output params string in md5sum_version.txt

Author: d4straub

modules/local/compare_sequences.nf

@@ -14,6 +14,7 @@ process COMPARE_SEQUENCES {
     val(similarity_threshold)        // Similarity threshold for maches of VSEARCH
     val(query_or_target)             // what reagion to evaluate (query,target,alignment) from params.expected_sequences_region
     val(trace_report_suffix)         // timestamp of pipeline info files
+    val(val_params_string)           // params map converted to string
 
     output:
     path("*.svg")                            , emit: svg
@@ -39,6 +40,7 @@ process COMPARE_SEQUENCES {
     # save unique tags to file
     echo "md5sum_version ${meta.id}" > "md5sum_version.txt"
     echo "trace_report_suffix ${trace_report_suffix}" >> "md5sum_version.txt"
+    echo "params ${val_params_string}" >> "md5sum_version.txt"
 
     # isolate warnings (when grep find no match, exit code is 1, "|| true" fixes that)
     grep "WARN -" "nucleotide-differences.log" | sed 's/^\\[1\\] //g' | sed 's/"//g' > Warnings.txt || true

subworkflows/local/comparison_wf.nf

@@ -5,6 +5,7 @@ include { COMPARE_PERFORMANCE     } from '../../modules/local/compare_performanc
 workflow COMPARISON_WF {
     take:
     val_md5sum_version     // md5sum of params appended by pipeline version
+    val_params_string      // params map converted to string
     trace_report_suffix    // params.trace_report_suffix that allows linkage to files in pipeline_info, such as pipeline_info/params_<trace_report_suffix>.json
     query_or_target        // region to evaluate
     ch_observed_sequences  // observed sequences (fasta)
@@ -24,7 +25,7 @@ workflow COMPARISON_WF {
         "query+target+ql+tl+qilo+qihi+tilo+tihi+gaps+mism+qstrand" )
 
     // Investigate mismatches per sample, plus barplot (y = number of sequences, x = number of mismatches)
-    COMPARE_SEQUENCES ( VSEARCH_USEARCHGLOBAL_BM.out.tsv, ch_observed_abundances, ch_expected_abundances.ifEmpty([]), similarity_threshold, query_or_target, trace_report_suffix )
+    COMPARE_SEQUENCES ( VSEARCH_USEARCHGLOBAL_BM.out.tsv, ch_observed_abundances, ch_expected_abundances.ifEmpty([]), similarity_threshold, query_or_target, trace_report_suffix, val_params_string )
     COMPARE_SEQUENCES.out.warnings.subscribe{ it ->
             if( it.countLines() > 0 ) { log.warn "about comparing sequences\n\n" + it.splitText().join("") }
         }

workflows/ampliseq.nf

@@ -1118,8 +1118,10 @@ workflow AMPLISEQ {
     // WORKFLOW: Comparison to expected
     //
     if ( params.expected_sequences ) {
+        def val_params_string = params.findAll{ it.key != 'trace_report_suffix' }.toString()
         COMPARISON_WF (
-            ( params.findAll{ it.key != 'trace_report_suffix' }.toString().md5() + "_${workflow.manifest.version}" ),  // md5sum of params (without variable time stamp in "trace_report_suffix") appended by pipeline version
+            ( val_params_string.md5() + "_${workflow.manifest.version}" ),  // md5sum of params (without variable time stamp in "trace_report_suffix") appended by pipeline version
+            val_params_string,
             params.trace_report_suffix, // record this as link to files in pipeline_info
             params.expected_sequences_region,
             run_qiime2 && !params.skip_abundance_tables ? QIIME2_EXPORT.out.abs_fasta : ch_dada2_fasta,  // observed sequences (fasta)