Merge main into full_test: resolve conflicts with test profiles

Author: Seqera AI

modules/xengsort_index.nf

@@ -10,13 +10,13 @@ process XENGSORT_INDEX {
     path "xengsort_index.*", emit: index_files
 
     script:
+    def args = task.ext.args ?: '-n 4500000000 -k 25'
     """
     xengsort index \\
         --index xengsort_index \\
         --host ${mouse_fasta} \\
         --graft ${human_fasta} \\
-        -n 4500000000 \\
-        -k 25
+        ${args}
      """
 
     // Add a stub block for minimal test

modules/xengsort_summary.nf

@@ -1,4 +1,5 @@
 process XENGSORT_SUMMARY {
+    container "ubuntu:22.04"
     publishDir "${params.outdir_base}/xengsort", mode: 'copy'
 
     input:

nextflow.config

@@ -40,19 +40,21 @@ profiles {
 
             // Specific configuration for memory-intensive processes
             withName: 'XENGSORT_CLASSIFY' {
-                memory = '4.GB'
+                memory = '8.GB'
                 cpus = 2
             }
 
             withName: 'XENGSORT_INDEX' {
                 memory = '2.GB'
                 cpus = 2
+                // Use much smaller index for test data to reduce memory requirements
+                ext.args = '-n 100000000 -k 25'
             }
         }
         params {
-            input = "${projectDir}/test_minimal/data/xengsort/samplesheet.csv"
-            hg38_fasta = "${projectDir}/test_minimal/data/xengsort/human.fa"
-            nsg_fasta = "${projectDir}/test_minimal/data/xengsort/mouse.fa"
+            input = "https://raw.githubusercontent.com/tylergross97/nextflow_xengsort/main/test_minimal/data/xengsort/samplesheet.csv"
+            hg38_fasta = "https://raw.githubusercontent.com/tylergross97/nextflow_xengsort/main/test_minimal/data/xengsort/human.fa"
+            nsg_fasta = "https://raw.githubusercontent.com/tylergross97/nextflow_xengsort/main/test_minimal/data/xengsort/mouse.fa"
             outdir_base = 'results_test_minimal'
             outdir_references = "results_test_minimal/references"
             outdir_fastp = "results_test_minimal/fastp"