From 952202ce753affba5cd332a0a7fce96afb02cf7c Mon Sep 17 00:00:00 2001
From: EladH1 <eladherz1@gmail.com>
Date: Tue, 4 Nov 2025 11:36:56 +0100
Subject: [PATCH 01/11] The previous script had issue of staging -> modified
 the summary_file .

---
 modules/nf-core/bbmap/bbsplit/main.nf | 33 ++++++---------------------
 1 file changed, 7 insertions(+), 26 deletions(-)
 mode change 100644 => 100755 modules/nf-core/bbmap/bbsplit/main.nf

diff --git a/modules/nf-core/bbmap/bbsplit/main.nf b/modules/nf-core/bbmap/bbsplit/main.nf
old mode 100644
new mode 100755
index da4e0a1b2..87f7e14d5
--- a/modules/nf-core/bbmap/bbsplit/main.nf
+++ b/modules/nf-core/bbmap/bbsplit/main.nf
@@ -2,6 +2,9 @@ process BBMAP_BBSPLIT {
     tag "$meta.id"
     label 'process_high'
     label 'error_retry'
+    
+    // Force copy mode to prevent index modifications
+    stageInMode 'copy'
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
@@ -38,8 +41,8 @@ process BBMAP_BBSPLIT {
     }
 
     def other_refs = []
-    other_ref_names.eachWithIndex { name, index ->
-        other_refs << "ref_${name}=${other_ref_paths[index]}"
+    other_ref_names.eachWithIndex { name, idx ->
+        other_refs << "ref_${name}=${other_ref_paths[idx]}"
     }
 
     def fastq_in=''
@@ -66,21 +69,7 @@ process BBMAP_BBSPLIT {
         refstats_cmd = 'refstats=' + prefix + '.stats.txt'
     }
     """
-
-    # When we stage in the index files the time stamps get disturbed, which
-    # bbsplit doesn't like. Fix the time stamps in its summaries. This needs to
-    # be done via Java to match what bbmap does
-
-    if [ $index ]; then
-        for summary_file in \$(find $index/ref/genome -name summary.txt); do
-            src=\$(grep '^source' "\$summary_file" | cut -f2- -d\$'\\t' | sed 's|.*/bbsplit|bbsplit|')
-            mod=\$(echo "System.out.println(java.nio.file.Files.getLastModifiedTime(java.nio.file.Paths.get(\\"\$src\\")).toMillis());" | jshell -J-Djdk.lang.Process.launchMechanism=vfork -)
-            sed "s|^last modified.*|last modified\\t\$mod|" "\$summary_file" > \${summary_file}.tmp && mv \${summary_file}.tmp \${summary_file}
-        done
-    fi
-
     # Run BBSplit
-
     bbsplit.sh \\
         -Xmx${avail_mem}M \\
         $index_files \\
@@ -90,14 +79,6 @@ process BBMAP_BBSPLIT {
         $refstats_cmd \\
         $args 2>| >(tee ${prefix}.log >&2)
 
-    # Summary files will have an absolute path that will make the index
-    # impossible to use in other processes- we can fix that
-
-    for summary_file in \$(find bbsplit/ref/genome -name summary.txt); do
-        src=\$(grep '^source' "\$summary_file" | cut -f2- -d\$'\\t' | sed 's|.*/bbsplit|bbsplit|')
-        sed "s|^source.*|source\\t\$src|" "\$summary_file" > \${summary_file}.tmp && mv \${summary_file}.tmp \${summary_file}
-    done
-
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
         bbmap: \$(bbversion.sh | grep -v "Duplicate cpuset")
@@ -107,7 +88,7 @@ process BBMAP_BBSPLIT {
     stub:
     def prefix = task.ext.prefix ?: "${meta.id}"
     def other_refs = ''
-    other_ref_names.eachWithIndex { name, index ->
+    other_ref_names.eachWithIndex { name, _idx ->
         other_refs += "echo '' | gzip > ${prefix}_${name}.fastq.gz"
     }
     """
@@ -128,4 +109,4 @@ process BBMAP_BBSPLIT {
         bbmap: \$(bbversion.sh | grep -v "Duplicate cpuset")
     END_VERSIONS
     """
-}
+}
\ No newline at end of file

From d9a288433ab308de7b00e0d130b29adf5d534744 Mon Sep 17 00:00:00 2001
From: EladH1 <eladherz1@gmail.com>
Date: Wed, 5 Nov 2025 11:12:59 +0100
Subject: [PATCH 02/11] bbsplit patch lint

---
 modules.json                                  |  3 +-
 .../nf-core/bbmap/bbsplit/bbmap-bbsplit.diff  | 97 +++++++++++++++++++
 2 files changed, 99 insertions(+), 1 deletion(-)
 create mode 100644 modules/nf-core/bbmap/bbsplit/bbmap-bbsplit.diff

