Merge pull request #110 from nf-core/dev

Dev -> Master for 2.1.1 release

Author: edmundmiller

CHANGELOG.md

@@ -3,6 +3,12 @@
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/)
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
+## v2.1.1 - 2023-02-17
+
+### Fixed
+
+- [[#109](https://github.com/nf-core/nascent/pull/109)] - Fixed bug where using AWS igenomes or passing a pre-made index fails because of an update to the module expects them to have a metamap. Generation was still working.
+
 ## v2.1.0 - 2023-02-15
 
 ### Added

nextflow.config

@@ -215,7 +215,7 @@ manifest {
     description     = """Global Run-On sequencing analysis pipeline"""
     mainScript      = 'main.nf'
     nextflowVersion = '!>=22.10.1'
-    version         = '2.1.0'
+    version         = '2.1.1'
     doi             = '10.5281/zenodo.7245273'
 }
 

subworkflows/local/prepare_genome.nf

@@ -88,13 +88,15 @@ workflow PREPARE_GENOME {
     //
     ch_bwa_index = Channel.empty()
     ch_dragmap = Channel.empty()
+    // TODO Turn this into a switch
     if ('bwa' in prepare_tool_indices) {
         if (params.bwa_index) {
             if (params.bwa_index.endsWith('.tar.gz')) {
                 ch_bwa_index = UNTAR_BWA_INDEX ( params.bwa_index ).untar
                 ch_versions = ch_versions.mix(UNTAR_BWA_INDEX.out.versions)
             } else {
-                ch_bwa_index = file(params.bwa_index)
+                // TODO Give the meta from basename or genome?
+                ch_bwa_index = [ [meta: "Genome"], file(params.bwa_index) ]
             }
         } else {
             ch_bwa_index = BWA_INDEX ( [ [:], ch_fasta ] ).index
@@ -106,7 +108,8 @@ workflow PREPARE_GENOME {
                 ch_bwa_index = UNTAR_BWA_INDEX ( [ [:], params.bwamem2_index ] ).untar
                 ch_versions = ch_versions.mix(UNTAR_BWA_INDEX.out.versions)
             } else {
-                ch_bwa_index = file(params.bwamem2_index)
+                // TODO Give the meta from basename or genome?
+                ch_bwa_index = [ [meta: "Genome"], file(params.bwamem2_index) ]
             }
         } else {
             ch_bwa_index = BWAMEM2_INDEX ( [ [:], ch_fasta ] ).index
@@ -115,10 +118,11 @@ workflow PREPARE_GENOME {
     } else if ('dragmap' in prepare_tool_indices) {
         if (params.dragmap) {
             if (params.dragmap.endsWith('.tar.gz')) {
-                ch_bwa_index = UNTAR_DRAGMAP_INDEX ( params.dragmap ).untar
+                ch_dragmap = UNTAR_DRAGMAP_INDEX ( params.dragmap ).untar
                 ch_versions = ch_versions.mix(UNTAR_DRAGMAP_INDEX.out.versions)
             } else {
-                ch_bwa_index = file(params.dragmap)
+                // TODO Give the meta from basename or genome?
+                ch_dragmap = [ [meta: "Genome"], file(params.dragmap) ]
             }
         } else {
             ch_dragmap = DRAGMAP_HASHTABLE( [ [:], ch_fasta ] ).hashmap

tests/pipeline/references.nf.test

@@ -0,0 +1,32 @@
+def igenomes_base = 's3://ngi-igenomes/igenomes'
+
+nextflow_pipeline {
+
+    name "Test passing references"
+    script "main.nf"
+
+    // https://github.com/nf-core/nascent/issues/106
+    test("Should work with BWA Index") {
+        // FIXME PINTS Fails because it doesn't find anything.
+        config 'tests/pipeline/skip_pints.config'
+        when {
+            params {
+                outdir = "$outputDir"
+                aligner = "bwa"
+                // TODO Update these to human
+                bwa_index = "${igenomes_base}/Saccharomyces_cerevisiae/Ensembl/R64-1-1/Sequence/BWAIndex/version0.6.0/"
+                fasta = "${igenomes_base}/Saccharomyces_cerevisiae/Ensembl/R64-1-1/Sequence/WholeGenomeFasta/genome.fa"
+                gtf = "${igenomes_base}/Saccharomyces_cerevisiae/Ensembl/R64-1-1/Annotation/Genes/genes.gtf"
+            }
+        }
+
+        then {
+            assert workflow.success
+            assert snapshot(
+                workflow.trace.tasks().size(),
+            ).match()
+        }
+
+    }
+
+}

tests/pipeline/references.nf.test.snap

@@ -0,0 +1,8 @@
+{
+    "Should work with BWA Index": {
+        "content": [
+            128
+        ],
+        "timestamp": "2023-02-16T23:30:58+0000"
+    }
+}

tests/pipeline/skip_pints.config

@@ -0,0 +1,5 @@
+process {
+    withName: PINTS_CALLER {
+        ext.when = false
+    }
+}