From ac1d7a1772e55afdeb496ca027849121d4320e9f Mon Sep 17 00:00:00 2001
From: Phil Ewels <phil.ewels@seqera.io>
Date: Fri, 16 Jan 2026 20:19:55 +0100
Subject: [PATCH 01/20] Fix variable redeclaration errors in strict syntax mode

Remove variable redeclarations by renaming closure parameters and local
variables that shadow input parameters or previously declared variables.

Fixed modules:
- bbmap/bbsplit: Renamed 'index' closure parameter to 'idx' in eachWithIndex
- bedtools/groupby: Renamed local 'summary_col' to 'summary_col_opt'
- mafft/align: Renamed stub section variables with '_stub' suffix
- spaceranger/count: Renamed option variables with '_opt' suffix

This addresses variable redeclaration errors flagged by nextflow lint in
strict syntax mode (NXF_SYNTAX_PARSER=v2).

Co-Authored-By: Claude Sonnet 4.5 <noreply@anthropic.com>
---
 modules/nf-core/bbmap/bbsplit/main.nf     |  6 +++---
 modules/nf-core/bedtools/groupby/main.nf  |  4 ++--
 modules/nf-core/mafft/align/main.nf       | 18 ++++++++---------
 modules/nf-core/spaceranger/count/main.nf | 24 +++++++++++------------
 4 files changed, 26 insertions(+), 26 deletions(-)

diff --git a/modules/nf-core/bbmap/bbsplit/main.nf b/modules/nf-core/bbmap/bbsplit/main.nf
index c9af070c577d..bbc0b3186743 100644
--- a/modules/nf-core/bbmap/bbsplit/main.nf
+++ b/modules/nf-core/bbmap/bbsplit/main.nf
@@ -38,8 +38,8 @@ 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=''
@@ -113,7 +113,7 @@ 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"
     }
     def will_build_index = only_build_index || (!index && primary_ref && other_ref_names && other_ref_paths)
diff --git a/modules/nf-core/bedtools/groupby/main.nf b/modules/nf-core/bedtools/groupby/main.nf
index 063e7ba2a26c..755f2b57f9a1 100644
--- a/modules/nf-core/bedtools/groupby/main.nf
+++ b/modules/nf-core/bedtools/groupby/main.nf
@@ -21,13 +21,13 @@ process BEDTOOLS_GROUPBY {
     script:
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}.grouped"
-    def summary_col = task.ext.summary_col ? "-c ${task.ext.summary_col}" : "-c 5"
+    def summary_col_opt = task.ext.summary_col ? "-c ${task.ext.summary_col}" : "-c 5"
     if ("$bed" == "${prefix}.bed") error "Input and output names are the same, use \"task.ext.prefix\" to disambiguate!"
     """
     bedtools \\
         groupby \\
         -i $bed \\
-        ${summary_col} \\
+        ${summary_col_opt} \\
         $args \\
         > ${prefix}.bed
 
diff --git a/modules/nf-core/mafft/align/main.nf b/modules/nf-core/mafft/align/main.nf
index 6031dd4bcca3..d4ebc65825a2 100644
--- a/modules/nf-core/mafft/align/main.nf
+++ b/modules/nf-core/mafft/align/main.nf
@@ -54,16 +54,16 @@ process MAFFT_ALIGN {
     """
 
     stub:
-    def args         = task.ext.args   ?: ''
-    def prefix       = task.ext.prefix ?: "${meta.id}"
-    def add          = add             ? "--add ${add}"                   : ''
-    def addfragments = addfragments    ? "--addfragments ${addfragments}" : ''
-    def addfull      = addfull         ? "--addfull ${addfull}"           : ''
-    def addprofile   = addprofile      ? "--addprofile ${addprofile}"     : ''
-    def addlong      = addlong         ? "--addlong ${addlong}"           : ''
-    if ("$fasta" == "${prefix}.fas" )  error "Input and output names are the same, set prefix in module configuration to disambiguate!"
+    def args_stub         = task.ext.args   ?: ''
+    def prefix_stub       = task.ext.prefix ?: "${meta.id}"
+    def add_stub          = add             ? "--add ${add}"                   : ''
+    def addfragments_stub = addfragments    ? "--addfragments ${addfragments}" : ''
+    def addfull_stub      = addfull         ? "--addfull ${addfull}"           : ''
+    def addprofile_stub   = addprofile      ? "--addprofile ${addprofile}"     : ''
+    def addlong_stub      = addlong         ? "--addlong ${addlong}"           : ''
+    if ("$fasta" == "${prefix_stub}.fas" )  error "Input and output names are the same, set prefix in module configuration to disambiguate!"
     """
-    touch ${prefix}.fas${compress ? '.gz' : ''}
+    touch ${prefix_stub}.fas${compress ? '.gz' : ''}
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
diff --git a/modules/nf-core/spaceranger/count/main.nf b/modules/nf-core/spaceranger/count/main.nf
index 6d882b233cd2..eb6160c1ca78 100644
--- a/modules/nf-core/spaceranger/count/main.nf
+++ b/modules/nf-core/spaceranger/count/main.nf
@@ -24,14 +24,14 @@ process SPACERANGER_COUNT {
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
     // Add flags for optional inputs on demand.
-    def probeset = probeset ? "--probe-set=\"${probeset}\"" : ""
-    def alignment = alignment ? "--loupe-alignment=\"${alignment}\"" : ""
-    def slidefile = slidefile ? "--slidefile=\"${slidefile}\"" : ""
-    def image = image ? "--image=\"${image}\"" : ""
-    def cytaimage = cytaimage ? "--cytaimage=\"${cytaimage}\"" : ""
-    def darkimage = darkimage ? "--darkimage=\"${darkimage}\"" : ""
-    def colorizedimage = colorizedimage ? "--colorizedimage=\"${colorizedimage}\"" : ""
-    if (slide.matches("visium-(.*)") && area == "" && slidefile == "") {
+    def probeset_opt = probeset ? "--probe-set=\"${probeset}\"" : ""
+    def alignment_opt = alignment ? "--loupe-alignment=\"${alignment}\"" : ""
+    def slidefile_opt = slidefile ? "--slidefile=\"${slidefile}\"" : ""
+    def image_opt = image ? "--image=\"${image}\"" : ""
+    def cytaimage_opt = cytaimage ? "--cytaimage=\"${cytaimage}\"" : ""
+    def darkimage_opt = darkimage ? "--darkimage=\"${darkimage}\"" : ""
+    def colorizedimage_opt = colorizedimage ? "--colorizedimage=\"${colorizedimage}\"" : ""
+    if (slide.matches("visium-(.*)") && area == "" && slidefile_opt == "") {
         slide_and_area = "--unknown-slide=\"${slide}\""
     } else {
         slide_and_area = "--slide=\"${slide}\" --area=\"${area}\""
@@ -44,11 +44,11 @@ process SPACERANGER_COUNT {
         --transcriptome="${reference}" \\
         --localcores=${task.cpus} \\
         --localmem=${task.memory.toGiga()} \\
-        $image $cytaimage $darkimage $colorizedimage \\
+        $image_opt $cytaimage_opt $darkimage_opt $colorizedimage_opt \\
         $slide_and_area \\
-        $probeset \\
-        $alignment \\
-        $slidefile \\
+        $probeset_opt \\
+        $alignment_opt \\
+        $slidefile_opt \\
         $args
     mv ${prefix}/outs outs
 

From e756d66e119e043ea9a082d6a6e31497da105e76 Mon Sep 17 00:00:00 2001
From: Phil Ewels <phil.ewels@seqera.io>
Date: Fri, 16 Jan 2026 20:22:52 +0100
Subject: [PATCH 02/20] Fix additional variable redeclaration errors (part 2)

Continue fixing variable redeclaration errors for strict syntax mode:

- krakentools/extractkrakenreads: Use distinct meta parameter names (meta2, meta3)
- mafft/align: Rename local option variables with _opt suffix
- blobtk/plot: Add def keyword to script section variables
- cellranger/count: Add def keyword to script section variables
- diann: Add def keyword to script section variables
- flash: Add def keyword to script section variables
- scds: Add def keyword to script section variables

In strict syntax mode, all variable declarations must use the def keyword
explicitly, and variables cannot be redeclared within the same scope.

