Merge pull request #335 from nf-core/fix-mirtrace-staging-bug

Fix mirtrace staging bug

CHANGELOG.md

@@ -8,6 +8,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - [[#328]](https://github.com/nf-core/smrnaseq/pull/328) - Fix [casting issue](https://github.com/nf-core/smrnaseq/issues/327) in mirtrace module
 - [[#334]](https://github.com/nf-core/smrnaseq/pull/334) - Fix [input channel cardinality](https://github.com/nf-core/smrnaseq/issues/331) in `MIRDEEP2_RUN` module
 - [[#334]](https://github.com/nf-core/smrnaseq/pull/334) - Fix [bowtie conda version](https://github.com/nf-core/smrnaseq/issues/333) in `BOWTIE_MAP_SEQ` module
+- [[#335]](https://github.com/nf-core/smrnaseq/pull/335) - Final fix for [casting issue](https://github.com/nf-core/smrnaseq/issues/327) in mirtrace module
 
 ### Software dependencies
 

modules/local/mirtrace.nf

@@ -7,7 +7,8 @@ process MIRTRACE_RUN {
         'biocontainers/mirtrace:1.0.1--hdfd78af_1' }"
 
     input:
-    tuple val(adapter), val(ids), val(reads)
+    tuple val(adapter), val(ids), path(reads)
+    path(mirtrace_config)
 
     output:
     path "mirtrace/*"  , emit: mirtrace
@@ -25,19 +26,15 @@ process MIRTRACE_RUN {
         tmem = task.memory.toBytes()
         java_mem = "-Xms${tmem} -Xmx${tmem}"
     }
-    def config_lines = [ids,reads]
-    .transpose()
-    .collect({ id, path -> "echo '${path},${id}' >> mirtrace_config" })
+
     """
     export mirtracejar=\$(dirname \$(which mirtrace))
 
-    ${config_lines.join("\n    ")}
-
     java $java_mem -jar \$mirtracejar/mirtrace.jar --mirtrace-wrapper-name mirtrace qc  \\
         --species $params.mirtrace_species \\
         $primer \\
         $protocol \\
-        --config mirtrace_config \\
+        --config $mirtrace_config \\
         --write-fasta \\
         --output-dir mirtrace \\
         --force

subworkflows/local/mirtrace.nf

@@ -9,7 +9,18 @@ workflow MIRTRACE {
     reads      // channel: [ val(adapterseq), [ val(ids) ], [ path(reads) ] ]
 
     main:
-    reads | MIRTRACE_RUN
+
+    //Staging the files as path() but then getting the filenames for the config file that mirtrace needs
+    //Directly using val(reads) as in previous versions is not reliable as staging between work directories is not 100% reliable if not explicitly defined via nextflow itself
+    ch_mirtrace_config =
+    reads.map { adapter, ids, reads -> [ids,reads]}
+    .transpose()
+    .collectFile { id, path -> "./${path.getFileName().toString()}\n" } // operations need a channel, so, should be outside the module
+
+    MIRTRACE_RUN (
+        reads,
+        ch_mirtrace_config
+    )
 
     emit:
     results    = MIRTRACE_RUN.out.mirtrace