diff --git a/modules.json b/modules.json
index aa20e9320..69270ed31 100644
--- a/modules.json
+++ b/modules.json
@@ -8,7 +8,8 @@
                     "bbmap/bbsplit": {
                         "branch": "master",
                         "git_sha": "8864afe586537bf562eac7b83349c26207f3cb4d",
-                        "installed_by": ["fastq_qc_trim_filter_setstrandedness", "modules"]
+                        "installed_by": ["fastq_qc_trim_filter_setstrandedness", "modules"],
+                        "patch": "modules/nf-core/bbmap/bbsplit/bbmap-bbsplit.diff"
                     },
                     "bedtools/genomecov": {
                         "branch": "master",
diff --git a/modules/nf-core/bbmap/bbsplit/bbmap-bbsplit.diff b/modules/nf-core/bbmap/bbsplit/bbmap-bbsplit.diff
new file mode 100644
index 000000000..93e8ab49e
--- /dev/null
+++ b/modules/nf-core/bbmap/bbsplit/bbmap-bbsplit.diff
@@ -0,0 +1,97 @@
+Changes in component 'nf-core/bbmap/bbsplit'
+'modules/nf-core/bbmap/bbsplit/meta.yml' is unchanged
+'modules/nf-core/bbmap/bbsplit/nextflow.config' was created
+'modules/nf-core/bbmap/bbsplit/environment.yml' is unchanged
+Changes in 'bbmap/bbsplit/main.nf':
+--- modules/nf-core/bbmap/bbsplit/main.nf
++++ modules/nf-core/bbmap/bbsplit/main.nf
+@@ -2,6 +2,9 @@
+     tag "$meta.id"
+     label 'process_high'
+     label 'error_retry'
++    
++    // Force copy mode to prevent index modifications
++    stageInMode 'copy'
+ 
+     conda "${moduleDir}/environment.yml"
+     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+@@ -38,8 +41,8 @@
+     }
+ 
+     def other_refs = []
+-    other_ref_names.eachWithIndex { name, index ->
+-        other_refs << "ref_${name}=${other_ref_paths[index]}"
++    other_ref_names.eachWithIndex { name, idx ->
++        other_refs << "ref_${name}=${other_ref_paths[idx]}"
+     }
+ 
+     def fastq_in=''
+@@ -66,21 +69,7 @@
+         refstats_cmd = 'refstats=' + prefix + '.stats.txt'
+     }
+     """
+-
+-    # When we stage in the index files the time stamps get disturbed, which
+-    # bbsplit doesn't like. Fix the time stamps in its summaries. This needs to
+-    # be done via Java to match what bbmap does
+-
+-    if [ $index ]; then
+-        for summary_file in \$(find $index/ref/genome -name summary.txt); do
+-            src=\$(grep '^source' "\$summary_file" | cut -f2- -d\$'\\t' | sed 's|.*/bbsplit|bbsplit|')
+-            mod=\$(echo "System.out.println(java.nio.file.Files.getLastModifiedTime(java.nio.file.Paths.get(\\"\$src\\")).toMillis());" | jshell -J-Djdk.lang.Process.launchMechanism=vfork -)
+-            sed "s|^last modified.*|last modified\\t\$mod|" "\$summary_file" > \${summary_file}.tmp && mv \${summary_file}.tmp \${summary_file}
+-        done
+-    fi
+-
+     # Run BBSplit
+-
+     bbsplit.sh \\
+         -Xmx${avail_mem}M \\
+         $index_files \\
+@@ -89,14 +78,6 @@
+         $fastq_out \\
+         $refstats_cmd \\
+         $args 2>| >(tee ${prefix}.log >&2)
+-
+-    # Summary files will have an absolute path that will make the index
+-    # impossible to use in other processes- we can fix that
+-
+-    for summary_file in \$(find bbsplit/ref/genome -name summary.txt); do
+-        src=\$(grep '^source' "\$summary_file" | cut -f2- -d\$'\\t' | sed 's|.*/bbsplit|bbsplit|')
+-        sed "s|^source.*|source\\t\$src|" "\$summary_file" > \${summary_file}.tmp && mv \${summary_file}.tmp \${summary_file}
+-    done
+ 
+     cat <<-END_VERSIONS > versions.yml
+     "${task.process}":
+@@ -107,7 +88,7 @@
+     stub:
+     def prefix = task.ext.prefix ?: "${meta.id}"
+     def other_refs = ''
+-    other_ref_names.eachWithIndex { name, index ->
++    other_ref_names.eachWithIndex { name, _idx ->
+         other_refs += "echo '' | gzip > ${prefix}_${name}.fastq.gz"
+     }
+     """
+@@ -128,4 +109,4 @@
+         bbmap: \$(bbversion.sh | grep -v "Duplicate cpuset")
+     END_VERSIONS
+     """
+-}
++}
+Changes in 'bbmap/bbsplit/tests/main.nf.test':
+--- modules/nf-core/bbmap/bbsplit/tests/main.nf.test
++++ modules/nf-core/bbmap/bbsplit/tests/main.nf.test
+@@ -3,10 +3,6 @@
+     name "Test Process BBMAP_BBSPLIT"
+     script "../main.nf"
+     process "BBMAP_BBSPLIT"
+-    tag "modules"
+-    tag "modules_nfcore"
+-    tag "bbmap"
+-    tag "bbmap/bbsplit"
+ 
+     test("sarscov2_se_fastq_fasta_chr22_fasta - index") {
+ 
+
+'modules/nf-core/bbmap/bbsplit/tests/main.nf.test.snap' is unchanged
+************************************************************

From 4819736fbf2c6cc4cb4e396f9e0315793f57e979 Mon Sep 17 00:00:00 2001
From: EladH1 <eladherz1@gmail.com>
Date: Wed, 5 Nov 2025 11:16:32 +0100
Subject: [PATCH 03/11] linting

---
 .github/workflows/linting.yml         | 14 +++++++-------
 .github/workflows/linting_comment.yml |  2 +-
 2 files changed, 8 insertions(+), 8 deletions(-)

diff --git a/.github/workflows/linting.yml b/.github/workflows/linting.yml
index 8b0f88c36..30e66026f 100644
--- a/.github/workflows/linting.yml
+++ b/.github/workflows/linting.yml
@@ -11,12 +11,12 @@ jobs:
   pre-commit:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4
+      - uses: actions/checkout@08c6903cd8c0fde910a37f88322edcfb5dd907a8 # v5
 
-      - name: Set up Python 3.13
-        uses: actions/setup-python@a26af69be951a213d495a4c3e4e4022e16d87065 # v5
+      - name: Set up Python 3.14
+        uses: actions/setup-python@e797f83bcb11b83ae66e0230d6156d7c80228e7c # v6
         with:
-          python-version: "3.13"
+          python-version: "3.14"
 
       - name: Install pre-commit
         run: pip install pre-commit
@@ -28,14 +28,14 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Check out pipeline code
-        uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4
+        uses: actions/checkout@08c6903cd8c0fde910a37f88322edcfb5dd907a8 # v5
 
       - name: Install Nextflow
         uses: nf-core/setup-nextflow@v2
 
-      - uses: actions/setup-python@a26af69be951a213d495a4c3e4e4022e16d87065 # v5
+      - uses: actions/setup-python@e797f83bcb11b83ae66e0230d6156d7c80228e7c # v6
         with:
-          python-version: "3.13"
+          python-version: "3.14"
           architecture: "x64"
 
       - name: read .nf-core.yml
diff --git a/.github/workflows/linting_comment.yml b/.github/workflows/linting_comment.yml
index d43797d9d..e6e9bc269 100644
--- a/.github/workflows/linting_comment.yml
+++ b/.github/workflows/linting_comment.yml
@@ -21,7 +21,7 @@ jobs:
         run: echo "pr_number=$(cat linting-logs/PR_number.txt)" >> $GITHUB_OUTPUT
 
       - name: Post PR comment
-        uses: marocchino/sticky-pull-request-comment@52423e01640425a022ef5fd42c6fb5f633a02728 # v2
+        uses: marocchino/sticky-pull-request-comment@773744901bac0e8cbb5a0dc842800d45e9b2b405 # v2
         with:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
           number: ${{ steps.pr_number.outputs.pr_number }}

From 8204ad975b3fd69dcee1198061f7b5b5a87dff7b Mon Sep 17 00:00:00 2001
From: EladH1 <eladherz1@gmail.com>
Date: Wed, 5 Nov 2025 11:46:55 +0100
Subject: [PATCH 04/11] bbsplit linting2

