diff --git a/configs/profiles.config b/configs/profiles.config index 24196a0..a1ba78c 100644 --- a/configs/profiles.config +++ b/configs/profiles.config @@ -1,4 +1,4 @@ -// Currently universal settings and params +// Currently universal setting docker.enabled = true wave.enabled = true aws.client.maxConnections = 1000 @@ -7,10 +7,6 @@ aws.client.connectionTimeout = 0 aws.client.socketTimeout = 0 nextflow.enable.moduleBinaries = true -params { - // Whether the underlying data is paired-end or single-end - single_end = new File(params.sample_sheet).text.readLines()[0].contains('fastq_2') ? false : true -} // Workflow run profiles profiles { diff --git a/configs/read_type.config b/configs/read_type.config new file mode 100644 index 0000000..cd55388 --- /dev/null +++ b/configs/read_type.config @@ -0,0 +1,6 @@ +// Universal flags for read type (single-end vs paired-end) + +params { + // Whether the underlying data is paired-end or single-end + single_end = new File(params.sample_sheet).text.readLines()[0].contains('fastq_2') ? false : true +} \ No newline at end of file diff --git a/configs/run.config b/configs/run.config index b405bb1..6da753a 100644 --- a/configs/run.config +++ b/configs/run.config @@ -34,4 +34,5 @@ includeConfig "${projectDir}/configs/containers.config" includeConfig "${projectDir}/configs/resources.config" includeConfig "${projectDir}/configs/profiles.config" includeConfig "${projectDir}/configs/output.config" +includeConfig "${projectDir}/configs/read_type.config" process.queue = "will-batch-queue" // AWS Batch job queue diff --git a/configs/run_dev_se.config b/configs/run_dev_se.config index 7025424..39080c0 100644 --- a/configs/run_dev_se.config +++ b/configs/run_dev_se.config @@ -30,4 +30,5 @@ includeConfig "${projectDir}/configs/containers.config" includeConfig "${projectDir}/configs/resources.config" includeConfig "${projectDir}/configs/profiles.config" includeConfig "${projectDir}/configs/output.config" +includeConfig "${projectDir}/configs/read_type.config" process.queue = "simon-batch-queue" // AWS Batch job queue diff --git a/tests/run.config b/tests/run.config index 320ef04..f4a4511 100644 --- a/tests/run.config +++ b/tests/run.config @@ -32,4 +32,5 @@ params { includeConfig "${projectDir}/configs/containers.config" includeConfig "${projectDir}/configs/profiles.config" +includeConfig "${projectDir}/configs/read_type.config" includeConfig "${projectDir}/configs/output.config" \ No newline at end of file diff --git a/tests/run_dev_se.config b/tests/run_dev_se.config index d3db01c..dc0709f 100644 --- a/tests/run_dev_se.config +++ b/tests/run_dev_se.config @@ -33,4 +33,5 @@ params { includeConfig "${projectDir}/configs/containers.config" includeConfig "${projectDir}/configs/profiles.config" -includeConfig "${projectDir}/configs/output.config" \ No newline at end of file +includeConfig "${projectDir}/configs/output.config" +includeConfig "${projectDir}/configs/read_type.config" \ No newline at end of file