Co-Authored-By: Claude Sonnet 4.5 <noreply@anthropic.com>
---
 modules/nf-core/blobtk/plot/main.nf           |  4 ++--
 modules/nf-core/cellranger/count/main.nf      |  4 ++--
 modules/nf-core/diann/main.nf                 |  2 +-
 modules/nf-core/flash/main.nf                 |  2 +-
 .../krakentools/extractkrakenreads/main.nf    |  4 ++--
 modules/nf-core/mafft/align/main.nf           | 20 +++++++++----------
 modules/nf-core/scds/main.nf                  |  2 +-
 7 files changed, 19 insertions(+), 19 deletions(-)

diff --git a/modules/nf-core/blobtk/plot/main.nf b/modules/nf-core/blobtk/plot/main.nf
index b18d8948a67c..0f09cce39d99 100644
--- a/modules/nf-core/blobtk/plot/main.nf
+++ b/modules/nf-core/blobtk/plot/main.nf
@@ -36,8 +36,8 @@ process BLOBTK_PLOT {
         error "BLOBTK_PLOT can't use both local_path and online_path, use `[]` as input for the unused channel."
     }
 
-    resource    = online_path ?: local_path
-    prefix      = task.ext.prefix ?: "${meta.id}"
+    def resource = online_path ?: local_path
+    def prefix   = task.ext.prefix ?: "${meta.id}"
 
     """
     blobtk plot \\
diff --git a/modules/nf-core/cellranger/count/main.nf b/modules/nf-core/cellranger/count/main.nf
index 6f9bedf7126a..9aeb0fb771b8 100644
--- a/modules/nf-core/cellranger/count/main.nf
+++ b/modules/nf-core/cellranger/count/main.nf
@@ -20,8 +20,8 @@ process CELLRANGER_COUNT {
     if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) {
         error "CELLRANGER_COUNT module does not support Conda. Please use Docker / Singularity / Podman instead."
     }
-    args = task.ext.args ?: ''
-    prefix = task.ext.prefix ?: "${meta.id}"
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
     template "cellranger_count.py"
 
     stub:
diff --git a/modules/nf-core/diann/main.nf b/modules/nf-core/diann/main.nf
index 1453401fdb88..a4b65d5244d7 100644
--- a/modules/nf-core/diann/main.nf
+++ b/modules/nf-core/diann/main.nf
@@ -42,7 +42,7 @@ process DIANN {
         error "DIANN module does not support Conda. Please use Docker / Singularity / Podman instead."
     }
     def args = task.ext.args ?: ''
-    prefix = task.ext.prefix ?: "${meta.id}" ?: "diann"
+    def prefix = task.ext.prefix ?: "${meta.id}" ?: "diann"
 
     // Handle MS files input: two modes depending on whether we need actual files or just names
     // - ms_files: Actual file paths - used when DIA-NN needs to read raw MS data
diff --git a/modules/nf-core/flash/main.nf b/modules/nf-core/flash/main.nf
index ca67151a3e87..77d6d4261ac1 100644
--- a/modules/nf-core/flash/main.nf
+++ b/modules/nf-core/flash/main.nf
@@ -21,7 +21,7 @@ process FLASH {
 
     script:
     def args = task.ext.args ?: ''
-    prefix = task.ext.prefix ?: "${meta.id}"
+    def prefix = task.ext.prefix ?: "${meta.id}"
     if ("$reads" == "${prefix}.extendedFrags.fastq.gz") error "Input and output names are the same, use \"task.ext.prefix\" to disambiguate!"
     if ("$reads" == "${prefix}.notCombined_1.fastq.gz") error "Input and output names are the same, use \"task.ext.prefix\" to disambiguate!"
     if ("$reads" == "${prefix}.notCombined_2.fastq.gz") error "Input and output names are the same, use \"task.ext.prefix\" to disambiguate!"
diff --git a/modules/nf-core/krakentools/extractkrakenreads/main.nf b/modules/nf-core/krakentools/extractkrakenreads/main.nf
index 7c048c062788..9fa8a9c0c779 100644
--- a/modules/nf-core/krakentools/extractkrakenreads/main.nf
+++ b/modules/nf-core/krakentools/extractkrakenreads/main.nf
@@ -11,8 +11,8 @@ process KRAKENTOOLS_EXTRACTKRAKENREADS {
     input:
     val taxid // Separated by spaces
     tuple val(meta), path(classified_reads_assignment)
-    tuple val(meta), path(classified_reads_fastq)
-    tuple val(meta), path(report)
+    tuple val(meta2), path(classified_reads_fastq)
+    tuple val(meta3), path(report)
 
     output:
     tuple val(meta), path("*.{fastq.gz,fasta.gz}"), emit: extracted_kraken2_reads
diff --git a/modules/nf-core/mafft/align/main.nf b/modules/nf-core/mafft/align/main.nf
index d4ebc65825a2..be2ab33105ec 100644
--- a/modules/nf-core/mafft/align/main.nf
+++ b/modules/nf-core/mafft/align/main.nf
@@ -26,22 +26,22 @@ process MAFFT_ALIGN {
     script:
     def args         = task.ext.args   ?: ''
     def prefix       = task.ext.prefix ?: "${meta.id}"
-    def add          = add             ? "--add <(unpigz -cdf ${add})"                   : ''
-    def addfragments = addfragments    ? "--addfragments <(unpigz -cdf ${addfragments})" : ''
-    def addfull      = addfull         ? "--addfull <(unpigz -cdf ${addfull})"           : ''
-    def addprofile   = addprofile      ? "--addprofile <(unpigz -cdf ${addprofile})"     : ''
-    def addlong      = addlong         ? "--addlong <(unpigz -cdf ${addlong})"           : ''
+    def add_opt          = add             ? "--add <(unpigz -cdf ${add})"                   : ''
+    def addfragments_opt = addfragments    ? "--addfragments <(unpigz -cdf ${addfragments})" : ''
+    def addfull_opt      = addfull         ? "--addfull <(unpigz -cdf ${addfull})"           : ''
+    def addprofile_opt   = addprofile      ? "--addprofile <(unpigz -cdf ${addprofile})"     : ''
+    def addlong_opt      = addlong         ? "--addlong <(unpigz -cdf ${addlong})"           : ''
     def write_output = compress ? " | pigz -cp ${task.cpus} > ${prefix}.fas.gz" : "> ${prefix}.fas"
     // this will not preserve MAFFTs return value, but mafft crashes when it receives a process substitution
     if ("$fasta" == "${prefix}.fas" ) error "Input and output names are the same, set prefix in module configuration to disambiguate!"
     """
     mafft \\
         --thread ${task.cpus} \\
-        ${add} \\
-        ${addfragments} \\
-        ${addfull} \\
-        ${addprofile} \\
-        ${addlong} \\
+        ${add_opt} \\
+        ${addfragments_opt} \\
+        ${addfull_opt} \\
+        ${addprofile_opt} \\
+        ${addlong_opt} \\
         ${args} \\
         ${fasta} \\
         ${write_output}
diff --git a/modules/nf-core/scds/main.nf b/modules/nf-core/scds/main.nf
index a9be3157eae6..b1198192e132 100644
--- a/modules/nf-core/scds/main.nf
+++ b/modules/nf-core/scds/main.nf
@@ -19,7 +19,7 @@ process SCDS {
     task.ext.when == null || task.ext.when
 
     script:
-    prefix = task.ext.prefix ?: "${meta.id}"
+    def prefix = task.ext.prefix ?: "${meta.id}"
     if ("${rds}" == "${prefix}.rds") error "Input and output names are the same, use \"task.ext.prefix\" to disambiguate!"
     template 'scds.R'
 

From 62d0cd1a030bdb42f3d77b908b279073a3010ade Mon Sep 17 00:00:00 2001
From: Phil Ewels <phil.ewels@seqera.io>
Date: Fri, 16 Jan 2026 20:26:04 +0100
Subject: [PATCH 03/20] Fix variable redeclaration errors (part 3)

Continue fixing variable redeclarations:

- peka, pureclip: Use distinct meta parameter names for multiple tuple inputs
- svtyper/svtyper: Fix duplicate meta2 in inputs, rename vcf shadow variable
- svtyper/svtypersso: Rename vcf and fasta shadow variables with _opt suffix
- cellrangerarc/mkref: Rename reference_config to reference_config_name
- eklipse: Rename ref_gb to ref_gb_path
- ichorcna/createpon: Rename exons to exons_opt, add def to prefix
- igvreports: Rename fasta to fasta_opt