---
 .../nf-core/bbmap/bbsplit/bbmap-bbsplit.diff  | 97 -------------------
 .../nf-core/bbmap/bbsplit/tests/main.nf.test  |  4 +
 2 files changed, 4 insertions(+), 97 deletions(-)
 delete mode 100644 modules/nf-core/bbmap/bbsplit/bbmap-bbsplit.diff

diff --git a/modules/nf-core/bbmap/bbsplit/bbmap-bbsplit.diff b/modules/nf-core/bbmap/bbsplit/bbmap-bbsplit.diff
deleted file mode 100644
index 93e8ab49e..000000000
--- a/modules/nf-core/bbmap/bbsplit/bbmap-bbsplit.diff
+++ /dev/null
@@ -1,97 +0,0 @@
-Changes in component 'nf-core/bbmap/bbsplit'
-'modules/nf-core/bbmap/bbsplit/meta.yml' is unchanged
-'modules/nf-core/bbmap/bbsplit/nextflow.config' was created
-'modules/nf-core/bbmap/bbsplit/environment.yml' is unchanged
-Changes in 'bbmap/bbsplit/main.nf':
---- modules/nf-core/bbmap/bbsplit/main.nf
-+++ modules/nf-core/bbmap/bbsplit/main.nf
-@@ -2,6 +2,9 @@
-     tag "$meta.id"
-     label 'process_high'
-     label 'error_retry'
-+    
-+    // Force copy mode to prevent index modifications
-+    stageInMode 'copy'
- 
-     conda "${moduleDir}/environment.yml"
-     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-@@ -38,8 +41,8 @@
-     }
- 
-     def other_refs = []
--    other_ref_names.eachWithIndex { name, index ->
--        other_refs << "ref_${name}=${other_ref_paths[index]}"
-+    other_ref_names.eachWithIndex { name, idx ->
-+        other_refs << "ref_${name}=${other_ref_paths[idx]}"
-     }
- 
-     def fastq_in=''
-@@ -66,21 +69,7 @@
-         refstats_cmd = 'refstats=' + prefix + '.stats.txt'
-     }
-     """
--
--    # When we stage in the index files the time stamps get disturbed, which
--    # bbsplit doesn't like. Fix the time stamps in its summaries. This needs to
--    # be done via Java to match what bbmap does
--
--    if [ $index ]; then
--        for summary_file in \$(find $index/ref/genome -name summary.txt); do
--            src=\$(grep '^source' "\$summary_file" | cut -f2- -d\$'\\t' | sed 's|.*/bbsplit|bbsplit|')
--            mod=\$(echo "System.out.println(java.nio.file.Files.getLastModifiedTime(java.nio.file.Paths.get(\\"\$src\\")).toMillis());" | jshell -J-Djdk.lang.Process.launchMechanism=vfork -)
--            sed "s|^last modified.*|last modified\\t\$mod|" "\$summary_file" > \${summary_file}.tmp && mv \${summary_file}.tmp \${summary_file}
--        done
--    fi
--
-     # Run BBSplit
--
-     bbsplit.sh \\
-         -Xmx${avail_mem}M \\
-         $index_files \\
-@@ -89,14 +78,6 @@
-         $fastq_out \\
-         $refstats_cmd \\
-         $args 2>| >(tee ${prefix}.log >&2)
--
--    # Summary files will have an absolute path that will make the index
--    # impossible to use in other processes- we can fix that
--
--    for summary_file in \$(find bbsplit/ref/genome -name summary.txt); do
--        src=\$(grep '^source' "\$summary_file" | cut -f2- -d\$'\\t' | sed 's|.*/bbsplit|bbsplit|')
--        sed "s|^source.*|source\\t\$src|" "\$summary_file" > \${summary_file}.tmp && mv \${summary_file}.tmp \${summary_file}
--    done
- 
-     cat <<-END_VERSIONS > versions.yml
-     "${task.process}":
-@@ -107,7 +88,7 @@
-     stub:
-     def prefix = task.ext.prefix ?: "${meta.id}"
-     def other_refs = ''
--    other_ref_names.eachWithIndex { name, index ->
-+    other_ref_names.eachWithIndex { name, _idx ->
-         other_refs += "echo '' | gzip > ${prefix}_${name}.fastq.gz"
-     }
-     """
-@@ -128,4 +109,4 @@
-         bbmap: \$(bbversion.sh | grep -v "Duplicate cpuset")
-     END_VERSIONS
-     """
--}
-+}
-Changes in 'bbmap/bbsplit/tests/main.nf.test':
---- modules/nf-core/bbmap/bbsplit/tests/main.nf.test
-+++ modules/nf-core/bbmap/bbsplit/tests/main.nf.test
-@@ -3,10 +3,6 @@
-     name "Test Process BBMAP_BBSPLIT"
-     script "../main.nf"
-     process "BBMAP_BBSPLIT"
--    tag "modules"
--    tag "modules_nfcore"
--    tag "bbmap"
--    tag "bbmap/bbsplit"
- 
-     test("sarscov2_se_fastq_fasta_chr22_fasta - index") {
- 
-
-'modules/nf-core/bbmap/bbsplit/tests/main.nf.test.snap' is unchanged
-************************************************************
diff --git a/modules/nf-core/bbmap/bbsplit/tests/main.nf.test b/modules/nf-core/bbmap/bbsplit/tests/main.nf.test
index 0674d247f..1f260d5f6 100644
--- a/modules/nf-core/bbmap/bbsplit/tests/main.nf.test
+++ b/modules/nf-core/bbmap/bbsplit/tests/main.nf.test
@@ -3,6 +3,10 @@ nextflow_process {
     name "Test Process BBMAP_BBSPLIT"
     script "../main.nf"
     process "BBMAP_BBSPLIT"
+    tag "modules"
+    tag "modules_nfcore"
+    tag "bbmap"
+    tag "bbmap/bbsplit"
 
     test("sarscov2_se_fastq_fasta_chr22_fasta - index") {
 

From 75b7c47afcc1a6445fcd5f1f407612a4b1bff614 Mon Sep 17 00:00:00 2001
From: EladH1 <eladherz1@gmail.com>
Date: Wed, 5 Nov 2025 11:58:52 +0100
Subject: [PATCH 05/11] lint pipe

