Umitools/dedup adding log and bug workaround

modules/nf-core/umitools/dedup/main.nf

@@ -12,7 +12,8 @@ process UMITOOLS_DEDUP {
     val get_output_stats
 
     output:
-    tuple val(meta), path("*.bam")             , emit: bam
+    tuple val(meta), path("${prefix}.bam")     , emit: bam
+    tuple val(meta), path("*.log")             , emit: log
     tuple val(meta), path("*edit_distance.tsv"), optional:true, emit: tsv_edit_distance
     tuple val(meta), path("*per_umi.tsv")      , optional:true, emit: tsv_per_umi
     tuple val(meta), path("*per_position.tsv") , optional:true, emit: tsv_umi_per_position
@@ -23,16 +24,18 @@ process UMITOOLS_DEDUP {
 
     script:
     def args = task.ext.args ?: ''
-    def prefix = task.ext.prefix ?: "${meta.id}"
+    prefix = task.ext.prefix ?: "${meta.id}"
     def paired = meta.single_end ? "" : "--paired"
-    def stats = get_output_stats ? "--output-stats $prefix" : ""
+    stats = get_output_stats ? "--output-stats ${prefix}" : ""
+    if ("$bam" == "${prefix}.bam") error "Input and output names are the same, set prefix in module configuration to disambiguate!"
 
     if (!(args ==~ /.*--random-seed.*/)) {args += " --random-seed=100"}
     """
     PYTHONHASHSEED=0 umi_tools \\
         dedup \\
         -I $bam \\
         -S ${prefix}.bam \\
+        -L ${prefix}.log \\
         $stats \\
         $paired \\
         $args

modules/nf-core/umitools/dedup/meta.yml

@@ -3,6 +3,7 @@ description: Deduplicate reads based on the mapping co-ordinate and the UMI atta
 keywords:
   - umitools
   - deduplication
+  - dedup
 tools:
   - umi_tools:
       description: >
@@ -40,6 +41,10 @@ output:
       type: file
       description: BAM file with deduplicated UMIs.
       pattern: "*.{bam}"
+  - log:
+      type: file
+      description: File with logging information
+      pattern: "*.{log}"
   - tsv_edit_distance:
       type: file
       description: Reports the (binned) average edit distance between the UMIs at each position.

tests/modules/nf-core/umitools/dedup/test.yml

@@ -35,6 +35,8 @@
     - path: output/umitools/test.umi_extract.log
       contains: ["Starting barcode extraction"]
     - path: output/umitools/versions.yml
+    - path: output/umitools/test.dedup.log
+      contains: ["# UMI-tools version:"]
 
 - name: umitools dedup test_umitools_dedup_paired_end_no_stats
   command: nextflow run ./tests/modules/nf-core/umitools/dedup -entry test_umitools_dedup_paired_end_no_stats -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/umitools/dedup/nextflow.config
@@ -63,6 +65,8 @@
     - path: output/umitools/test.umi_extract.log
       contains: ["Starting barcode extraction"]
     - path: output/umitools/versions.yml
+    - path: output/umitools/test.dedup.log
+      contains: ["# UMI-tools version:"]
 
 - name: umitools dedup test_umitools_dedup_paired_end_stats
   command: nextflow run ./tests/modules/nf-core/umitools/dedup -entry test_umitools_dedup_paired_end_stats -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/umitools/dedup/nextflow.config
@@ -97,3 +101,5 @@
     - path: output/umitools/test.umi_extract.log
       contains: ["Starting barcode extraction"]
     - path: output/umitools/versions.yml
+    - path: output/umitools/test.dedup.log
+      contains: ["# UMI-tools version:"]