luslab-umitools | Cleanup for submission

tools/umi_tools/environment.yml

@@ -2,10 +2,6 @@
 #   conda env create -f environment.yml
 name: nfcore-module-umitools
 channels:
-  - conda-forge
   - bioconda
-  - defaults
 dependencies:
-  
-  ## bioconda packages, see above
   - umi_tools=1.0.1

tools/umi_tools/main.nf

@@ -23,28 +23,25 @@ process umitools_dedup {
     shell:
 
     // Init
-    error_message = ""
+    internal_prog = "umi_tools dedup"
-    args_exist = "false"
+    internal_args = "--log=${sample_id}.dedup.log"
-    internal_prog = "umi_tools dedup "
-    internal_args = ""
 
     // Check main args string exists and strip whitespace
     if(params.umitools_dedup_args) {
-        internal_args = params.umitools_dedup_args
+        ext_args = params.umitools_dedup_args
-        internal_args = internal_args.trim() + " --log=${sample_id}.dedup.log "
+        internal_args += " " + ext_args.trim()
-        args_exist = "true"
     }
-    else {
+
-        error_message = "params.umitools_dedup_args does not exist, please define to run this module."
+    // Contruct CL line
+    internal_cl = "${internal_prog} ${internal_args} -I $bam -S ${sample_id}.dedup.bam --output-stats=${sample_id}"
+
+    // Log
+    if (params.verbose){
+        println ("[MODULE] umi_tools/dedup exec: " + internal_cl)
     }
 
     //SHELL
     """
-    if ${args_exist}; then
+    ${internal_cl}
-        ${internal_prog}${internal_args}-I $bam -S ${sample_id}.dedup.bam --output-stats=${sample_id}
-    else
-        echo "${error_message}" 1>&2
-        exit 1
-    fi
     """
 }

tools/umi_tools/test/main.nf

@@ -60,11 +60,6 @@ Channel
 --------------------------------------------------------------------------------------*/
 
 workflow {
-    // Logging
-    if (params.verbose){
-        println ("[MODULE] umi_tools/dedup ARGS: " + params.umitools_dedup_args)
-    }
-
     // Run dedup
     umitools_dedup ( ch_test_meta_bambai )
 

tools/umi_tools/umi_tools.yml

@@ -13,11 +13,12 @@ tools:
         documentation: https://umi-tools.readthedocs.io/en/latest/
 processes:
     - dedup:
-        opperation: |
+        operation: |
             Set command args to params.umitools_dedup_args
-            The program will execute with the following pattern: umi_tools dedeup ARGS -I $bam -S SAMPLE_ID.dedup.bam --output-stats=SAMPLE_ID
+            The program will execute with the following pattern:
+                umi_tools dedup --log={SAMPLE_ID}.dedup.log {params.umitools_dedup_args} -I {SAMPLE_ID}.bam -S {SAMPLE_ID}.dedup.bam --output-stats={SAMPLE_ID}
         description: |
-            Groups PCR duplicates and deduplicates reads to yield one read per group. 
+            Groups PCR duplicates and de-duplicates reads to yield one read per group. 
             Use this when you want to remove the PCR duplicates prior to any downstream analysis.
         input:
             - sample_id:
@@ -33,10 +34,10 @@ processes:
             - dedupBam:
                 type: tuple
                 description: A tuple of samples id and output bam file
-                pattern: *SAMPLE_ID.dedup.bam
+                pattern: [sample_id, *SAMPLE_ID.dedup.bam]
             - report:
                 type: file
-                description: Log file for the umi_tools opperation
+                description: Log file for the umi_tools operation
                 pattern: *SAMPLE_ID.dedup.log
 authors:
     - @candiceh08