---
 modules.json | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/modules.json b/modules.json
index 69270ed31..aa20e9320 100644
--- a/modules.json
+++ b/modules.json
@@ -8,8 +8,7 @@
                     "bbmap/bbsplit": {
                         "branch": "master",
                         "git_sha": "8864afe586537bf562eac7b83349c26207f3cb4d",
-                        "installed_by": ["fastq_qc_trim_filter_setstrandedness", "modules"],
-                        "patch": "modules/nf-core/bbmap/bbsplit/bbmap-bbsplit.diff"
+                        "installed_by": ["fastq_qc_trim_filter_setstrandedness", "modules"]
                     },
                     "bedtools/genomecov": {
                         "branch": "master",

From 628d041b6cbf436d2c72419ee7f3469502bb7fe9 Mon Sep 17 00:00:00 2001
From: Jonathan Manning <jonathan.manning@seqera.io>
Date: Thu, 13 Nov 2025 12:45:22 +0000
Subject: [PATCH 06/11] Revert bbsplit staging changes to allow proper module
 update

---
 .github/workflows/linting.yml                 | 14 ++++----
 .github/workflows/linting_comment.yml         |  2 +-
 modules/nf-core/bbmap/bbsplit/main.nf         | 33 +++++++++++++++----
 .../nf-core/bbmap/bbsplit/tests/main.nf.test  |  4 ---
 4 files changed, 34 insertions(+), 19 deletions(-)
 mode change 100755 => 100644 modules/nf-core/bbmap/bbsplit/main.nf

diff --git a/.github/workflows/linting.yml b/.github/workflows/linting.yml
index 30e66026f..8b0f88c36 100644
--- a/.github/workflows/linting.yml
+++ b/.github/workflows/linting.yml
@@ -11,12 +11,12 @@ jobs:
   pre-commit:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@08c6903cd8c0fde910a37f88322edcfb5dd907a8 # v5
+      - uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4
 
-      - name: Set up Python 3.14
-        uses: actions/setup-python@e797f83bcb11b83ae66e0230d6156d7c80228e7c # v6
+      - name: Set up Python 3.13
+        uses: actions/setup-python@a26af69be951a213d495a4c3e4e4022e16d87065 # v5
         with:
-          python-version: "3.14"
+          python-version: "3.13"
 
       - name: Install pre-commit
         run: pip install pre-commit
@@ -28,14 +28,14 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Check out pipeline code
-        uses: actions/checkout@08c6903cd8c0fde910a37f88322edcfb5dd907a8 # v5
+        uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4
 
       - name: Install Nextflow
         uses: nf-core/setup-nextflow@v2
 
-      - uses: actions/setup-python@e797f83bcb11b83ae66e0230d6156d7c80228e7c # v6
+      - uses: actions/setup-python@a26af69be951a213d495a4c3e4e4022e16d87065 # v5
         with:
-          python-version: "3.14"
+          python-version: "3.13"
           architecture: "x64"
 
       - name: read .nf-core.yml
diff --git a/.github/workflows/linting_comment.yml b/.github/workflows/linting_comment.yml
index e6e9bc269..d43797d9d 100644
--- a/.github/workflows/linting_comment.yml
+++ b/.github/workflows/linting_comment.yml
@@ -21,7 +21,7 @@ jobs:
         run: echo "pr_number=$(cat linting-logs/PR_number.txt)" >> $GITHUB_OUTPUT
 
       - name: Post PR comment
-        uses: marocchino/sticky-pull-request-comment@773744901bac0e8cbb5a0dc842800d45e9b2b405 # v2
+        uses: marocchino/sticky-pull-request-comment@52423e01640425a022ef5fd42c6fb5f633a02728 # v2
         with:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
           number: ${{ steps.pr_number.outputs.pr_number }}
diff --git a/modules/nf-core/bbmap/bbsplit/main.nf b/modules/nf-core/bbmap/bbsplit/main.nf
old mode 100755
new mode 100644
index 87f7e14d5..da4e0a1b2
--- a/modules/nf-core/bbmap/bbsplit/main.nf
+++ b/modules/nf-core/bbmap/bbsplit/main.nf
@@ -2,9 +2,6 @@ process BBMAP_BBSPLIT {
     tag "$meta.id"
     label 'process_high'
     label 'error_retry'
-    
-    // Force copy mode to prevent index modifications
-    stageInMode 'copy'
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
@@ -41,8 +38,8 @@ process BBMAP_BBSPLIT {
     }
 
     def other_refs = []
-    other_ref_names.eachWithIndex { name, idx ->
-        other_refs << "ref_${name}=${other_ref_paths[idx]}"
+    other_ref_names.eachWithIndex { name, index ->
+        other_refs << "ref_${name}=${other_ref_paths[index]}"
     }
 
     def fastq_in=''
@@ -69,7 +66,21 @@ process BBMAP_BBSPLIT {
         refstats_cmd = 'refstats=' + prefix + '.stats.txt'
     }
     """
+
+    # When we stage in the index files the time stamps get disturbed, which
+    # bbsplit doesn't like. Fix the time stamps in its summaries. This needs to
+    # be done via Java to match what bbmap does
+
+    if [ $index ]; then
+        for summary_file in \$(find $index/ref/genome -name summary.txt); do
+            src=\$(grep '^source' "\$summary_file" | cut -f2- -d\$'\\t' | sed 's|.*/bbsplit|bbsplit|')
+            mod=\$(echo "System.out.println(java.nio.file.Files.getLastModifiedTime(java.nio.file.Paths.get(\\"\$src\\")).toMillis());" | jshell -J-Djdk.lang.Process.launchMechanism=vfork -)
+            sed "s|^last modified.*|last modified\\t\$mod|" "\$summary_file" > \${summary_file}.tmp && mv \${summary_file}.tmp \${summary_file}
+        done
+    fi
+
     # Run BBSplit
+
     bbsplit.sh \\
         -Xmx${avail_mem}M \\
         $index_files \\
@@ -79,6 +90,14 @@ process BBMAP_BBSPLIT {
         $refstats_cmd \\
         $args 2>| >(tee ${prefix}.log >&2)
 