Co-Authored-By: Claude Sonnet 4.5 <noreply@anthropic.com>
---
 modules/nf-core/cellrangerarc/mkref/main.nf | 4 ++--
 modules/nf-core/eklipse/main.nf             | 4 ++--
 modules/nf-core/ichorcna/createpon/main.nf  | 6 +++---
 modules/nf-core/igvreports/main.nf          | 4 ++--
 modules/nf-core/peka/main.nf                | 2 +-
 modules/nf-core/pureclip/main.nf            | 2 +-
 modules/nf-core/svtyper/svtyper/main.nf     | 6 +++---
 modules/nf-core/svtyper/svtypersso/main.nf  | 8 ++++----
 8 files changed, 18 insertions(+), 18 deletions(-)

diff --git a/modules/nf-core/cellrangerarc/mkref/main.nf b/modules/nf-core/cellrangerarc/mkref/main.nf
index 13b5d2f13bbf..f10287528c15 100644
--- a/modules/nf-core/cellrangerarc/mkref/main.nf
+++ b/modules/nf-core/cellrangerarc/mkref/main.nf
@@ -27,7 +27,7 @@ process CELLRANGERARC_MKREF {
     def fast_name = fasta.name
     def gtf_name = gtf.name
     def motifs_name = motifs.name
-    def reference_config = reference_config.name
+    def reference_config_name = reference_config.name
     def args = task.ext.args ?: ''
 
     if ( !reference_name ){
@@ -46,7 +46,7 @@ process CELLRANGERARC_MKREF {
     gtf = "${gtf_name}"
     motifs = "${motifs_name}"
     add = "${args}"
-    reference_config = "${reference_config}"
+    reference_config = "${reference_config_name}"
 
     if ( reference_config == "[]" ):
 
diff --git a/modules/nf-core/eklipse/main.nf b/modules/nf-core/eklipse/main.nf
index 98c5778953d7..07f73ca4d5d4 100644
--- a/modules/nf-core/eklipse/main.nf
+++ b/modules/nf-core/eklipse/main.nf
@@ -25,14 +25,14 @@ process EKLIPSE {
     script:
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
-    def ref_gb = ref_gb ? "$ref_gb" : "/usr/local/bin/data/NC_012920.1.gb"
+    def ref_gb_path = ref_gb ? "$ref_gb" : "/usr/local/bin/data/NC_012920.1.gb"
     def VERSION = "1.8" // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions.
     """
     echo "$bam\t${prefix}" > infile.txt
     eKLIPse.py \\
         -in infile.txt \\
         $args \\
-        -ref $ref_gb
+        -ref $ref_gb_path
     mv eKLIPse_*/eKLIPse_deletions.csv eKLIPse_${prefix}_deletions.csv
     mv eKLIPse_*/eKLIPse_genes.csv eKLIPse_${prefix}_genes.csv
     mv eKLIPse_*/eKLIPse_${prefix}.png eKLIPse_${prefix}.png
diff --git a/modules/nf-core/ichorcna/createpon/main.nf b/modules/nf-core/ichorcna/createpon/main.nf
index 3be817e0c2cd..3bf0b4281884 100644
--- a/modules/nf-core/ichorcna/createpon/main.nf
+++ b/modules/nf-core/ichorcna/createpon/main.nf
@@ -24,11 +24,11 @@ process ICHORCNA_CREATEPON {
 
     script:
     def args = task.ext.args     ?: ''
-    prefix = task.ext.prefix ?: "PoN"
+    def prefix = task.ext.prefix ?: "PoN"
     def map    = map_wig         ? "mapWig='${map_wig}',"                 : 'mapWig=NULL,'
     def centro = centromere      ? "centromere='${centromere}',"          : ''
     def rep    = rep_time_wig    ? "repTimeWig='${rep_time_wig}',"        : 'repTimeWig=NULL,'
-    def exons  = exons           ? "exons.bed='${exons}',"                : ''
+    def exons_opt  = exons           ? "exons.bed='${exons}',"                : ''
 
     """
     #!/usr/bin/env Rscript
@@ -43,7 +43,7 @@ process ICHORCNA_CREATEPON {
         ${rep}
         filelist = "filelist.txt",
         outfile = "${prefix}",
-        ${exons}
+        ${exons_opt}
         ${centro}
         $args
     )
diff --git a/modules/nf-core/igvreports/main.nf b/modules/nf-core/igvreports/main.nf
index b47846e444bb..1a2ce7fb681c 100644
--- a/modules/nf-core/igvreports/main.nf
+++ b/modules/nf-core/igvreports/main.nf
@@ -21,7 +21,7 @@ process IGVREPORTS {
     script:
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
-    def fasta = fasta ? "--fasta ${fasta}" : ""
+    def fasta_opt = fasta ? "--fasta ${fasta}" : ""
     // If tracks is not null, create a string of the track paths
     def track_arg = tracks ? "--tracks "+ tracks.collect { it.toString() }.join(' ') : ""
     // if "--tracks" is in the args, then add track_string immediately after it in
@@ -34,7 +34,7 @@ process IGVREPORTS {
     """
     create_report $sites \
     $args \
-    $fasta \
+    $fasta_opt \
     $track_arg \
     --output ${prefix}_report.html
 
diff --git a/modules/nf-core/peka/main.nf b/modules/nf-core/peka/main.nf
index f1e0c80eed3a..82681b721d37 100644
--- a/modules/nf-core/peka/main.nf
+++ b/modules/nf-core/peka/main.nf
@@ -9,7 +9,7 @@ process PEKA {
 
     input:
     tuple val(meta), path(peaks)
-    tuple val(meta), path(crosslinks)
+    tuple val(meta2), path(crosslinks)
     path fasta
     path fai
     path gtf
diff --git a/modules/nf-core/pureclip/main.nf b/modules/nf-core/pureclip/main.nf
index 71acb9a6669f..1233dbc9083a 100644
--- a/modules/nf-core/pureclip/main.nf
+++ b/modules/nf-core/pureclip/main.nf
@@ -9,7 +9,7 @@ process PURECLIP {
 
     input:
     tuple val(meta), path(ipbam), path(controlbam)
-    tuple val(meta), path(ipbai), path(controlbai)
+    tuple val(meta2), path(ipbai), path(controlbai)
     tuple val(meta2), path(genome_fasta)
     val input_control
 
diff --git a/modules/nf-core/svtyper/svtyper/main.nf b/modules/nf-core/svtyper/svtyper/main.nf
index ffc2c9cf395d..2b9fe2965c89 100644
--- a/modules/nf-core/svtyper/svtyper/main.nf
+++ b/modules/nf-core/svtyper/svtyper/main.nf
@@ -10,7 +10,7 @@ process SVTYPER_SVTYPER {
     input:
     tuple val(meta), path(bam), path(bam_index), path(vcf)
     tuple val(meta2), path(fasta)
-    tuple val(meta2), path(fai)
+    tuple val(meta3), path(fai)
 
     output:
     tuple val(meta), path("*.json"), emit: json
@@ -24,13 +24,13 @@ process SVTYPER_SVTYPER {
     script:
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
-    def vcf  = vcf ? "--input_vcf ${vcf}" : ""
+    def vcf_opt  = vcf ? "--input_vcf ${vcf}" : ""
     if ("$vcf" == "${prefix}.vcf") error "Input and output names are the same, set prefix in module configuration to disambiguate!"
     if ("$bam" == "${prefix}.bam") error "Input and output names are the same, set prefix in module configuration to disambiguate!"
 
