Merge pull request #81 from asp8200/fix_getGenomeAttribute

Add fct getGenomeAttribute to main.nf
nf-core · Mar 13, 2024 · b6bcae3 · b6bcae3
2 parents cc7ad45 + 5608a1e
commit b6bcae3
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -8,15 +8,18 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 ### `Added`
 
 - [#73](https://github.com/nf-core/bamtofastq/pull/73) Sync TEMPLATE with tools 2.12
+- [#75](https://github.com/nf-core/bamtofastq/pull/75), [#78](https://github.com/nf-core/bamtofastq/pull/78) Sync TEMPLATE with tools 2.13
+- [#80](https://github.com/nf-core/bamtofastq/pull/80) Sync TEMPLATE with tools 2.13.1
 
 ### `Changed`
 
-- [#74](https://github.com/nf-core/bamtofastq/pull/74) Update to samtools to v1.19.2.
-- [#76](https://github.com/nf-core/bamtofastq/pull/76) Update modules cat/fastq and samtools/view.
+- [#74](https://github.com/nf-core/bamtofastq/pull/74) Update to samtools to v1.19.2
+- [#76](https://github.com/nf-core/bamtofastq/pull/76) Update modules cat/fastq and samtools/view
 
 ### `Fixed`
 
-- [#77](https://github.com/nf-core/bamtofastq/pull/77) Fix detection of paired-end or single-end for input with less than 1000 reads.
+- [#77](https://github.com/nf-core/bamtofastq/pull/77) Fix detection of paired-end or single-end for input with less than 1000 reads
+- [#81](https://github.com/nf-core/bamtofastq/pull/81) Add function `getGenomeAttribute` to `main.nf` and remove it from `subworkflows/local/utils_nfcore_bamtofastq_pipeline/main.nf`
 
 ### `Dependencies`
 

diff --git a/main.nf b/main.nf
@@ -21,8 +21,6 @@ include { BAMTOFASTQ  } from './workflows/bamtofastq'
 include { PIPELINE_INITIALISATION } from './subworkflows/local/utils_nfcore_bamtofastq_pipeline'
 include { PIPELINE_COMPLETION     } from './subworkflows/local/utils_nfcore_bamtofastq_pipeline'
 
-include { getGenomeAttribute      } from './subworkflows/local/utils_nfcore_bamtofastq_pipeline'
-
 /*
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
     GENOME PARAMETER VALUES
@@ -106,6 +104,25 @@ workflow {
     )
 }
 
+/*
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+    FUNCTIONS
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+*/
+
+//
+// Get attribute from genome config file e.g. fasta
+//
+
+def getGenomeAttribute(attribute) {
+    if (params.genomes && params.genome && params.genomes.containsKey(params.genome)) {
+        if (params.genomes[ params.genome ].containsKey(attribute)) {
+            return params.genomes[ params.genome ][ attribute ]
+        }
+    }
+    return null
+}
+
 /*
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
     THE END

diff --git a/subworkflows/local/utils_nfcore_bamtofastq_pipeline/main.nf b/subworkflows/local/utils_nfcore_bamtofastq_pipeline/main.nf
@@ -149,18 +149,6 @@ def validateInputParameters() {
     genomeExistsError()
 }
 
-//
-// Get attribute from genome config file e.g. fasta
-//
-def getGenomeAttribute(attribute) {
-    if (params.genomes && params.genome && params.genomes.containsKey(params.genome)) {
-        if (params.genomes[ params.genome ].containsKey(attribute)) {
-            return params.genomes[ params.genome ][ attribute ]
-        }
-    }
-    return null
-}
-
 //
 // Exit pipeline if incorrect --genome key provided
 //