+    # Summary files will have an absolute path that will make the index
+    # impossible to use in other processes- we can fix that
+
+    for summary_file in \$(find bbsplit/ref/genome -name summary.txt); do
+        src=\$(grep '^source' "\$summary_file" | cut -f2- -d\$'\\t' | sed 's|.*/bbsplit|bbsplit|')
+        sed "s|^source.*|source\\t\$src|" "\$summary_file" > \${summary_file}.tmp && mv \${summary_file}.tmp \${summary_file}
+    done
+
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
         bbmap: \$(bbversion.sh | grep -v "Duplicate cpuset")
@@ -88,7 +107,7 @@ process BBMAP_BBSPLIT {
     stub:
     def prefix = task.ext.prefix ?: "${meta.id}"
     def other_refs = ''
-    other_ref_names.eachWithIndex { name, _idx ->
+    other_ref_names.eachWithIndex { name, index ->
         other_refs += "echo '' | gzip > ${prefix}_${name}.fastq.gz"
     }
     """
@@ -109,4 +128,4 @@ process BBMAP_BBSPLIT {
         bbmap: \$(bbversion.sh | grep -v "Duplicate cpuset")
     END_VERSIONS
     """
-}
\ No newline at end of file
+}
diff --git a/modules/nf-core/bbmap/bbsplit/tests/main.nf.test b/modules/nf-core/bbmap/bbsplit/tests/main.nf.test
index 1f260d5f6..0674d247f 100644
--- a/modules/nf-core/bbmap/bbsplit/tests/main.nf.test
+++ b/modules/nf-core/bbmap/bbsplit/tests/main.nf.test
@@ -3,10 +3,6 @@ nextflow_process {
     name "Test Process BBMAP_BBSPLIT"
     script "../main.nf"
     process "BBMAP_BBSPLIT"
-    tag "modules"
-    tag "modules_nfcore"
-    tag "bbmap"
-    tag "bbmap/bbsplit"
 
     test("sarscov2_se_fastq_fasta_chr22_fasta - index") {
 

From 439396c6b00305ae41726f24bdfc149d431bb813 Mon Sep 17 00:00:00 2001
From: Jonathan Manning <jonathan.manning@seqera.io>
Date: Thu, 13 Nov 2025 12:53:13 +0000
Subject: [PATCH 07/11] Update bbmap/bbsplit module to latest version
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

This updates the bbmap/bbsplit module to address staging issues
reported in the original PR.

🤖 Generated with [Claude Code](https://claude.com/claude-code)

Co-Authored-By: Claude <noreply@anthropic.com>
---
 modules.json                                  |   2 +-
 modules/nf-core/bbmap/bbsplit/main.nf         |  45 ++--
 modules/nf-core/bbmap/bbsplit/meta.yml        |  70 +++---
 .../nf-core/bbmap/bbsplit/tests/main.nf.test  |  64 ++----
 .../bbmap/bbsplit/tests/main.nf.test.snap     | 199 ++----------------
 5 files changed, 108 insertions(+), 272 deletions(-)

diff --git a/modules.json b/modules.json
index aa20e9320..920c05cd7 100644
--- a/modules.json
+++ b/modules.json
@@ -7,7 +7,7 @@
                 "nf-core": {
                     "bbmap/bbsplit": {
                         "branch": "master",
-                        "git_sha": "8864afe586537bf562eac7b83349c26207f3cb4d",
+                        "git_sha": "b5114f2bb0aa49281e1292d0c8b1433e368c0ed3",
                         "installed_by": ["fastq_qc_trim_filter_setstrandedness", "modules"]
                     },
                     "bedtools/genomecov": {
diff --git a/modules/nf-core/bbmap/bbsplit/main.nf b/modules/nf-core/bbmap/bbsplit/main.nf
index da4e0a1b2..2deebbec7 100644
--- a/modules/nf-core/bbmap/bbsplit/main.nf
+++ b/modules/nf-core/bbmap/bbsplit/main.nf
@@ -10,13 +10,13 @@ process BBMAP_BBSPLIT {
 
     input:
     tuple val(meta), path(reads)
-    path  index
+    path  index, name: 'input_index'
     path  primary_ref
     tuple val(other_ref_names), path(other_ref_paths)
     val   only_build_index
 
     output:
-    path "bbsplit"                            , optional:true, emit: index
+    path "bbsplit_index"                      , optional:true, emit: index
     tuple val(meta), path('*primary*fastq.gz'), optional:true, emit: primary_fastq
     tuple val(meta), path('*fastq.gz')        , optional:true, emit: all_fastq
     tuple val(meta), path('*txt')             , optional:true, emit: stats
@@ -46,16 +46,17 @@ process BBMAP_BBSPLIT {
     def fastq_out=''
     def index_files=''
     def refstats_cmd=''
+    def use_index = index ? true : false
 
     if (only_build_index) {
         if (primary_ref && other_ref_names && other_ref_paths) {
-            index_files = 'ref_primary=' +primary_ref + ' ' + other_refs.join(' ') + ' path=bbsplit'
+            index_files = 'ref_primary=' +primary_ref + ' ' + other_refs.join(' ') + ' path=bbsplit_build'
         } else {
             log.error 'ERROR: Please specify as input a primary fasta file along with names and paths to non-primary fasta files.'
         }
     } else {
         if (index) {
-            index_files = "path=$index"
+            index_files = "path=index_writable"
         } else if (primary_ref && other_ref_names && other_ref_paths) {
             index_files = "ref_primary=${primary_ref} ${other_refs.join(' ')}"
         } else {
@@ -67,15 +68,18 @@ process BBMAP_BBSPLIT {
     }
     """
 
-    # When we stage in the index files the time stamps get disturbed, which
-    # bbsplit doesn't like. Fix the time stamps in its summaries. This needs to
-    # be done via Java to match what bbmap does
+    # If using a pre-built index, copy it to avoid modifying input files in place,
+    # then fix timestamps. When we stage in the index files the time stamps get
+    # disturbed, which bbsplit doesn't like. Fix the time stamps in its summaries.
+    # This needs to be done via Java to match what bbmap does.
+    if [ "$use_index" == "true" ]; then
+        cp -rL input_index index_writable
 
-    if [ $index ]; then
-        for summary_file in \$(find $index/ref/genome -name summary.txt); do
-            src=\$(grep '^source' "\$summary_file" | cut -f2- -d\$'\\t' | sed 's|.*/bbsplit|bbsplit|')
+        for summary_file in \$(find index_writable/ref/genome -name summary.txt); do
+            # Extract the path from summary.txt and update it to point to index_writable
+            src=\$(grep '^source' "\$summary_file" | cut -f2- -d\$'\\t' | sed 's|.*/ref/|index_writable/ref/|')
             mod=\$(echo "System.out.println(java.nio.file.Files.getLastModifiedTime(java.nio.file.Paths.get(\\"\$src\\")).toMillis());" | jshell -J-Djdk.lang.Process.launchMechanism=vfork -)
-            sed "s|^last modified.*|last modified\\t\$mod|" "\$summary_file" > \${summary_file}.tmp && mv \${summary_file}.tmp \${summary_file}
+            sed -e 's|bbsplit_index/ref|index_writable/ref|' -e "s|^last modified.*|last modified\\t\$mod|" "\$summary_file" > \${summary_file}.tmp && mv \${summary_file}.tmp \${summary_file}
         done
     fi
 
