add db and fastq_input parameter checks (#12)

* added catch for missing db and fastq_input parameters * added pip to fluviewer conda environment * Revert "added catch for missing db and fastq_input parameters" This reverts commit 0067cd6. * added check for db and fastq_input parameters --------- Co-authored-by: John Palmer <[email protected]>
BCCDC-PHL · Jul 4, 2024 · 9944834 · 9944834
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commit 9944834
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diff --git a/environments/fluviewer.yml b/environments/fluviewer.yml
@@ -14,5 +14,6 @@ dependencies:
   - freebayes=1.3.6
   - pandas=2.0.3
   - seaborn=0.12.2
+  - pip=24.0
   - pip:
     - git+https://github.com/BCCDC-PHL/[email protected]
diff --git a/main.nf b/main.nf
@@ -66,6 +66,11 @@ workflow {
 
 
     main:
+
+    if (params.db == 'NO_FILE' || params.fastq_input == 'NO_FILE') {
+      error "ERROR: Missing required inputs. '--fastq_input' and '--db' parameters are mandatory."
+    }
+
     // Provenance channel starts with just the sample IDs
     // These will be joined to various provenance files as they are generated
     ch_provenance = ch_fastq_input.map{ it -> it[0] }

diff --git a/nextflow.config b/nextflow.config
@@ -11,7 +11,7 @@ params {
     profile = false
     cache = ''
     outdir = 'results'
-    fastq_input = ''
+    fastq_input = 'NO_FILE'
     illumina_suffixes = ['*_R{1,2}_001', '*_R{1,2}', '*_{1,2}' ]
     fastq_exts = ['.fastq.gz', '.fq.gz', '.fastq', '.fq']
     fastq_search_path = makeFastqSearchPath( illumina_suffixes, fastq_exts )