update config

Author: YanyanLiuBio

.github/workflows/nextflow-ci.yml

@@ -24,6 +24,8 @@ jobs:
         curl -s https://get.nextflow.io | bash
         sudo mv nextflow /usr/local/bin
         nextflow -version
+      env:
+        NXF_VER: 25.10.4
 
     - name: Run Nextflow pipeline with test profile
       run: |

.gitignore

@@ -8,6 +8,7 @@ bam_test_output/
 ci_output/
 barcode/
 other/
+temp_test/
 
 # Latch
 files_for_latch/

nextflow.config

@@ -32,8 +32,8 @@ process {
   memory = '4 GB'
   cpus   = 1
 
-  withName:DORADO_DEMUX            { container = 'genomicpariscentre/dorado:1.1.1'; memory = '8 GB'; cpus = 2 }
-  withName:COMBINE_BARCODES        { container = 'ubuntu:20.04' }
+  withName:DORADO_DEMUX            { container = 'genomicpariscentre/dorado:1.2.0'; memory = '8 GB'; cpus = 2 }
+  withName:COMBINE_BARCODES        { container = 'quay.io/biocontainers/samtools:1.21--h50ea8bc_0' }
   withName:EXTRACT_HEADER          { container = 'quay.io/biocontainers/pysam:0.22.0--py39hcada746_0' }
   withName:REHEADER_READS          { container = 'seqwell/python:v2.0' }
   withName:CUTADAPT_TRIM           { container = 'quay.io/biocontainers/cutadapt:5.0--py310h1fe012e_0' }