diff --git a/conf/modules.config b/conf/modules.config index 8430be2d..3c150832 100644 --- 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 index c7f130ca..c80fc1ed 100644 --- 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 index 764148d9..4a79fd46 100644 --- 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