refactor: use Channel.fromPath(type:'dir') for fastq screen

obviates need to mount/bind db dir to container
CCBR · Sep 19, 2023 · c3f487b · c3f487b
1 parent 9c96c9b
commit c3f487b
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Showing 3 changed files with 6 additions and 8 deletions.
diff --git a/conf/modules.config b/conf/modules.config
@@ -15,10 +15,4 @@ process {
             saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
         ]
     }
-    withName: FASTQ_SCREEN {
-        // use bind for singularity and volume for docker
-        containerOptions = { workflow.containerEngine == 'singularity' ?
-            "--mount type=bind,src=$params.fastq_screen.db_dir,dst=$params.fastq_screen.db_dir" :
-            "--volume $params.fastq_screen.db_dir:$params.fastq_screen.db_dir "}
-    }
 }
diff --git a/modules/local/qc.nf b/modules/local/qc.nf
@@ -35,7 +35,8 @@ process FASTQ_SCREEN {
     container = "${params.containers.fastq_screen}"
 
     input:
-        tuple val(meta), path(fastq), path(conf)
+        tuple val(meta), path(fastq), path(conf), path(db_dir)
+
     output:
         path("${meta.id}*_screen.*"), emit: screen
 

diff --git a/subworkflows/local/qc.nf b/subworkflows/local/qc.nf
@@ -33,7 +33,10 @@ workflow QC {
     main:
         raw_fastqs.combine(Channel.value("raw")) | FASTQC_RAW
         trimmed_fastqs.combine(Channel.value("trimmed")) | FASTQC_TRIMMED
-        trimmed_fastqs.combine(Channel.fromPath(params.fastq_screen.conf)) | FASTQ_SCREEN
+        trimmed_fastqs
+          .combine(Channel.fromPath(params.fastq_screen.conf, checkIfExists: true))
+          .combine(Channel.fromPath(params.fastq_screen.db_dir,
+                                    type: 'dir', checkIfExists: true)) | FASTQ_SCREEN
 
         PRESEQ(aligned_bam)
         // when preseq fails, write NAs for the stats that are calculated from its log