\
+            $args
+
+        strip_suffix() {
+            local result=\$1
+            # Strip any file extensions.
+            echo "\${result%%.*}"
+        }
+
+        printf "%s\\n" ${fastqs} | while read FASTQ; do \\
+            PREFIX="\$(strip_suffix "\${FASTQ}")"
 
-#    for fastq in "${fastqs.join('\" \"')}"; do \\
-    for fastq in ${fastqs}; do \\
-        PREFIX=\$(echo \$fastq)
             krakenuniq \\
                 --db $db \\
                 --threads $task.cpus \\
@@ -56,9 +63,8 @@ process KRAKENUNIQ_PRELOADEDKRAKENUNIQ {
                 $unclassified_option \\
                 $classified_option \\
                 $output_option \\
-            $paired \\
                 $args2 \\
-            \$fastq
+                "\${FASTQ}"
         done
 
         $compress_reads_command
@@ -68,29 +74,28 @@ process KRAKENUNIQ_PRELOADEDKRAKENUNIQ {
             krakenuniq: \$(echo \$(krakenuniq --version 2>&1) | sed 's/^.*KrakenUniq version //; s/ .*\$//')
         END_VERSIONS
         """
-
+    } else {
-    stub:
-    def args = task.ext.args ?: ''
-    def args2 = task.ext.args ?: ''
-
-    def paired       = meta.single_end ? "" : "--paired"
-    def classified   = meta.single_end ? '"\$PREFIX".classified.fastq'   : '"\$PREFIX".classified#.fastq'
-    def unclassified = meta.single_end ? '"\$PREFIX".unclassified.fastq' : '"\$PREFIX".unclassified#.fastq'
-    def classified_option = save_output_fastqs ? "--classified-out ${classified}" : ""
-    def unclassified_option = save_output_fastqs ? "--unclassified-out ${unclassified}" : ""
-    def output_option = save_output ? '--output "\$PREFIX".krakenuniq.classified.txt' : ""
-    def report = report_file ? '--report-file "\$PREFIX".krakenuniq.report.txt' : ""
-    def compress_reads_command = save_output_fastqs ? "echo 'gzip --no-name *.fastq'" : ""
         """
-    echo "krakenuniq \\
+        krakenuniq \\
-        $args \\
             --db $db \\
-        --preload $ram_chunk_size \\
+            --preload \\
-        --threads $task.cpus"
+            --preload-size $ram_chunk_size \\
+            --threads $task.cpus \\
+            $args
 
-    for fastq in "${fastqs.join('\" \"')}"; do \\
+        strip_suffix() {
-        PREFIX=\$(echo \$fastq)
+            local result
-        echo "krakenuniq \\
+            read result
+            # Strip any trailing dot or underscore.
+            result="\${result%_}"
+            echo "\${result%.}"
+        }
+
+        printf "%s %s\\n" ${fastqs} | while read FASTQ; do \\
+            read -r -a FASTQ <<< "\${FASTQ}"
+            PREFIX="\$(printf "%s\\n" "\${FASTQ[@]}" |  sed -e 'N;s/^\\(.*\\).*\\n\\1.*\$/\\1\\n\\1/;D' | strip_suffix)"
+
+            krakenuniq \\
                 --db $db \\
                 --threads $task.cpus \\
                 $report \\
@@ -98,14 +103,9 @@ process KRAKENUNIQ_PRELOADEDKRAKENUNIQ {
                 $unclassified_option \\
                 $classified_option \\
                 $output_option \\
-            $paired \\
+                --paired \\
                 $args2 \\
-            \$fastq"
+                "\${FASTQ[@]}"
-
-        touch "\$PREFIX".classified.fastq.gz
-        touch "\$PREFIX".krakenuniq.classified.txt
-        touch "\$PREFIX".krakenuniq.report.txt
-        touch "\$PREFIX".unclassified.fastq.gz
         done
 
