Test parsing actions tbprofiler version for proper provenance output (#59)

* test parsing actions tbprofiler version for provenance

* fix syntax

* test raw version outputs in github actions

* remove 2>&1 from the version command that causes bad output in github actions testing

* test removing mamba

* remove use mamba comment

Author: taranewman

modules/tbprofiler.nf

@@ -92,7 +92,7 @@ process tbprofiler {
     printf -- "- process_name: tbprofiler\\n"                  >> ${sample_id}_tbprofiler_provenance.yml
     printf -- "  tools:\\n"                                    >> ${sample_id}_tbprofiler_provenance.yml
     printf -- "    - tool_name: tb-profiler\\n"                >> ${sample_id}_tbprofiler_provenance.yml
-    printf -- "      tool_version: \$(tb-profiler profile --version 2>&1 | cut -d ' ' -f 3)\\n" >> ${sample_id}_tbprofiler_provenance.yml
+    printf -- "      tool_version: \$(tb-profiler profile --version | cut -d ' ' -f 3)\\n" >> ${sample_id}_tbprofiler_provenance.yml
     printf -- "      subcommand: profile\\n"                   >> ${sample_id}_tbprofiler_provenance.yml
     printf -- "      parameters:\\n"                           >> ${sample_id}_tbprofiler_provenance.yml
     printf -- "        - parameter: --platform\\n"             >> ${sample_id}_tbprofiler_provenance.yml

nextflow.config

@@ -54,7 +54,6 @@ def parsePipelineName(name) {
 profiles {
     conda {
 	conda.enabled = true
-	conda.useMamba = true
 	process.conda = "$baseDir/environments/environment.yml"
 	if (params.cache){
 	    conda.cacheDir = params.cache