finalise nextflow version

Author: ch99l

.github/workflows/smoke_test.yml

@@ -12,7 +12,7 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        nextflow_version: ["25.04.0", "latest-stable"]
+        nextflow_version: ["26.04.0", "latest-stable"]
         profile:
           - test_sc_fastq
           - test_sc_bam
@@ -39,7 +39,6 @@ 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

@@ -34,7 +34,7 @@ This pipeline performs context-aware transcript discovery and quantification fro
 
 ### **Installation** 
 Install the following dependencies before running the pipeline:
-- [Nextflow](https://www.nextflow.io/docs/latest/install.html) ≥ 25.04.0
+- [Nextflow](https://www.nextflow.io/docs/latest/install.html) ≥ 26.04.0
 - [Docker](https://docs.docker.com/engine/install/ubuntu/) (or [Singularity](https://docs.sylabs.io/guides/3.0/user-guide/installation.html) if you do not have user permissions for Docker). 
 
 ### **General Usage** 
@@ -44,9 +44,6 @@ 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 \
@@ -247,9 +244,6 @@ 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
 
@@ -286,9 +280,6 @@ 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 \
@@ -307,9 +298,6 @@ 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 \

main.nf

@@ -1,7 +1,5 @@
 #! /usr/bin/env nextflow
 
-nextflow.enable.dsl=2
-
 include { DECOMPRESS as DECOMPRESS_GENOME }     from './modules/decompress.nf'
 include { DECOMPRESS as DECOMPRESS_ANNOTATION } from './modules/decompress.nf'
 include { PREPARE_INPUT_STANDARD } from './subworkflows/prepare_input_standard.nf'
@@ -37,8 +35,8 @@ workflow {
     ch_genome     = channel.value(file(params.genome,     checkIfExists: true))
     ch_annotation = channel.value(file(params.annotation, checkIfExists: true))
 
-    ch_genome     = params.genome.endsWith('.gz')     ? DECOMPRESS_GENOME(ch_genome).file         : ch_genome
-    ch_annotation = params.annotation.endsWith('.gz') ? DECOMPRESS_ANNOTATION(ch_annotation).file : ch_annotation
+    ch_genome     = params.genome.toString().endsWith('.gz')     ? DECOMPRESS_GENOME(ch_genome).file         : ch_genome
+    ch_annotation = params.annotation.toString().endsWith('.gz') ? DECOMPRESS_ANNOTATION(ch_annotation).file : ch_annotation
 
     // load config files
     ch_barcode_coordinate_config = file("${projectDir}/assets/10x_config/barcode_coordinate_config.csv", checkIfExists: true)
@@ -47,15 +45,13 @@ workflow {
 
     // parsing samplesheet csv file
     ch_input = channel.fromPath(params.input, checkIfExists: true)
-    .ifEmpty { error "Cannot find samplesheet file: ${params.input}" }
     .map { file ->
         if (file.extension != "csv") {
             error "Invalid samplesheet. Must be a CSV file."
         }
         return file
     }
 
-    // TODO: Add Visium-HD and non-standard routing
     ch_standard  = ch_input.splitCsv(header:true, sep:',')
     ch_n_samples = ch_standard.count()
 

nextflow.config

@@ -4,7 +4,7 @@ manifest {
     author      = 'Andre Sim, Chin Hao Lee, Min Hao Ling'
     version     = 'v0.9-beta'
     mainScript  = 'main.nf'
-    nextflowVersion = '>=25.04.0'
+    nextflowVersion = '>=26.04.0'
 }
 
 params {