@@ -92,11 +96,15 @@ process BBMAP_BBSPLIT {
 
     # Summary files will have an absolute path that will make the index
     # impossible to use in other processes- we can fix that
+    if [ -d bbsplit_build/ref/genome ]; then
+        for summary_file in \$(find bbsplit_build/ref/genome -name summary.txt); do
+            src=\$(grep '^source' "\$summary_file" | cut -f2- -d\$'\\t' | sed 's|.*/bbsplit_build|bbsplit_index|')
+            sed "s|^source.*|source\\t\$src|" "\$summary_file" > \${summary_file}.tmp && mv \${summary_file}.tmp \${summary_file}
+        done
 
-    for summary_file in \$(find bbsplit/ref/genome -name summary.txt); do
-        src=\$(grep '^source' "\$summary_file" | cut -f2- -d\$'\\t' | sed 's|.*/bbsplit|bbsplit|')
-        sed "s|^source.*|source\\t\$src|" "\$summary_file" > \${summary_file}.tmp && mv \${summary_file}.tmp \${summary_file}
-    done
+        # Atomically rename the completed index
+        mv bbsplit_build bbsplit_index
+    fi
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
@@ -110,11 +118,14 @@ process BBMAP_BBSPLIT {
     other_ref_names.eachWithIndex { name, index ->
         other_refs += "echo '' | gzip > ${prefix}_${name}.fastq.gz"
     }
+    def will_build_index = only_build_index || (!index && primary_ref && other_ref_names && other_ref_paths)
     """
-    if [ ! -d bbsplit ]; then
-        mkdir bbsplit
+    # Create index directory if building an index (either only_build_index or on-the-fly)
+    if [ "${will_build_index}" == "true" ]; then
+        mkdir -p bbsplit_index
     fi
 
+    # Only create output files if splitting (not just building index)
     if ! (${only_build_index}); then
         echo '' | gzip >  ${prefix}_primary.fastq.gz
         ${other_refs}
diff --git a/modules/nf-core/bbmap/bbsplit/meta.yml b/modules/nf-core/bbmap/bbsplit/meta.yml
index 081aeb2b3..b496849ad 100644
--- a/modules/nf-core/bbmap/bbsplit/meta.yml
+++ b/modules/nf-core/bbmap/bbsplit/meta.yml
@@ -25,31 +25,33 @@ input:
         description: |
           List of input FastQ files of size 1 and 2 for single-end and paired-end data,
           respectively.
-  - - index:
-        type: directory
-        description: Directory to place generated index
-        pattern: "*"
-  - - primary_ref:
-        type: file
-        description: Path to the primary reference
-        pattern: "*"
+        ontologies: []
+  - index:
+      type: directory
+      description: Directory to place generated index
+      pattern: "*"
+  - primary_ref:
+      type: file
+      description: Path to the primary reference
+      pattern: "*"
+      ontologies: []
   - - other_ref_names:
         type: list
         description: List of other reference ids apart from the primary
     - other_ref_paths:
         type: list
         description: Path to other references paths corresponding to "other_ref_names"
-  - - only_build_index:
-        type: string
-        description: true = only build index; false = mapping
+  - only_build_index:
+      type: string
+      description: true = only build index; false = mapping
 output:
-  - index:
-      - bbsplit:
-          type: directory
-          description: Directory with index files
-          pattern: "bbsplit"
-  - primary_fastq:
-      - meta:
+  index:
+    - bbsplit_index:
+        type: directory
+        description: Directory with index files
+        pattern: "bbsplit_index"
+  primary_fastq:
+    - - meta:
           type: map
           description: |
             Groovy Map containing sample information
@@ -58,8 +60,10 @@ output:
           type: file
           description: Output reads that map to the primary reference
           pattern: "*primary*fastq.gz"
-  - all_fastq:
-      - meta:
+          ontologies:
+            - edam: http://edamontology.org/format_3989 # GZIP format
+  all_fastq:
+    - - meta:
           type: map
           description: |
             Groovy Map containing sample information
@@ -68,8 +72,10 @@ output:
           type: file
           description: All reads mapping to any of the references
           pattern: "*fastq.gz"
-  - stats:
-      - meta:
+          ontologies:
+            - edam: http://edamontology.org/format_3989 # GZIP format
+  stats:
+    - - meta:
           type: map
           description: |
             Groovy Map containing sample information
@@ -78,8 +84,9 @@ output:
           type: file
           description: Tab-delimited text file containing mapping statistics
           pattern: "*.txt"
-  - log:
-      - meta:
+          ontologies: []
+  log:
+    - - meta:
           type: map
           description: |
             Groovy Map containing sample information
@@ -88,14 +95,19 @@ output:
           type: file
           description: Log file
           pattern: "*.log"
-  - versions:
-      - versions.yml:
-          type: file
-          description: File containing software versions
-          pattern: "versions.yml"
+          ontologies: []
+  versions:
+    - versions.yml:
+        type: file
+        description: File containing software versions
+        pattern: "versions.yml"
+        ontologies:
+          - edam: http://edamontology.org/format_3750 # YAML
 authors:
   - "@joseespinosa"
   - "@drpatelh"
+  - "@pinin4fjords"
 maintainers:
   - "@joseespinosa"
   - "@drpatelh"
+  - "@pinin4fjords"
\ No newline at end of file
diff --git a/modules/nf-core/bbmap/bbsplit/tests/main.nf.test b/modules/nf-core/bbmap/bbsplit/tests/main.nf.test
index 0674d247f..2f942f39c 100644
--- a/modules/nf-core/bbmap/bbsplit/tests/main.nf.test
+++ b/modules/nf-core/bbmap/bbsplit/tests/main.nf.test
@@ -3,8 +3,12 @@ nextflow_process {
     name "Test Process BBMAP_BBSPLIT"
     script "../main.nf"
     process "BBMAP_BBSPLIT"
+    tag "modules"
+    tag "modules_nfcore"
+    tag "bbmap"
+    tag "bbmap/bbsplit"
 
-    test("sarscov2_se_fastq_fasta_chr22_fasta - index") {
+    test("sarscov2_se_fastq_fasta_chr22_fasta - build index") {
 
         when {
             process {
@@ -31,7 +35,7 @@ nextflow_process {
         }
     }
 
-    test("sarscov2_se_fastq_fasta_chr22_fasta - index - stub") {
+    test("sarscov2_se_fastq_fasta_chr22_fasta - build index - stub") {
 
         options "-stub"
 
@@ -52,13 +56,12 @@ nextflow_process {
 
         then {
             assertAll(
-                { assert process.success },
-                { assert snapshot(process.out).match() }
+                { assert process.success }
             )
         }
     }
 
