Merge branch 'single-read-raw-clean' into single-read-profile

naobservatory · Dec 4, 2024 · 3648257 · 3648257
2 parents 6216f77 + 3fe2bd2
commit 3648257
Show file tree

Hide file tree

Showing 6 changed files with 12 additions and 6 deletions.
diff --git 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
@@ -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
+}
diff --git 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 "${projectDir}/configs/read_type.config"
 process.queue = "will-batch-queue" // AWS Batch job queue
diff --git a/configs/run_dev_se.config b/configs/run_dev_se.config
@@ -30,4 +30,5 @@ includeConfig "${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
@@ -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"
diff --git 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 "${projectDir}/configs/output.config"
+includeConfig "${projectDir}/configs/output.config"
+includeConfig "${projectDir}/configs/read_type.config"