Fix deacon CLI flags and decontaminate process name collision

The RUN_DEACON process still uses the old zcat-pipe-pigz pattern and the deprecated --log flag from before deacon v0.5.0. Deacon now handles compressed I/O and threading natively, and the flag was renamed to --summary. This commit updates RUN_DEACON to use deacon's native I/O with --output and --summary.

The DECONTAMINATE subworkflow also has a bug where it unconditionally calls both INDEX_CONTAMINANTS and GET_INDEX, then invokes RUN_DEACON twice with each result. This causes a Nextflow process name collision and means both code paths always run regardless of which parameters the user actually provided. This commit restructures the subworkflow to branch on whether the user supplied a local FASTA (contam_fasta) or a remote pre-built index URL (contam_link), running only the appropriate path.

Author: nrminor

modules/deacon.nf

@@ -60,9 +60,10 @@ process RUN_DEACON {
     script:
     def dbName = file(contam_index).getSimpleName()
     """
-    zcat ${reads} \
-    | deacon filter ${contam_index} --log ${dbName}.log.json \
-    | pigz > ${barcode}.decontam.fastq.gz
+    deacon filter ${contam_index} ${reads} \
+        --output ${barcode}.decontam.fastq.gz \
+        --summary ${dbName}.summary.json \
+        --threads ${task.cpus}
     """
 
 }

subworkflows/decontaminate.nf

@@ -6,15 +6,20 @@ workflow DECONTAMINATE {
     ch_contam_fasta
 
     main:
+    def has_local_fasta = params.contam_fasta && file(params.contam_fasta).isFile()
 
-    INDEX_CONTAMINANTS(ch_contam_fasta)
+    ch_built_index = has_local_fasta
+        ? INDEX_CONTAMINANTS(ch_contam_fasta)
+        : Channel.empty()
 
-    RUN_DEACON(ch_fastqs.combine(INDEX_CONTAMINANTS.out))
+    ch_fetched_index = (!has_local_fasta && params.contam_link)
+        ? GET_INDEX()
+        : Channel.empty()
 
-    GET_INDEX()
+    ch_index = ch_built_index.mix(ch_fetched_index)
 
-    RUN_DEACON(ch_fastqs.combine(GET_INDEX.out))
+    ch_decontaminated = RUN_DEACON(ch_fastqs.combine(ch_index))
 
     emit:
-    RUN_DEACON.out
+    ch_decontaminated
 }

subworkflows/quality_control.nf

@@ -14,7 +14,7 @@ workflow QUALITY_CONTROL {
     ch_contam_fasta
 
     main:
-    if ( params.contam_fasta && file(params.contam_fasta).isFile() ) {
+    if ( (params.contam_fasta && file(params.contam_fasta).isFile()) || params.contam_link ) {
         DECONTAMINATE(
             ch_reads,
             ch_contam_fasta