include nextflow strict parser export

Author: ch99l

.github/workflows/smoke_test.yml

@@ -39,6 +39,7 @@ jobs:
           version: ${{ matrix.nextflow_version }}
       - name: Run ${{ matrix.profile }}
         run: |
+          export NXF_SYNTAX_PARSER=v2
           nextflow run . -profile test_base,${{ matrix.profile }},docker \
             ${{ matrix.quantification_mode && format('--quantification_mode {0}', matrix.quantification_mode) || '' }} \
             ${{ matrix.bam_only && '--bam_only' || '' }}

README.md

@@ -44,6 +44,9 @@ To run the pipeline, you must provide a samplesheet, reference genome, and refer
 
 Use the command below to run the pipeline on the test data provided in `examples/`
 ``` 
+# Required for Nextflow < 26.04
+export NXF_SYNTAX_PARSER=v2
+
 nextflow run main.nf \
   --input examples/samplesheet_test_sc_fastq.csv \
   --genome examples/GRCh38.primary_assembly.genome.chr21.fa.gz \
@@ -244,6 +247,9 @@ Example data and pre-configured profiles are provided in `examples/` to run the
 | `test_custom` | Custom chemistry, single-sample ONT run from demultiplexed BAM |
 
 ```bash
+# Required for Nextflow < 26.04
+export NXF_SYNTAX_PARSER=v2
+
 # Single-cell: test from FASTQ input
 nextflow run . -profile test_base,test_sc_fastq,singularity
 
@@ -280,6 +286,9 @@ custom_example,examples/custom_example.bam,my_custom_chemistry,ONT
 The `--bam_only` flag stops the pipeline after genome alignment, saving BAM files to `output/bam/`. This is useful when you want to inspect the aligned reads or run downstream steps separately.
 
 ```bash
+# Required for Nextflow < 26.04
+export NXF_SYNTAX_PARSER=v2
+
 nextflow run main.nf \
   --input examples/samplesheet_test_sc_fastq.csv \
   --genome examples/GRCh38.primary_assembly.genome.chr21.fa.gz \
@@ -298,6 +307,9 @@ sample,path,chemistry,technology
 ```
 
 ```bash
+# Required for Nextflow < 26.04
+export NXF_SYNTAX_PARSER=v2
+
 nextflow run main.nf \
   --input examples/samplesheet_test_sc_bam.csv \
   --genome examples/GRCh38.primary_assembly.genome.chr21.fa.gz \