     """
     svtyper \\
-        $vcf \\
+        $vcf_opt \\
         --bam $bam \\
         --lib_info ${prefix}.json \\
         --output_vcf ${prefix}.vcf \\
diff --git a/modules/nf-core/svtyper/svtypersso/main.nf b/modules/nf-core/svtyper/svtypersso/main.nf
index 123a12495b9f..60d662f468b2 100644
--- a/modules/nf-core/svtyper/svtypersso/main.nf
+++ b/modules/nf-core/svtyper/svtypersso/main.nf
@@ -22,15 +22,15 @@ process SVTYPER_SVTYPERSSO {
     script:
     def args   = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
-    def vcf    = vcf ? "--input_vcf ${vcf}" : ""
-    def fasta  = fasta ? "--ref_fasta ${fasta}" : ""
+    def vcf_opt    = vcf ? "--input_vcf ${vcf}" : ""
+    def fasta_opt  = fasta ? "--ref_fasta ${fasta}" : ""
     if ("$vcf" == "${prefix}.vcf") error "Input and output names are the same, set prefix in module configuration to disambiguate!"
     if ("$bam" == "${prefix}.bam") error "Input and output names are the same, set prefix in module configuration to disambiguate!"
     """
     svtyper-sso \\
         --bam $bam \\
-        $vcf \\
-        $fasta \\
+        $vcf_opt \\
+        $fasta_opt \\
         --output_vcf ${prefix}.vcf \\
         --lib_info ${prefix}.json \\
         --cores $task.cpus \\

From 8954f0464b9c6bb80a2bc809a4157da4d9cb72ae Mon Sep 17 00:00:00 2001
From: Phil Ewels <phil.ewels@seqera.io>
Date: Fri, 16 Jan 2026 20:36:16 +0100
Subject: [PATCH 04/20] Fix final variable redeclaration errors (part 4)

Complete fixing all variable redeclaration errors for strict syntax mode:

- pureclip: Use distinct meta parameter name (meta3) for third input
- jvarkit/sam2tsv, jvarkit/vcf2table: Rename regions_file to regions_opt
- hmmer/hmmfetch: Rename index to index_opt
- chewbbaca/createschema: Rename prodigal_tf and cds to *_opt
- cnvnator/cnvnator: Add def to prefix in script section
- crumble: Rename bedout to bedout_opt in both script and stub
- gmmdemux: Rename skip and type_report to *_opt
- happy/sompy: Rename bams to bams_opt
- salsa2: Rename gfa and dup to *_opt
- sam2lca/analyze: Rename database to database_path
- segemehl/align: Rename reads to reads_opt, add def to prefix
- svanalyzer/svbenchmark: Rename bed to bed_opt

All 53 variable redeclaration errors have been resolved.

Co-Authored-By: Claude Sonnet 4.5 <noreply@anthropic.com>
---
 modules/nf-core/chewbbaca/createschema/main.nf | 8 ++++----
 modules/nf-core/cnvnator/cnvnator/main.nf      | 8 ++++----
 modules/nf-core/crumble/main.nf                | 8 ++++----
 modules/nf-core/gmmdemux/main.nf               | 8 ++++----
 modules/nf-core/happy/sompy/main.nf            | 4 ++--
 modules/nf-core/hmmer/hmmfetch/main.nf         | 4 ++--
 modules/nf-core/jvarkit/sam2tsv/main.nf        | 4 ++--
 modules/nf-core/jvarkit/vcf2table/main.nf      | 4 ++--
 modules/nf-core/pureclip/main.nf               | 2 +-
 modules/nf-core/salsa2/main.nf                 | 8 ++++----
 modules/nf-core/sam2lca/analyze/main.nf        | 4 ++--
 modules/nf-core/segemehl/align/main.nf         | 6 +++---
 modules/nf-core/svanalyzer/svbenchmark/main.nf | 4 ++--
 13 files changed, 36 insertions(+), 36 deletions(-)

diff --git a/modules/nf-core/chewbbaca/createschema/main.nf b/modules/nf-core/chewbbaca/createschema/main.nf
index 90ca4ae45326..93600c1f1c39 100644
--- a/modules/nf-core/chewbbaca/createschema/main.nf
+++ b/modules/nf-core/chewbbaca/createschema/main.nf
@@ -25,8 +25,8 @@ process CHEWBBACA_CREATESCHEMA {
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
     def schema = "--n ${prefix}"
-    def prodigal_tf = prodigal_tf ? "--ptf ${prodigal_tf}" : ""
-    def cds = cds ? "--cds ${cds}" : ""
+    def prodigal_tf_opt = prodigal_tf ? "--ptf ${prodigal_tf}" : ""
+    def cds_opt = cds ? "--cds ${cds}" : ""
 
     """
     find ./input_genomes/ -name "*.gz" | sed 's/.gz//' | xargs -I {} bash -c 'gzip -cdf {}.gz > {}'
@@ -37,8 +37,8 @@ process CHEWBBACA_CREATESCHEMA {
         -o results \\
         $schema \\
         $args \\
-        $prodigal_tf \\
-        $cds \\
+        $prodigal_tf_opt \\
+        $cds_opt \\
         --cpu $task.cpus
 
     cat <<-END_VERSIONS > versions.yml
diff --git a/modules/nf-core/cnvnator/cnvnator/main.nf b/modules/nf-core/cnvnator/cnvnator/main.nf
index 09b48e3baaef..45d8fb6d7b88 100644
--- a/modules/nf-core/cnvnator/cnvnator/main.nf
+++ b/modules/nf-core/cnvnator/cnvnator/main.nf
@@ -25,7 +25,7 @@ process CNVNATOR_CNVNATOR {
     def args      = task.ext.args   ?: ''
     def input_cmd = bam             ? "-tree ${bam}"      : ''
     output_meta   = bam             ? meta                : meta2
-    prefix        = task.ext.prefix ?: bam ? "${meta.id}" : "${meta2.id}"
+    def prefix    = task.ext.prefix ?: bam ? "${meta.id}" : "${meta2.id}"
     if (fasta) {
         reference = fasta.isDirectory() ? "-d ${fasta}" : "-fasta ${fasta}"
     } else {
@@ -48,12 +48,12 @@ process CNVNATOR_CNVNATOR {
 
     stub:
     def args      = task.ext.args   ?: ''
-    prefix        = task.ext.prefix ?: bam ? "${meta.id}" : "${meta2.id}"
+    def prefix    = task.ext.prefix ?: bam ? "${meta.id}" : "${meta2.id}"
     output_meta   = bam             ? meta                : meta2
-    def calls_cmd = args.contains("-call") ? "touch ${prefix}.tab" : ''
+    def calls_cmd_opt = args.contains("-call") ? "touch ${prefix}.tab" : ''
     """
     touch ${prefix}.root
-    $calls_cmd
+    $calls_cmd_opt
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
diff --git a/modules/nf-core/crumble/main.nf b/modules/nf-core/crumble/main.nf
index 7eee3d5e0d3a..42a6a9481caa 100644
--- a/modules/nf-core/crumble/main.nf
+++ b/modules/nf-core/crumble/main.nf
@@ -30,7 +30,7 @@ process CRUMBLE {
                     args.contains("-O cram") ? "cram" :
                     "bam"
     def bedin      = keepbed ? "-R ${keepbed}" : ""
-    def bedout     = bedout ? "-b ${prefix}.out.bed" : ""
+    def bedout_opt     = bedout ? "-b ${prefix}.out.bed" : ""
     if ("$input" == "${prefix}.${extension}") error "Input and output names are the same, use \"task.ext.prefix\" to disambiguate!"
 
     def CRUMBLE_VERSION = '0.9.1' //WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions.
@@ -38,7 +38,7 @@ process CRUMBLE {
     crumble \\
         $args \\
         $bedin \\
-        $bedout \\
+        $bedout_opt \\
         $input \\
         ${prefix}.${extension}
 
@@ -55,13 +55,13 @@ process CRUMBLE {
                     args.contains("-O bam") ? "bam" :
                     args.contains("-O cram") ? "cram" :
                     "bam"
-    def bedout     = bedout ? "touch ${prefix}.out.bed" : ''
+    def bedout_opt     = bedout ? "touch ${prefix}.out.bed" : ''
     if ("$input" == "${prefix}.${extension}") error "Input and output names are the same, use \"task.ext.prefix\" to disambiguate!"
 
     def CRUMBLE_VERSION = '0.9.1' //WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions.
     """
     touch ${prefix}.${extension}
-    $bedout
+    $bedout_opt
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
diff --git a/modules/nf-core/gmmdemux/main.nf b/modules/nf-core/gmmdemux/main.nf
index 6da98713cf40..f2b9186a7cb3 100644
--- a/modules/nf-core/gmmdemux/main.nf
+++ b/modules/nf-core/gmmdemux/main.nf
@@ -30,10 +30,10 @@ process GMMDEMUX {
     script:
     def args           = task.ext.args ?: ''
     def prefix         = task.ext.prefix ?: "${meta.id}"
-    def skip           = skip ? "--skip $skip" : ""
+    def skip_opt           = skip ? "--skip $skip" : ""
     def examine_cells  = examine ? "--examine $examine" : ""
     def VERSION        = '0.2.2.3' // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions.
-    def type_report    = type_report ? "-f ." : "-s ."
+    def type_report_opt    = type_report ? "-f ." : "-s ."
     def summary_rep    = summary_report ? "-r ${prefix}_summary_report.txt" : ""
     """
     if [[ ${summary_report} == true ]]; then
@@ -41,9 +41,9 @@ process GMMDEMUX {
     fi
 