-    test("sarscov2_se_fastq_fasta_chr22_fasta") {
+    test("sarscov2_se_fastq_fasta_chr22_fasta - split with prebuilt index") {
 
         setup {
 
@@ -87,58 +90,27 @@ nextflow_process {
                         file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true)
                     ])
                     input[1] = BBMAP_BBSPLIT_INDEX.out.index
-                    input[2] = Channel.of(file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true))
-                    input[3] = Channel.of([
-                        [ 'human' ], // meta map
-                        file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr22/sequence/chr22_23800000-23980000.fa', checkIfExists: true)
-                    ])
+                    input[2] = []
+                    input[3] = [[], []]
                     input[4] = false
                     """
                 }
         }
 
         then {
-            def filesToExclude = [
-                "info.txt",
-                "reflist.txt",
-                "scaffolds.txt.gz",
-                "summary.txt"
-            ]
-
-            def outputFiles = []
-            def outputDirectory = new File(process.out.index[0])
-            outputDirectory.eachFileRecurse { file ->
-                if (file.isFile()){
-                    outputFiles << file
-                    }
-            }
-
-            def filesExist = filesToExclude.every { excludeName ->
-                outputFiles.any { file ->
-                    file.getName().endsWith(excludeName) && file.exists()
-                }
-            }
-
-            def filteredFiles = outputFiles
-                .findAll { file ->
-                    !filesToExclude.any { excludeName ->
-                        file.getName().endsWith(excludeName)
-                    }
-                }.sort{ it.getName()}
-
             assertAll(
                 { assert process.success },
                 { assert path(process.out.log[0][1]).text.contains("If you wish to regenerate the index") },
-                { assert filesExist : "One or more files to exclude do not exist" },
                 { assert snapshot(
-                    filteredFiles,
+                    process.out.primary_fastq,
+                    process.out.stats,
                     process.out.versions
                 ).match()}
             )
         }
     }
 
-    test("sarscov2_se_fastq_fasta_chr22_fasta - stub") {
+    test("sarscov2_se_fastq_fasta_chr22_fasta - split with prebuilt index - stub") {
 
         options "-stub"
 
@@ -169,11 +141,8 @@ nextflow_process {
                         file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true)
                     ])
                     input[1] = BBMAP_BBSPLIT_INDEX.out.index
-                    input[2] = Channel.of(file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true))
-                    input[3] = Channel.of([
-                        [ 'human' ], // meta map
-                        file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr22/sequence/chr22_23800000-23980000.fa', checkIfExists: true)
-                    ])
+                    input[2] = []
+                    input[3] = [[], []]
                     input[4] = false
                 """
             }
@@ -181,8 +150,7 @@ nextflow_process {
 
         then {
             assertAll(
-                { assert process.success },
-                { assert snapshot(process.out).match() }
+                { assert process.success }
             )
         }
     }
diff --git a/modules/nf-core/bbmap/bbsplit/tests/main.nf.test.snap b/modules/nf-core/bbmap/bbsplit/tests/main.nf.test.snap
index 656d3ed05..7e739a663 100644
--- a/modules/nf-core/bbmap/bbsplit/tests/main.nf.test.snap
+++ b/modules/nf-core/bbmap/bbsplit/tests/main.nf.test.snap
@@ -1,12 +1,23 @@
 {
-    "sarscov2_se_fastq_fasta_chr22_fasta": {
+    "sarscov2_se_fastq_fasta_chr22_fasta - split with prebuilt index": {
         "content": [
             [
-                "chr1.chrom.gz:md5,8fec4c63ec642613ad10adf4cc2e6ade",
-                "chr1_index_k13_c13_b1.block:md5,385913c1e84b77dc7bf36288ee1c8706",
-                "chr1_index_k13_c13_b1.block2.gz:md5,2556b45206835a0ff7078d683b5fd6e2",
-                "merged_ref_9222711925172838098.fa.gz:md5,983cef447fb28394b88a5b49b3579f0c",
-                "namelist.txt:md5,45e7a4cdc7a11a39ada56844ca3a1e30"
+                [
+                    {
+                        "id": "test",
+                        "single_end": true
+                    },
+                    "test_primary.fastq.gz:md5,4161df271f9bfcd25d5845a1e220dbec"
+                ]
+            ],
+            [
+                [
+                    {
+                        "id": "test",
+                        "single_end": true
+                    },
+                    "test.stats.txt:md5,2cbf69b72e5f4f8508306b54e8fe2861"
+                ]
             ],
             [
                 "versions.yml:md5,b75d21d7649b5a512e7b54dd15cd3eba"
@@ -14,11 +25,11 @@
         ],
         "meta": {
             "nf-test": "0.9.2",
-            "nextflow": "24.10.5"
+            "nextflow": "25.10.0"
         },
-        "timestamp": "2025-03-12T18:57:32.958846"
+        "timestamp": "2025-11-07T12:36:23.511852"
     },
-    "sarscov2_se_fastq_fasta_chr22_fasta - index": {
+    "sarscov2_se_fastq_fasta_chr22_fasta - build index": {
         "content": [
             [
                 "versions.yml:md5,b75d21d7649b5a512e7b54dd15cd3eba"
@@ -26,174 +37,8 @@
         ],
         "meta": {
             "nf-test": "0.9.2",
-            "nextflow": "24.10.5"
-        },
-        "timestamp": "2025-03-12T18:57:12.155636"
-    },
-    "sarscov2_se_fastq_fasta_chr22_fasta - index - stub": {
-        "content": [
-            {
-                "0": [
-                    [
-                        
-                    ]
-                ],
-                "1": [
-                    
-                ],
-                "2": [
-                    
-                ],
-                "3": [
-                    
-                ],
-                "4": [
-                    [
-                        {
-                            
-                        },
-                        "null.log:md5,d41d8cd98f00b204e9800998ecf8427e"
-                    ]
-                ],
-                "5": [
-                    "versions.yml:md5,b75d21d7649b5a512e7b54dd15cd3eba"
-                ],
-                "all_fastq": [
-                    
-                ],
-                "index": [
-                    [
-                        
-                    ]
-                ],
-                "log": [
-                    [
-                        {
-                            
-                        },
-                        "null.log:md5,d41d8cd98f00b204e9800998ecf8427e"
-                    ]
-                ],
-                "primary_fastq": [
-                    
-                ],
-                "stats": [
-                    
-                ],
-                "versions": [
-                    "versions.yml:md5,b75d21d7649b5a512e7b54dd15cd3eba"
-                ]
-            }
-        ],
-        "meta": {
-            "nf-test": "0.9.2",
-            "nextflow": "24.10.5"
-        },
-        "timestamp": "2025-03-12T18:57:17.177351"
-    },
-    "sarscov2_se_fastq_fasta_chr22_fasta - stub": {
-        "content": [
-            {
-                "0": [
-                    [
-                        
-                    ]
-                ],
-                "1": [
-                    [
-                        {
-                            "id": "test",
-                            "single_end": true
-                        },
-                        "test_primary.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
-                    ]
-                ],
-                "2": [
-                    [
-                        {
-                            "id": "test",
-                            "single_end": true
-                        },
-                        [
-                            "test_human.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940",
-                            "test_primary.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
-                        ]
-                    ]
-                ],
-                "3": [
-                    [
-                        {
-                            "id": "test",
-                            "single_end": true
-                        },
-                        "test.stats.txt:md5,d41d8cd98f00b204e9800998ecf8427e"
-                    ]
-                ],
-                "4": [
-                    [
-                        {
-                            "id": "test",
-                            "single_end": true
-                        },
-                        "test.log:md5,d41d8cd98f00b204e9800998ecf8427e"
-                    ]
-                ],
-                "5": [
-                    "versions.yml:md5,b75d21d7649b5a512e7b54dd15cd3eba"
-                ],
-                "all_fastq": [
-                    [
-                        {
-                            "id": "test",
-                            "single_end": true
-                        },
-                        [
-                            "test_human.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940",
-                            "test_primary.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
-                        ]
-                    ]
-                ],
-                "index": [
-                    [
-                        
-                    ]
-                ],
-                "log": [
-                    [
-                        {
-                            "id": "test",
-                            "single_end": true
-                        },
-                        "test.log:md5,d41d8cd98f00b204e9800998ecf8427e"
-                    ]
-                ],
-                "primary_fastq": [
-                    [
-                        {
-                            "id": "test",
-                            "single_end": true
-                        },
-                        "test_primary.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
-                    ]
-                ],
-                "stats": [
-                    [
-                        {
-                            "id": "test",
-                            "single_end": true
-                        },
-                        "test.stats.txt:md5,d41d8cd98f00b204e9800998ecf8427e"
-                    ]
-                ],
-                "versions": [
-                    "versions.yml:md5,b75d21d7649b5a512e7b54dd15cd3eba"
-                ]
-            }
-        ],
-        "meta": {
-            "nf-test": "0.9.2",
-            "nextflow": "24.10.5"
+            "nextflow": "25.10.0"
         },
-        "timestamp": "2025-03-12T18:57:42.233549"
+        "timestamp": "2025-11-07T11:05:45.517832"
     }
 }
\ No newline at end of file

