From 531975c004dfd573c43a3663f330256289e7f123 Mon Sep 17 00:00:00 2001
From: Natalia Garcia <natalia.garcia@nanoporetech.com>
Date: Wed, 27 May 2026 11:59:11 +0000
Subject: [PATCH] Template updates: sort threads param

---
 lib/common.nf  | 4 ++--
 lib/ingress.nf | 7 +++++--
 main.nf        | 1 +
 3 files changed, 8 insertions(+), 4 deletions(-)

diff --git a/lib/common.nf b/lib/common.nf
index 32ccd05..1aed50d 100644
--- a/lib/common.nf
+++ b/lib/common.nf
@@ -93,7 +93,7 @@ process minimap2_alignment {
         def fastq_input_cmd = "touch reads.header && fastcat --reheader reads/*"
         def bam_or_fastq_input = params.bam ? bam_input_cmd : fastq_input_cmd
         def minimap2_opts = bsargs["minimap2_opts"]
-        
+        def sort_threads = bsargs["sort_threads"]
     """
     rm -rf bamstats_results
     mkdir bamstats_results
@@ -103,7 +103,7 @@ process minimap2_alignment {
         | workflow-glue reheader_samstream reads.header \
             --insert \$'@PG\\tID:reset\\tPN:samtools\\tCL:${reset_cmd_body}' \
             --insert \$'@PG\\tID:fastq\\tPN:samtools\\tCL:${fastq_cmd_body}' \
-        | samtools sort -u -O BAM - \
+        | samtools sort -@ ${sort_threads} -u -O BAM - \
         | tee >(samtools view --reference ${reference} \
             --write-index -o reads.${align_ext}##idx##reads.${align_ext}.${index_ext} -) \
         | bamstats -s ${meta.alias} -u \
diff --git a/lib/ingress.nf b/lib/ingress.nf
index 35c502c..d457634 100644
--- a/lib/ingress.nf
+++ b/lib/ingress.nf
@@ -182,6 +182,7 @@ def add_number_of_reads_to_meta(ch, String input_type_format) {
  *  - "alignment_threads": number of threads to use for alignment process (default: 6)
  *  - "output_xam_fmt": alignment output format, `bam` outputs a BAM file with index (.bam, .bai),
        `cram` outputs a CRAM file with index (.cram, .crai)
+ *  - "sort_threads": number of threads to use for sorting aligned reads (default: 1)
  * @param aln_ref_ch: optional channel with a reference tuple (ref, ref_idx) to align against.
  *  If provided alignment will be attempted if inputs are unaligned or not already aligned to this ref.
  * @return: channel of `[Map(alias, barcode, type, ...), Path|null, Path|null]`.
@@ -337,7 +338,8 @@ def fastq_ingress(Map arguments, aln_ref_ch = null)
  *  - "alignment_threads": number of threads to use for alignment process (default: 6)
  *  - "output_xam_fmt": alignment output format, `bam` outputs an BAM file with index (.bam, .bai),
        `cram` outputs a CRAM file with index (.cram, .crai)
-*   - "force_alignment": boolean. Run alignment regardless of inputs.
+ *  - "sort_threads": number of threads to use for sorting aligned reads (default: 1)
+ *  - "force_alignment": boolean. Run alignment regardless of inputs.
  * @param aln_ref_ch: optional channel with a reference tuple (ref, ref_idx) to align against.
  *  If provided alignment will be attempted if inputs are unaligned or not already aligned to this ref.
  * @return: channel of `[Map(alias, barcode, type, ...), Path|null, Path|null]`.
@@ -985,7 +987,8 @@ Map parse_arguments(String func_name, Map arguments, Map extra_kwargs=[:]) {
         "minimap2_memory": ["8GB", "15GB", "31GB"],
         "minimap2_opts": "-x lr:hq",
         "alignment_threads": 6,
-        "output_xam_fmt": "bam" // or cram
+        "output_xam_fmt": "bam", // or cram
+        "sort_threads": 1 // TODO hook this up for ingress sorts as well
     ]
     ArgumentParser parser = new ArgumentParser(
         args: required_args,
diff --git a/main.nf b/main.nf
index d808e89..88b5af7 100644
--- a/main.nf
+++ b/main.nf
@@ -232,6 +232,7 @@ workflow {
         "analyse_fail": params.analyse_fail,
         "fastcat_extra_args": "",
         "required_sample_types": [],
+        "sort_threads": 3,
     ]
 
     if (params.fastq) {