Fix ch_transcripts and ch_pubids for AWS

CHANGELOG.md

@@ -9,6 +9,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - [PR #27](https://github.com/nf-core/denovotranscript/pull/27) - Update spades resources and usage instructions
 - [PR #28](https://github.com/nf-core/denovotranscript/pull/28) - Template update for nf-core/tools v3.1.0
 - [PR #29](https://github.com/nf-core/denovotranscript/pull/29) - Template update for nf-core/tools v3.1.1
+- [PR #30](https://github.com/nf-core/denovotranscript/pull/30) - Fix ch_transcripts and ch_pubids for AWS
 
 ## v1.1.0 - [2024-11-28]
 

conf/test_full.config

@@ -10,6 +10,15 @@
 ----------------------------------------------------------------------------------------
 */
 
+process {
+    resourceLimits = [
+        cpus: 20,
+        memory: '200.GB',
+        time: '20.h'
+    ]
+    maxRetries    = 1
+}
+
 params {
     config_profile_name        = 'Full test profile'
     config_profile_description = 'Full test dataset to check pipeline function'

modules/local/orp_transrate/main.nf

@@ -34,6 +34,12 @@ process ORP_TRANSRATE {
     gunzip -c ${reads[0]} > ${prefix}_1.fq
     gunzip -c ${reads[1]} > ${prefix}_2.fq
 
+    # Ruby (a dependency of transrate) requires a writable tmp directory
+    mkdir ./tmp
+    export TMPDIR=./tmp
+    export TEMP=./tmp
+    export TMP=./tmp
+
     transrate \\
         --assembly $fasta \\
         --left ${prefix}_1.fq \\

workflows/denovotranscript.nf

@@ -202,12 +202,16 @@ workflow DENOVOTRANSCRIPT {
             ch_versions = ch_versions.mix(EVIGENE_TR2AACDS.out.versions)
 
             ch_transcripts = EVIGENE_TR2AACDS.out.okayset.map { meta, dir ->
-                def mrna_file = file("$dir/*okay.mrna")
-                return [ meta, mrna_file ]}
+                def mrna_file = dir.listFiles().find { it.name.endsWith('.okay.mrna') }
+                if (!mrna_file) throw new Exception("No .okay.mrna file found in ${dir}")
+                return [ meta, mrna_file ]
+            }
 
             ch_pubids = EVIGENE_TR2AACDS.out.okayset.map { meta, dir ->
-                def pubids_file = file("$dir/*.pubids")
-                return [ meta, pubids_file ]}
+                def pubids_file = dir.listFiles().find { it.name.endsWith('.pubids') }
+                if (!pubids_file) throw new Exception("No .pubids file found in ${dir}")
+                return [ meta, pubids_file ]
+            }
             //
             // MODULE: TX2GENE
             //