From 411ac4fcef1074b0865a74c7d4b9680473d4baaf Mon Sep 17 00:00:00 2001
From: Jonathan Manning <jonathan.manning@seqera.io>
Date: Thu, 13 Nov 2025 12:56:05 +0000
Subject: [PATCH 08/11] Update CHANGELOG.md to credit Elad Herzog for PR #1617
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

🤖 Generated with [Claude Code](https://claude.com/claude-code)

Co-Authored-By: Claude <noreply@anthropic.com>
---
 CHANGELOG.md | 5 +++++
 1 file changed, 5 insertions(+)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index d42fcdde3..d5c45983f 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -7,9 +7,14 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ### Credits
 
+Special thanks to the following for their contributions to the release:
+
+- [Elad Herzog](https://github.com/EladH1)
+
 ### Enhancements and fixes
 
 - [PR #1608](https://github.com/nf-core/rnaseq/pull/1608) - Bump version after release 3.21.0
+- [PR #1617](https://github.com/nf-core/rnaseq/pull/1617) - Update bbmap/bbsplit module
 
 ## [[3.21.0](https://github.com/nf-core/rnaseq/releases/tag/3.21.0)] - 2025-09-18
 

From 8a5e38b5e2e9c184617b9e838dad2b7f8d5ca629 Mon Sep 17 00:00:00 2001
From: Jonathan Manning <jonathan.manning@seqera.io>
Date: Thu, 13 Nov 2025 14:52:10 +0000
Subject: [PATCH 09/11] Fix maintainers list formatting in meta.yml

---
 modules/nf-core/bbmap/bbsplit/meta.yml | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/modules/nf-core/bbmap/bbsplit/meta.yml b/modules/nf-core/bbmap/bbsplit/meta.yml
index b496849ad..3075bcd99 100644
--- a/modules/nf-core/bbmap/bbsplit/meta.yml
+++ b/modules/nf-core/bbmap/bbsplit/meta.yml
@@ -110,4 +110,5 @@ authors:
 maintainers:
   - "@joseespinosa"
   - "@drpatelh"
-  - "@pinin4fjords"
\ No newline at end of file
+  - "@pinin4fjords"
+  

From d2d9f87a91b6ea2ab47d25fe025243d773dd4223 Mon Sep 17 00:00:00 2001
From: Jonathan Manning <jonathan.manning@seqera.io>
Date: Thu, 13 Nov 2025 14:54:43 +0000
Subject: [PATCH 10/11] Remove trailing whitespace in meta.yml

---
 modules/nf-core/bbmap/bbsplit/meta.yml | 1 -
 1 file changed, 1 deletion(-)

diff --git a/modules/nf-core/bbmap/bbsplit/meta.yml b/modules/nf-core/bbmap/bbsplit/meta.yml
index 3075bcd99..66f87cce0 100644
--- a/modules/nf-core/bbmap/bbsplit/meta.yml
+++ b/modules/nf-core/bbmap/bbsplit/meta.yml
@@ -111,4 +111,3 @@ maintainers:
   - "@joseespinosa"
   - "@drpatelh"
   - "@pinin4fjords"
-  

From 2e2c75c95052479978a04156557e07f5d2fe9bec Mon Sep 17 00:00:00 2001
From: Jonathan Manning <jonathan.manning@seqera.io>
Date: Thu, 13 Nov 2025 15:10:52 +0000
Subject: [PATCH 11/11] Update git_sha for bbmap/bbsplit module

---
 modules.json | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/modules.json b/modules.json
index 920c05cd7..a62301a56 100644
--- a/modules.json
+++ b/modules.json
@@ -7,7 +7,7 @@
                 "nf-core": {
                     "bbmap/bbsplit": {
                         "branch": "master",
-                        "git_sha": "b5114f2bb0aa49281e1292d0c8b1433e368c0ed3",
+                        "git_sha": "fa1477128e0ff24675c8f56d6c334fcc323025c4",
                         "installed_by": ["fastq_qc_trim_filter_setstrandedness", "modules"]
                     },
                     "bedtools/genomecov": {