fix: Specify skip params in param checks (#35)

Signed-off-by: jvfe <[email protected]>
dalmolingroup · Apr 9, 2024 · 93c08ba · 93c08ba
1 parent 5b1cca1
commit 93c08ba
Showing 1 changed file with 3 additions and 2 deletions.
diff --git a/workflows/euryale.nf b/workflows/euryale.nf
@@ -73,8 +73,9 @@ def multiqc_report = []
 
 workflow EURYALE {
     if (params.reference_fasta == null && params.diamond_db == null && params.skip_alignment == false) { exit 1, 'A reference fasta (--reference_fasta) or a DIAMOND db (--diamond_db) must be specified' }
-    if (params.run_kaiju == true && params.kaiju_db == null) {exit 1, 'A Kaiju tar.gz database must be specified with --kaiju_db'}
-    if (params.run_kraken2 == true && params.kraken2_db == null) {exit 1, 'A Kraken2 database must be specified with --kraken2_db'}
+    if (params.run_kaiju == true && params.kaiju_db == null && params.skip_classification == false) {exit 1, 'A Kaiju tar.gz database must be specified with --kaiju_db'}
+    if (params.run_kraken2 == true && params.kraken2_db == null && params.skip_classification == false) {exit 1, 'A Kraken2 database must be specified with --kraken2_db'}
+    if (params.id_mapping == null && params.skip_functional == false) {exit 1, 'An ID mapping file is necessary if you want to run functional annotation'}
     if (params.host_fasta == null && params.bowtie2_db == null && params.skip_host_removal == false) {exit 1, 'Either a host reference FASTA (--host_fasta) or a pre-built bowtie2 index (--bowtie2_db) must be specified'}
 
     ch_versions = Channel.empty()