check incompatible params with sidle

nf-core · Mar 13, 2024 · dd3698e · dd3698e
1 parent 221a554
commit dd3698e
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Showing 2 changed files with 18 additions and 5 deletions.
diff --git a/lib/WorkflowAmpliseq.groovy b/lib/WorkflowAmpliseq.groovy
@@ -131,6 +131,19 @@ class WorkflowAmpliseq {
         if ( params.orf_end && ( ( ( params.orf_end + 1 ) - params.orf_start ) % 3 != 0 ) ) {
             Nextflow.error("Incompatible parameters: The difference of  `--orf_end` and `--orf_start` must be a multiple of 3.")
         }
+
+        // When multi-region analysis is used, some parameter combinations are required or not allowed:
+        if ( params.input_multiregion ) {
+            if ( (params.dada_ref_tax_custom || params.dada_ref_taxonomy) && !params.skip_dada_taxonomy ) {
+                Nextflow.error("Incompatible parameters: Multiple region analysis with `--input_multiregion` does not work with `--dada_ref_tax_custom`, `--dada_ref_taxonomy`")
+            }
+            if ( params.cut_its ) {
+                Nextflow.error("Incompatible parameters: Multiple region analysis with `--input_multiregion` does not work with `--cut_its`")
+            }
+            if ( params.vsearch_cluster || params.filter_ssu || params.min_len_asv || params.max_len_asv || params.filter_codons ) {
+                log.warn "Incompatible parameters: Multiple region analysis with `--input_multiregion` ignores any of `--vsearch_cluster`, `--filter_ssu`, `--min_len_asv`, `--max_len_asv`, `--filter_codons`, `--cut_its`"
+            }
+        }
     }
 
     //

diff --git a/workflows/ampliseq.nf b/workflows/ampliseq.nf
@@ -472,12 +472,12 @@ workflow AMPLISEQ {
         // forward results to downstream analysis if multi region
         ch_dada2_asv = SIDLE_WF.out.table_tsv
         ch_dada2_fasta = Channel.empty()
-        // TODO Any ASV post-clustering param is not allowed:
+        // Any ASV post-clustering param is not allowed:
         // - solved by '!params.input_multiregion' for vsearch_cluster, filter_ssu, min_len_asv, max_len_asv, filter_codons
-        // - not solved: cut_its
-        // TODO Must have params:
-        // solved by '!params.input_multiregion' for skip_report
-        // not solved: skip_dada_taxonomy
+        // - solved in 'lib/WorkflowAmpliseq.groovy': cut_its
+        // Must have params:
+        // - solved by '!params.input_multiregion' for skip_report
+        // - solved in 'lib/WorkflowAmpliseq.groovy': skip_dada_taxonomy
     } else {
         // forward results to downstream analysis if single region
         ch_dada2_fasta = DADA2_MERGE.out.fasta