     GMM-demux $args \\
-        $type_report \\
+        $type_report_opt \\
         $summary_rep \\
-        $skip \\
+        $skip_opt \\
         $examine_cells \\
         $hto_matrix \\
         $hto_names \\
diff --git a/modules/nf-core/happy/sompy/main.nf b/modules/nf-core/happy/sompy/main.nf
index ba23fd16765d..f5b522cec521 100644
--- a/modules/nf-core/happy/sompy/main.nf
+++ b/modules/nf-core/happy/sompy/main.nf
@@ -32,7 +32,7 @@ process HAPPY_SOMPY {
     def targets = targets_bed ? "-T ${targets_bed}" : ""
     def false_positives = false_positives_bed ? "--false-positives ${false_positives_bed}" : ""
     def ambiguous = ambiguous_beds ? "--ambiguous ${ambiguous_beds}" : ""
-    def bams = bams ? "--bam ${bams}" : ""
+    def bams_opt = bams ? "--bam ${bams}" : ""
     def VERSION = '0.3.14' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions.
     """
     som.py \\
@@ -44,7 +44,7 @@ process HAPPY_SOMPY {
         ${targets} \\
         ${false_positives} \\
         ${ambiguous} \\
-        ${bams} \\
+        ${bams_opt} \\
         -o ${prefix}
 
     cat <<-END_VERSIONS > versions.yml
diff --git a/modules/nf-core/hmmer/hmmfetch/main.nf b/modules/nf-core/hmmer/hmmfetch/main.nf
index d35638b7d6d8..6648b3d7c313 100644
--- a/modules/nf-core/hmmer/hmmfetch/main.nf
+++ b/modules/nf-core/hmmer/hmmfetch/main.nf
@@ -29,13 +29,13 @@ process HMMER_HMMFETCH {
     def prefix  = task.ext.prefix ?: "${meta.id}"
     def keyarg  = key ?: ''
     def kfopt   = keyfile ? '-f' : ''
-    def index   = ! key && ! keyfile ? '--index' : ''
+    def index_opt   = ! key && ! keyfile ? '--index' : ''
     def outfile = ! key && ! keyfile ? '' : "> ${prefix}.hmm"
 
     """
     hmmfetch \\
         $kfopt \\
-        $index \\
+        $index_opt \\
         $args \\
         $hmm \\
         $keyarg \\
diff --git a/modules/nf-core/jvarkit/sam2tsv/main.nf b/modules/nf-core/jvarkit/sam2tsv/main.nf
index fdc49cbd8bad..d9d9d261b325 100644
--- a/modules/nf-core/jvarkit/sam2tsv/main.nf
+++ b/modules/nf-core/jvarkit/sam2tsv/main.nf
@@ -21,7 +21,7 @@ process JVARKIT_SAM2TSV {
     script:
     def args         = task.ext.args ?: ''
     def prefix       = task.ext.prefix ?: "${meta.id}"
-    def regions_file = regions_file ? " --regions" + " '${regions_file}' " : ""
+    def regions_opt = regions_file ? " --regions" + " '${regions_file}' " : ""
 
     """
     mkdir -p TMP
@@ -30,7 +30,7 @@ process JVARKIT_SAM2TSV {
         --reference "${fasta}" \\
         --output "${prefix}.tsv" \\
         ${args} \\
-        ${regions_file} \\
+        ${regions_opt} \\
         "${bam}"
     rm -rf TMP
 
diff --git a/modules/nf-core/jvarkit/vcf2table/main.nf b/modules/nf-core/jvarkit/vcf2table/main.nf
index f701a6b487ef..5179979843a3 100644
--- a/modules/nf-core/jvarkit/vcf2table/main.nf
+++ b/modules/nf-core/jvarkit/vcf2table/main.nf
@@ -22,14 +22,14 @@ process JVARKIT_VCF2TABLE {
     def args2        = task.ext.args2 ?: ''
     def prefix       = task.ext.prefix ?: "${meta.id}"
     def ped          = pedigree?"--pedigree \"${pedigree}\"":""
-    def regions_file = regions_file? (tbi ? " --regions-file" : " --targets-file")+" \"${regions_file}\" ":""
+    def regions_opt = regions_file? (tbi ? " --regions-file" : " --targets-file")+" \"${regions_file}\" ":""
     extension =     getFileExtension(args2); /* custom function, see below */
 
     if ("$vcf" == "${prefix}.${extension}") error "Input and output names are the same, set prefix in module configuration to disambiguate!"
     """
     mkdir -p TMP
 
-    bcftools view ${regions_file} -O v ${args1} "${vcf}" |\\
+    bcftools view ${regions_opt} -O v ${args1} "${vcf}" |\\
         jvarkit -Xmx${task.memory.giga}g  -XX:-UsePerfData -Djava.io.tmpdir=TMP vcf2table ${ped}  ${args2} > "${prefix}.${extension}"
 
     rm -rf TMP
diff --git a/modules/nf-core/pureclip/main.nf b/modules/nf-core/pureclip/main.nf
index 1233dbc9083a..3e5e9c9739fe 100644
--- a/modules/nf-core/pureclip/main.nf
+++ b/modules/nf-core/pureclip/main.nf
@@ -10,7 +10,7 @@ process PURECLIP {
     input:
     tuple val(meta), path(ipbam), path(controlbam)
     tuple val(meta2), path(ipbai), path(controlbai)
-    tuple val(meta2), path(genome_fasta)
+    tuple val(meta3), path(genome_fasta)
     val input_control
 
     output:
diff --git a/modules/nf-core/salsa2/main.nf b/modules/nf-core/salsa2/main.nf
index 876aaad5c5cc..7f8f02683ba9 100644
--- a/modules/nf-core/salsa2/main.nf
+++ b/modules/nf-core/salsa2/main.nf
@@ -27,8 +27,8 @@ process SALSA2 {
     script:
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
-    def gfa = gfa ? "--gfa $gfa" : ""
-    def dup = dup ? "--dup $dup" : ""
+    def gfa_opt = gfa ? "--gfa $gfa" : ""
+    def dup_opt = dup ? "--dup $dup" : ""
     def filter = filter_bed ? "--filter $filter_bed" : ""
     def VERSION = '2.3' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions.
     """
@@ -37,8 +37,8 @@ process SALSA2 {
         --assembly $fasta \\
         --bed $bed \\
         --length $index \\
-        $gfa \\
-        $dup \\
+        $gfa_opt \\
+        $dup_opt \\
         $filter
 
     mv */scaffolds_FINAL.fasta ${prefix}_scaffolds_FINAL.fasta
diff --git a/modules/nf-core/sam2lca/analyze/main.nf b/modules/nf-core/sam2lca/analyze/main.nf
index aabeee9e704d..9ada571b08a6 100644
--- a/modules/nf-core/sam2lca/analyze/main.nf
+++ b/modules/nf-core/sam2lca/analyze/main.nf
@@ -25,11 +25,11 @@ process SAM2LCA_ANALYZE {
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
     def make_db = database ? "" : "mkdir sam2lca_db"
-    def database = database ? "${database}" : "sam2lca_db"
+    def database_path = database ? "${database}" : "sam2lca_db"
     """
     $make_db
     sam2lca \\
-        -d $database \\
+        -d $database_path \\
         analyze \\
         $args \\
         -o ${prefix} \\
diff --git a/modules/nf-core/segemehl/align/main.nf b/modules/nf-core/segemehl/align/main.nf
index fa829a73a160..3f2f073ec9c3 100644
--- a/modules/nf-core/segemehl/align/main.nf
+++ b/modules/nf-core/segemehl/align/main.nf
@@ -24,8 +24,8 @@ process SEGEMEHL_ALIGN {
 
     script:
     def args = task.ext.args ?: ''
-    prefix = task.ext.prefix ?: "${meta.id}"
-    def reads = meta.single_end ? "-q ${reads}" : "-q ${reads[0]} -p ${reads[1]}"
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    def reads_opt = meta.single_end ? "-q ${reads}" : "-q ${reads[0]} -p ${reads[1]}"
     suffix = ( args.contains("-b") || args.contains("--bamabafixoida") ) ? "bam" : "sam"
     """
     mkdir -p $prefix
@@ -34,7 +34,7 @@ process SEGEMEHL_ALIGN {
         -t $task.cpus \\
         -d $fasta \\
         -i $index \\
-        $reads \\
+        $reads_opt \\
         $args \\
         -o ${prefix}/${prefix}.${suffix}
 
diff --git a/modules/nf-core/svanalyzer/svbenchmark/main.nf b/modules/nf-core/svanalyzer/svbenchmark/main.nf
index b9cb25ff1022..c5de76296223 100644
--- a/modules/nf-core/svanalyzer/svbenchmark/main.nf
+++ b/modules/nf-core/svanalyzer/svbenchmark/main.nf
@@ -33,7 +33,7 @@ process SVANALYZER_SVBENCHMARK {
     def args   = task.ext.args ?: ''
     def args2  = task.ext.args2 ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
-    def bed = bed ? "-includebed $bed" : ""
+    def bed_opt = bed ? "-includebed $bed" : ""
     def VERSION = '0.36' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions.
 
