Metaphlan4 update: add --index (#3604)

* Add --index to metaphlan * correct --input_type
nf-core · Jul 6, 2023 · 31ec447 · 31ec447
1 parent c5b528d
commit 31ec447
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Showing 2 changed files with 4 additions and 2 deletions.
diff --git a/modules/nf-core/metaphlan/metaphlan/main.nf b/modules/nf-core/metaphlan/metaphlan/main.nf
@@ -23,12 +23,13 @@ process METAPHLAN_METAPHLAN {
     script:
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
-    def input_type  = ("$input".endsWith(".fastq.gz") || "$input".endsWith(".fq.gz")) ? "--input_type fastq" :  ("$input".contains(".fasta")) ? "--input_type fasta" : ("$input".endsWith(".bowtie2out.txt")) ? "--input_type bowtie2out" : "--input_type sam"
+    def input_type = "$input" =~ /.*\.(fastq|fq)/ ? "--input_type fastq" : "$input" =~ /.*\.(fasta|fna|fa)/ ? "--input_type fasta" : "$input".endsWith(".bowtie2out.txt") ? "--input_type bowtie2out" : "--input_type sam"
     def input_data  = ("$input_type".contains("fastq")) && !meta.single_end ? "${input[0]},${input[1]}" : "$input"
     def bowtie2_out = "$input_type" == "--input_type bowtie2out" || "$input_type" == "--input_type sam" ? '' : "--bowtie2out ${prefix}.bowtie2out.txt"
 
     """
     BT2_DB=`find -L "${metaphlan_db_latest}" -name "*rev.1.bt2l" -exec dirname {} \\;`
+    BT2_DB_INDEX=`find -L ${metaphlan_db_latest} -name "*.rev.1.bt2l" | sed 's/\\.rev.1.bt2l\$//' | sed 's/.*\\///'`
 
     metaphlan \\
         --nproc $task.cpus \\
@@ -37,6 +38,7 @@ process METAPHLAN_METAPHLAN {
         $args \\
         $bowtie2_out \\
         --bowtie2db \$BT2_DB \\
+        --index \$BT2_DB_INDEX \\
         --biom ${prefix}.biom \\
         --output_file ${prefix}_profile.txt
 

diff --git a/tests/modules/nf-core/metaphlan/metaphlan/main.nf b/tests/modules/nf-core/metaphlan/metaphlan/main.nf
@@ -53,7 +53,7 @@ workflow test_metaphlan_sam {
     db    = [ [], file('https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/delete_me/metaphlan4_database.tar.gz', checkIfExists: true) ]
 
     UNTAR ( db )
-    SAMTOOLS_VIEW ( input, [] ,[])
+    SAMTOOLS_VIEW ( input, [[],[]], [])
     METAPHLAN_METAPHLAN ( SAMTOOLS_VIEW.out.sam, UNTAR.out.untar.map{ it[1] } )
 }