Merge pull request #170 from nf-core/fix-forward-stranded

Fix "Access to undefined parameter `forwardStranded`" warnings
nf-core · Oct 21, 2024 · f84692e · f84692e
2 parents f61aac0 + f458d8b
commit f84692e
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Showing 3 changed files with 12 additions and 2 deletions.
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -18,6 +18,10 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - [#137](https://github.com/nf-core/nascent/pull/137) - Use singularity containers for PINTS
 - [#142](https://github.com/nf-core/nascent/pull/142) - Updated CHM13 references
 
+### Fixed
+
+- [#170](https://github.com/nf-core/nascent/pull/170) - Remove "Access to undefined parameter forwardStranded" warnings
+
 ## v2.2.0 - 2024-03-05
 
 ### Added

diff --git a/modules/local/dreg_prep/main.nf b/modules/local/dreg_prep/main.nf
@@ -11,6 +11,7 @@ process DREG_PREP {
     input:
     tuple val(meta), path(bam_file), val(index)
     path  sizes
+    val assay_type
 
     output:
     tuple val(meta), path("${prefix}.pos.bw"), path("${prefix}.neg.bw"), emit: dreg_bigwig
@@ -21,6 +22,10 @@ process DREG_PREP {
 
     script:
     prefix = task.ext.prefix ?: "${meta.id}"
+    // NOTE https://github.com/hyulab/PINTS/blob/700f2c44b967413a19fc6b66bd876b53b6f31002/pints/io_engine.py#L436-L446
+    def forwardStranded_assays = ["PROseq", "mNETseq"]
+    def forwardStranded = forwardStranded_assays.contains(assay_type)
+
     if (meta.single_end) {
         """
         echo "Creating BigWigs suitable as inputs to dREG"
@@ -74,7 +79,7 @@ process DREG_PREP {
         echo "bedGraph to bigwig done"
         """
     } else {
-        if (params.forwardStranded) {
+        if (forwardStranded) {
             """
             samtools view -@ $task.cpus -bf 0x2 ${bam_file} | samtools sort -n -@ $task.cpus \\
                 > ${prefix}.dreg.bam

diff --git a/subworkflows/local/coverage_graphs.nf b/subworkflows/local/coverage_graphs.nf
@@ -61,7 +61,8 @@ workflow COVERAGE_GRAPHS {
 
     DREG_PREP (
         bam_bai,
-        sizes
+        sizes,
+        params.assay_type,
     )
 
     emit:
-Original file line number
+Diff line change
@@ Expand Up / @@ -61,7 +61,8 @@ workflow COVERAGE_GRAPHS { @@
         DREG_PREP (
             bam_bai,
-            sizes
+            sizes,
+            params.assay_type,
         )
         emit:
@@ Expand Down @@