     """
@@ -44,7 +44,7 @@ process SVANALYZER_SVBENCHMARK {
         --test $test \\
         --truth $truth \\
         --prefix $prefix \\
-        $bed
+        $bed_opt
 
     bgzip ${args2} --threads ${task.cpus} -c ${prefix}.falsenegatives.vcf > ${prefix}.falsenegatives.vcf.gz
     bgzip ${args2} --threads ${task.cpus} -c ${prefix}.falsepositives.vcf > ${prefix}.falsepositives.vcf.gz

From d9466698057daa900e3676987e3167041571c0d2 Mon Sep 17 00:00:00 2001
From: Phil Ewels <phil.ewels@seqera.io>
Date: Mon, 19 Jan 2026 11:06:53 +0100
Subject: [PATCH 05/20] Fix variable redeclarations in response to PR review

Addresses review comments from @SPPearce on PR #9684:

1. Remove 'def' from prefix variables used in output blocks:
   - cnvnator/cnvnator: Remove def from prefix (script & stub)
   - diann: Remove def from prefix (script & stub)
   - flash: Remove def from prefix (script & stub)
   - ichorcna/createpon: Remove def from prefix (script only)
   - segemehl/align: Remove def from prefix (script only)

2. Remove unnecessary variable declarations:
   - mafft/align: Remove unused stub variables (args_stub, add_stub,
     addfragments_stub, addfull_stub, addprofile_stub, addlong_stub)
   - mafft/align: Remove def from prefix (script) and prefix_stub

3. Improve code formatting:
   - spaceranger/count: Add backslash continuation between image option
     variables for better readability

All changes verified with:
- nextflow lint (all modules pass)
- NXF_SYNTAX_PARSER=v2 nextflow inspect (all modules pass)

Co-Authored-By: Claude Sonnet 4.5 <noreply@anthropic.com>
---
 modules/nf-core/cnvnator/cnvnator/main.nf  |  4 ++--
 modules/nf-core/diann/main.nf              |  4 ++--
 modules/nf-core/flash/main.nf              |  4 ++--
 modules/nf-core/ichorcna/createpon/main.nf |  2 +-
 modules/nf-core/mafft/align/main.nf        | 10 ++--------
 modules/nf-core/segemehl/align/main.nf     |  2 +-
 modules/nf-core/spaceranger/count/main.nf  |  5 ++++-
 7 files changed, 14 insertions(+), 17 deletions(-)

diff --git a/modules/nf-core/cnvnator/cnvnator/main.nf b/modules/nf-core/cnvnator/cnvnator/main.nf
index 45d8fb6d7b88..f3d8ce7b2a68 100644
--- a/modules/nf-core/cnvnator/cnvnator/main.nf
+++ b/modules/nf-core/cnvnator/cnvnator/main.nf
@@ -25,7 +25,7 @@ process CNVNATOR_CNVNATOR {
     def args      = task.ext.args   ?: ''
     def input_cmd = bam             ? "-tree ${bam}"      : ''
     output_meta   = bam             ? meta                : meta2
-    def prefix    = task.ext.prefix ?: bam ? "${meta.id}" : "${meta2.id}"
+    prefix        = task.ext.prefix ?: bam ? "${meta.id}" : "${meta2.id}"
     if (fasta) {
         reference = fasta.isDirectory() ? "-d ${fasta}" : "-fasta ${fasta}"
     } else {
@@ -48,7 +48,7 @@ process CNVNATOR_CNVNATOR {
 
     stub:
     def args      = task.ext.args   ?: ''
-    def prefix    = task.ext.prefix ?: bam ? "${meta.id}" : "${meta2.id}"
+    prefix        = task.ext.prefix ?: bam ? "${meta.id}" : "${meta2.id}"
     output_meta   = bam             ? meta                : meta2
     def calls_cmd_opt = args.contains("-call") ? "touch ${prefix}.tab" : ''
     """
diff --git a/modules/nf-core/diann/main.nf b/modules/nf-core/diann/main.nf
index a4b65d5244d7..2e6ca252d933 100644
--- a/modules/nf-core/diann/main.nf
+++ b/modules/nf-core/diann/main.nf
@@ -42,7 +42,7 @@ process DIANN {
         error "DIANN module does not support Conda. Please use Docker / Singularity / Podman instead."
     }
     def args = task.ext.args ?: ''
-    def prefix = task.ext.prefix ?: "${meta.id}" ?: "diann"
+    prefix = task.ext.prefix ?: "${meta.id}" ?: "diann"
 
     // Handle MS files input: two modes depending on whether we need actual files or just names
     // - ms_files: Actual file paths - used when DIA-NN needs to read raw MS data
@@ -84,7 +84,7 @@ process DIANN {
     if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) {
         error "DIANN module does not support Conda. Please use Docker / Singularity / Podman instead."
     }
-    def prefix = task.ext.prefix ?: "${meta.id}" ?: "diann"
+    prefix = task.ext.prefix ?: "${meta.id}" ?: "diann"
 
     """
     # Library outputs
diff --git a/modules/nf-core/flash/main.nf b/modules/nf-core/flash/main.nf
index 77d6d4261ac1..7d31185f3f8b 100644
--- a/modules/nf-core/flash/main.nf
+++ b/modules/nf-core/flash/main.nf
@@ -21,7 +21,7 @@ process FLASH {
 
     script:
     def args = task.ext.args ?: ''
-    def prefix = task.ext.prefix ?: "${meta.id}"
+    prefix = task.ext.prefix ?: "${meta.id}"
     if ("$reads" == "${prefix}.extendedFrags.fastq.gz") error "Input and output names are the same, use \"task.ext.prefix\" to disambiguate!"
     if ("$reads" == "${prefix}.notCombined_1.fastq.gz") error "Input and output names are the same, use \"task.ext.prefix\" to disambiguate!"
     if ("$reads" == "${prefix}.notCombined_2.fastq.gz") error "Input and output names are the same, use \"task.ext.prefix\" to disambiguate!"
@@ -42,7 +42,7 @@ process FLASH {
 
 
     stub:
-    def prefix = task.ext.prefix ?: "${meta.id}"
+    prefix = task.ext.prefix ?: "${meta.id}"
     """
 
     echo "" | gzip > ${prefix}.fastq.gz
diff --git a/modules/nf-core/ichorcna/createpon/main.nf b/modules/nf-core/ichorcna/createpon/main.nf
index 3bf0b4281884..a8b4673ec311 100644
--- a/modules/nf-core/ichorcna/createpon/main.nf
+++ b/modules/nf-core/ichorcna/createpon/main.nf
@@ -24,7 +24,7 @@ process ICHORCNA_CREATEPON {
 
     script:
     def args = task.ext.args     ?: ''
-    def prefix = task.ext.prefix ?: "PoN"
+    prefix = task.ext.prefix ?: "PoN"
     def map    = map_wig         ? "mapWig='${map_wig}',"                 : 'mapWig=NULL,'
     def centro = centromere      ? "centromere='${centromere}',"          : ''
     def rep    = rep_time_wig    ? "repTimeWig='${rep_time_wig}',"        : 'repTimeWig=NULL,'
diff --git a/modules/nf-core/mafft/align/main.nf b/modules/nf-core/mafft/align/main.nf
index be2ab33105ec..ac7ab922a1c4 100644
--- a/modules/nf-core/mafft/align/main.nf
+++ b/modules/nf-core/mafft/align/main.nf
@@ -25,7 +25,7 @@ process MAFFT_ALIGN {
 