         $compress_reads_command
@@ -116,3 +116,109 @@ process KRAKENUNIQ_PRELOADEDKRAKENUNIQ {
         END_VERSIONS
         """
     }
+
+    stub:
+    def args = task.ext.args ?: ''
+    def args2 = task.ext.args ?: ''
+
+    def classified   = meta.single_end ? '"\${PREFIX}.classified.fastq"'   : '"\${PREFIX}.classified#.fastq"'
+    def unclassified = meta.single_end ? '"\${PREFIX}.unclassified.fastq"' : '"\${PREFIX}.unclassified#.fastq"'
+    def classified_option = save_output_fastqs ? "--classified-out ${classified}" : ''
+    def unclassified_option = save_output_fastqs ? "--unclassified-out ${unclassified}" : ''
+    def output_option = save_output ? '--output "\${PREFIX}.krakenuniq.classified.txt"' : ''
+    def report = report_file ? '--report-file "\${PREFIX}.krakenuniq.report.txt"' : ''
+    def compress_reads_command = save_output_fastqs ? 'gzip --no-name *.fastq' : ''
+    if (meta.single_end) {
+        """
+        echo krakenuniq \\
+            --db $db \\
+            --preload \\
+            --preload-size $ram_chunk_size \\
+            --threads $task.cpus \\
+            $args
+
+        strip_suffix() {
+            local result=\$1
+            # Strip any file extensions.
+            echo "\${result%%.*}"
+        }
+
+        printf "%s\\n" ${fastqs} | while read FASTQ; do \\
+            echo "\${FASTQ}"
+            PREFIX="\$(strip_suffix "\${FASTQ}")"
+            echo "\${PREFIX}"
+
+            echo krakenuniq \\
+                --db $db \\
+                --threads $task.cpus \\
+                $report \\
+                $output_option \\
+                $unclassified_option \\
+                $classified_option \\
+                $output_option \\
+                $args2 \\
+                "\${FASTQ}"
+
+            touch "\${PREFIX}.classified.fastq.gz"
+            touch "\${PREFIX}.krakenuniq.classified.txt"
+            touch "\${PREFIX}.krakenuniq.report.txt"
+            touch "\${PREFIX}.unclassified.fastq.gz"
+        done
+
+        echo $compress_reads_command
+
+        cat <<-END_VERSIONS > versions.yml
+        "${task.process}":
+            krakenuniq: \$(echo \$(krakenuniq --version 2>&1) | sed 's/^.*KrakenUniq version //; s/ .*\$//')
+        END_VERSIONS
+        """
+    } else {
+        """
+        echo krakenuniq \\
+            --db $db \\
+            --preload \\
+            --preload-size $ram_chunk_size \\
+            --threads $task.cpus \\
+            $args
+
+        strip_suffix() {
+            local result
+            read result
+            # Strip any trailing dot or underscore.
+            result="\${result%_}"
+            echo "\${result%.}"
+        }
+
+        printf "%s %s\\n" ${fastqs} | while read FASTQ; do \\
+            read -r -a FASTQ <<< "\${FASTQ}"
+            echo "\${FASTQ[@]}"
+            PREFIX="\$(printf "%s\\n" "\${FASTQ[@]}" |  sed -e 'N;s/^\\(.*\\).*\\n\\1.*\$/\\1\\n\\1/;D' | strip_suffix)"
+            echo "\${PREFIX}"
+
+            echo krakenuniq \\
+                --db $db \\
+                --threads $task.cpus \\
+                $report \\
+                $output_option \\
+                $unclassified_option \\
+                $classified_option \\
+                $output_option \\
+                --paired \\
+                $args2 \\
+                "\${FASTQ[@]}"
+
+            touch "\${PREFIX}.classified_1.fastq.gz" "\${PREFIX}.classified_2.fastq.gz"
+            touch "\${PREFIX}.krakenuniq.classified.txt"
+            touch "\${PREFIX}.krakenuniq.report.txt"
+            touch "\${PREFIX}.unclassified_1.fastq.gz" "\${PREFIX}.unclassified_2.fastq.gz"
+        done
+
+        echo $compress_reads_command
+
+        cat <<-END_VERSIONS > versions.yml
+        "${task.process}":
+            krakenuniq: \$(echo \$(krakenuniq --version 2>&1) | sed 's/^.*KrakenUniq version //; s/ .*\$//')
+        END_VERSIONS
+        """
+    }
+}

modules/nf-core/krakenuniq/preloadedkrakenuniq/meta.yml

@@ -51,13 +51,13 @@ output:
       description: |
         Reads classified as belonging to any of the taxa
         on the KrakenUniq database.
-      pattern: "*{fastq.gz}"
+      pattern: "*.fastq.gz"
   - unclassified_reads_fastq:
       type: file
       description: |
         Reads not classified to any of the taxa
         on the KrakenUniq database.
-      pattern: "*{fastq.gz}"
+      pattern: "*.fastq.gz"
   - classified_assignment:
       type: file
       description: |
@@ -68,10 +68,11 @@ output:
       description: |
         KrakenUniq report containing stats about classified
         and not classifed reads.
-      pattern: "*.{report.txt}"
+      pattern: "*.report.txt"
   - versions:
       type: file
       description: File containing software versions
       pattern: "versions.yml"
 authors:
   - "@mjamy"
+  - "@Midnighter"