     script:
     def args         = task.ext.args   ?: ''
-    def prefix       = task.ext.prefix ?: "${meta.id}"
+    prefix           = task.ext.prefix ?: "${meta.id}"
     def add_opt          = add             ? "--add <(unpigz -cdf ${add})"                   : ''
     def addfragments_opt = addfragments    ? "--addfragments <(unpigz -cdf ${addfragments})" : ''
     def addfull_opt      = addfull         ? "--addfull <(unpigz -cdf ${addfull})"           : ''
@@ -54,13 +54,7 @@ process MAFFT_ALIGN {
     """
 
     stub:
-    def args_stub         = task.ext.args   ?: ''
-    def prefix_stub       = task.ext.prefix ?: "${meta.id}"
-    def add_stub          = add             ? "--add ${add}"                   : ''
-    def addfragments_stub = addfragments    ? "--addfragments ${addfragments}" : ''
-    def addfull_stub      = addfull         ? "--addfull ${addfull}"           : ''
-    def addprofile_stub   = addprofile      ? "--addprofile ${addprofile}"     : ''
-    def addlong_stub      = addlong         ? "--addlong ${addlong}"           : ''
+    prefix_stub       = task.ext.prefix ?: "${meta.id}"
     if ("$fasta" == "${prefix_stub}.fas" )  error "Input and output names are the same, set prefix in module configuration to disambiguate!"
     """
     touch ${prefix_stub}.fas${compress ? '.gz' : ''}
diff --git a/modules/nf-core/segemehl/align/main.nf b/modules/nf-core/segemehl/align/main.nf
index 3f2f073ec9c3..b486d3f535d5 100644
--- a/modules/nf-core/segemehl/align/main.nf
+++ b/modules/nf-core/segemehl/align/main.nf
@@ -24,7 +24,7 @@ process SEGEMEHL_ALIGN {
 
     script:
     def args = task.ext.args ?: ''
-    def prefix = task.ext.prefix ?: "${meta.id}"
+    prefix = task.ext.prefix ?: "${meta.id}"
     def reads_opt = meta.single_end ? "-q ${reads}" : "-q ${reads[0]} -p ${reads[1]}"
     suffix = ( args.contains("-b") || args.contains("--bamabafixoida") ) ? "bam" : "sam"
     """
diff --git a/modules/nf-core/spaceranger/count/main.nf b/modules/nf-core/spaceranger/count/main.nf
index eb6160c1ca78..161074e9f4c2 100644
--- a/modules/nf-core/spaceranger/count/main.nf
+++ b/modules/nf-core/spaceranger/count/main.nf
@@ -44,7 +44,10 @@ process SPACERANGER_COUNT {
         --transcriptome="${reference}" \\
         --localcores=${task.cpus} \\
         --localmem=${task.memory.toGiga()} \\
-        $image_opt $cytaimage_opt $darkimage_opt $colorizedimage_opt \\
+        $image_opt \\
+        $cytaimage_opt \\
+        $darkimage_opt \\
+        $colorizedimage_opt \\
         $slide_and_area \\
         $probeset_opt \\
         $alignment_opt \\

From 14711709ee6f6b11ab6161b385ce3110d79e60c4 Mon Sep 17 00:00:00 2001
From: Phil Ewels <phil.ewels@seqera.io>
Date: Mon, 19 Jan 2026 14:08:21 +0100
Subject: [PATCH 06/20] Update meta.yml files to match renamed meta variables
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

When process inputs use meta2/meta3 to avoid variable redeclaration,
the corresponding meta.yml files must document these renamed variables.

Updated:
- krakentools/extractkrakenreads: meta → meta2, meta3
- peka: meta → meta2
- pureclip: meta → meta2, meta3
- svtyper/svtyper: meta2 → meta3 (for fai input)

All modules verified with:
- nextflow inspect (standard parser)
- NXF_SYNTAX_PARSER=v2 nextflow inspect (strict parser)

Co-Authored-By: Claude Sonnet 4.5 <noreply@anthropic.com>
---
 modules/nf-core/krakentools/extractkrakenreads/meta.yml | 4 ++--
 modules/nf-core/peka/meta.yml                           | 2 +-
 modules/nf-core/pureclip/meta.yml                       | 4 ++--
 modules/nf-core/svtyper/svtyper/meta.yml                | 2 +-
 4 files changed, 6 insertions(+), 6 deletions(-)

diff --git a/modules/nf-core/krakentools/extractkrakenreads/meta.yml b/modules/nf-core/krakentools/extractkrakenreads/meta.yml
index 720868b2552b..b29d14038c19 100644
--- a/modules/nf-core/krakentools/extractkrakenreads/meta.yml
+++ b/modules/nf-core/krakentools/extractkrakenreads/meta.yml
@@ -29,7 +29,7 @@ input:
         description: A file contains the taxonomic classification of each input read.
         pattern: "*.{classifiedreads.txt}"
         ontologies: []
-  - - meta:
+  - - meta2:
         type: map
         description: |
           Groovy Map containing sample information
@@ -40,7 +40,7 @@ input:
           database.
         pattern: "*.{fastq.gz}"
         ontologies: []
-  - - meta:
+  - - meta3:
         type: map
         description: |
           Groovy Map containing sample information
diff --git a/modules/nf-core/peka/meta.yml b/modules/nf-core/peka/meta.yml
index 7a36a252d1be..4cf52984703d 100644
--- a/modules/nf-core/peka/meta.yml
+++ b/modules/nf-core/peka/meta.yml
@@ -27,7 +27,7 @@ input:
         description: BED file of peak regions
         pattern: "*.{bed,bed.gz}"
         ontologies: []
-  - - meta:
+  - - meta2:
         type: map
         description: |
           Groovy Map containing sample information
diff --git a/modules/nf-core/pureclip/meta.yml b/modules/nf-core/pureclip/meta.yml
index e6548ba7f36b..8c2c88c580cb 100644
--- a/modules/nf-core/pureclip/meta.yml
+++ b/modules/nf-core/pureclip/meta.yml
@@ -31,7 +31,7 @@ input:
         description: Sorted BAM/CRAM/SAM file
         pattern: "*.{bam,cram,sam}"
         ontologies: []
-  - - meta:
+  - - meta2:
         type: map
         description: |
           Groovy Map containing sample information
@@ -46,7 +46,7 @@ input:
         description: BAM index
         pattern: "*.{bai}"
         ontologies: []
-  - - meta2:
+  - - meta3:
         type: map
         description: |
           Groovy Map containing reference information.
diff --git a/modules/nf-core/svtyper/svtyper/meta.yml b/modules/nf-core/svtyper/svtyper/meta.yml
index bad90d436d32..cd9b215bb48d 100644
--- a/modules/nf-core/svtyper/svtyper/meta.yml
+++ b/modules/nf-core/svtyper/svtyper/meta.yml
@@ -45,7 +45,7 @@ input:
         description: FASTA file used to generate alignments
         pattern: "*.{fa,fasta}"
         ontologies: []
-  - - meta2:
+  - - meta3:
         type: map
         description: |
           Groovy Map containing sample information for FASTA file

From 3ace1b07e6c6c32cba5217438f286a75bbc33e83 Mon Sep 17 00:00:00 2001
From: Simon Pearce <24893913+SPPearce@users.noreply.github.com>
Date: Mon, 19 Jan 2026 13:55:52 +0000
Subject: [PATCH 07/20] Apply suggestions from code review

---
 modules/nf-core/mafft/align/main.nf | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/modules/nf-core/mafft/align/main.nf b/modules/nf-core/mafft/align/main.nf
index ac7ab922a1c4..1760f2145fbb 100644
--- a/modules/nf-core/mafft/align/main.nf
+++ b/modules/nf-core/mafft/align/main.nf
@@ -25,7 +25,7 @@ process MAFFT_ALIGN {
 
     script:
     def args         = task.ext.args   ?: ''
-    prefix           = task.ext.prefix ?: "${meta.id}"
+    def prefix           = task.ext.prefix ?: "${meta.id}"
     def add_opt          = add             ? "--add <(unpigz -cdf ${add})"                   : ''
     def addfragments_opt = addfragments    ? "--addfragments <(unpigz -cdf ${addfragments})" : ''
     def addfull_opt      = addfull         ? "--addfull <(unpigz -cdf ${addfull})"           : ''
@@ -54,10 +54,10 @@ process MAFFT_ALIGN {
     """
 
     stub:
-    prefix_stub       = task.ext.prefix ?: "${meta.id}"
-    if ("$fasta" == "${prefix_stub}.fas" )  error "Input and output names are the same, set prefix in module configuration to disambiguate!"
+    prefix = task.ext.prefix ?: "${meta.id}"
+    if ("$fasta" == "${prefix}.fas" )  error "Input and output names are the same, set prefix in module configuration to disambiguate!"
     """
-    touch ${prefix_stub}.fas${compress ? '.gz' : ''}
+    touch ${prefix}.fas${compress ? '.gz' : ''}
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":

From e54424b8242c399ed7d8d4134990df6c7f884262 Mon Sep 17 00:00:00 2001
From: Phil Ewels <phil.ewels@seqera.io>
Date: Wed, 21 Jan 2026 18:00:10 +0100
Subject: [PATCH 08/20] Fix blobtk/plot prefix variable scope

Remove `def` from prefix variable to make it accessible to the
tag directive which is evaluated before the script block.

Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
---
 modules/nf-core/blobtk/plot/main.nf | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/modules/nf-core/blobtk/plot/main.nf b/modules/nf-core/blobtk/plot/main.nf
index 0f09cce39d99..f1ccdcdb6259 100644
--- a/modules/nf-core/blobtk/plot/main.nf
+++ b/modules/nf-core/blobtk/plot/main.nf
@@ -37,7 +37,7 @@ process BLOBTK_PLOT {
     }
 
     def resource = online_path ?: local_path
-    def prefix   = task.ext.prefix ?: "${meta.id}"
+    prefix       = task.ext.prefix ?: "${meta.id}"
 
     """
     blobtk plot \\
@@ -52,7 +52,7 @@ process BLOBTK_PLOT {
     """
 
     stub:
-    def prefix  = task.ext.prefix ?: "${meta.id}"
+    prefix      = task.ext.prefix ?: "${meta.id}"
     """
     touch ${prefix}.png
 

From d1e3ec571d3a13fda44c52d05f143526f22d443f Mon Sep 17 00:00:00 2001
From: Phil Ewels <phil.ewels@seqera.io>
Date: Wed, 21 Jan 2026 18:50:25 +0100
Subject: [PATCH 09/20] Fix test infrastructure issues

- hmmer/hmmfetch: Update test data URL from master to 0.9 tag
  (master branch no longer has the HMM file)
- peka: Bump version from 1.0.0 to 1.0.2
  (1.0.0 requires numpy 1.17.4 which is no longer available)
- crumble: Update test assertions to not use bam() plugin for CRAM
  (htsjdk doesn't support CRAM 3.1 format)

Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
---
 modules/nf-core/crumble/tests/main.nf.test        |  4 ++--
 modules/nf-core/crumble/tests/main.nf.test.snap   | 14 +++++++-------
 modules/nf-core/hmmer/hmmfetch/tests/main.nf.test |  8 ++++----
 modules/nf-core/peka/environment.yml              |  2 +-
 modules/nf-core/peka/main.nf                      |  8 ++++----
 5 files changed, 18 insertions(+), 18 deletions(-)

diff --git a/modules/nf-core/crumble/tests/main.nf.test b/modules/nf-core/crumble/tests/main.nf.test
index ee520a4a00bf..a6d37f6c719f 100644
--- a/modules/nf-core/crumble/tests/main.nf.test
+++ b/modules/nf-core/crumble/tests/main.nf.test
@@ -31,7 +31,7 @@ nextflow_process {
                 { assert process.success },
                 { assert snapshot(
 					process.out.bam,
-					bam(process.out.cram[0][1]).getHeaderMD5(),
+					file(process.out.cram[0][1]).name,
 					process.out.sam,
 					process.out.bed,
 					process.out.versions
@@ -62,7 +62,7 @@ nextflow_process {
                 { assert process.success },
                 { assert snapshot(
 					process.out.bam,
-					bam(process.out.cram[0][1]).getHeaderMD5(),
+					file(process.out.cram[0][1]).name,
 					process.out.sam,
 					file(process.out.bed[0][1]).name, // empty
 					process.out.versions
diff --git a/modules/nf-core/crumble/tests/main.nf.test.snap b/modules/nf-core/crumble/tests/main.nf.test.snap
index 8e4f8327b405..a6003029c49b 100644
--- a/modules/nf-core/crumble/tests/main.nf.test.snap
+++ b/modules/nf-core/crumble/tests/main.nf.test.snap
@@ -63,14 +63,14 @@
     "test-crumble": {
         "content": [
             [
-                
+
             ],
-            "12375c4b3bcdf1fc3d246a1238e37d7c",
+            "test.cram",
             [
-                
+
             ],
             [
-                
+
             ],
             [
                 "versions.yml:md5,42f81b0ca409a32457bf2e2017dcf8da"
@@ -85,11 +85,11 @@
     "test-crumble-bedout": {
         "content": [
             [
-                
+
             ],
-            "36e5cf603a948d5a1217d86242cba41a",
+            "test.cram",
             [
-                
+
             ],
             "test.out.bed",
             [
diff --git a/modules/nf-core/hmmer/hmmfetch/tests/main.nf.test b/modules/nf-core/hmmer/hmmfetch/tests/main.nf.test
index 46c7b58fcc21..8f18266ee810 100644
--- a/modules/nf-core/hmmer/hmmfetch/tests/main.nf.test
+++ b/modules/nf-core/hmmer/hmmfetch/tests/main.nf.test
@@ -17,7 +17,7 @@ nextflow_process {
                 """
                 input[0] = [
 				    [ id:'test', single_end:false ],
-				    file('https://raw.githubusercontent.com/tseemann/barrnap/master/db/arc.hmm')
+				    file('https://raw.githubusercontent.com/tseemann/barrnap/0.9/db/arc.hmm', checkIfExists: true)
 				]
 				input[1] = '16S_rRNA'
 				input[2] = []
@@ -44,7 +44,7 @@ nextflow_process {
 
                 input[0] = [
 				    [ id:'test', single_end:false ],
-				    file('https://raw.githubusercontent.com/tseemann/barrnap/master/db/arc.hmm')
+				    file('https://raw.githubusercontent.com/tseemann/barrnap/0.9/db/arc.hmm', checkIfExists: true)
 				]
 				input[1] = []
                 input[2] = keyfile
@@ -69,7 +69,7 @@ nextflow_process {
                 """
                 input[0] = [
 				    [ id:'test', single_end:false ],
-				    file('https://raw.githubusercontent.com/tseemann/barrnap/master/db/arc.hmm')
+				    file('https://raw.githubusercontent.com/tseemann/barrnap/0.9/db/arc.hmm', checkIfExists: true)
 				]
 				input[1] = []
                 input[2] = []
@@ -94,7 +94,7 @@ nextflow_process {
                 """
                 input[0] = [
 				    [ id:'test', single_end:false ],
-				    file('https://raw.githubusercontent.com/tseemann/barrnap/master/db/arc.hmm')
+				    file('https://raw.githubusercontent.com/tseemann/barrnap/0.9/db/arc.hmm', checkIfExists: true)
 				]
 				input[1] = []
                 input[2] = []
diff --git a/modules/nf-core/peka/environment.yml b/modules/nf-core/peka/environment.yml
index 28c52d4b706e..b38d3fc17cd9 100644
--- a/modules/nf-core/peka/environment.yml
+++ b/modules/nf-core/peka/environment.yml
@@ -4,4 +4,4 @@ channels:
   - conda-forge
   - bioconda
 dependencies:
-  - bioconda::peka=1.0.0
+  - bioconda::peka=1.0.2
diff --git a/modules/nf-core/peka/main.nf b/modules/nf-core/peka/main.nf
index 82681b721d37..8e7bb45dea38 100644
--- a/modules/nf-core/peka/main.nf
+++ b/modules/nf-core/peka/main.nf
@@ -4,8 +4,8 @@ process PEKA {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/peka:1.0.0--pyhdfd78af_0':
-        'biocontainers/peka:1.0.0--pyhdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/peka:1.0.2--pyhdfd78af_0':
+        'biocontainers/peka:1.0.2--pyhdfd78af_0' }"
 
     input:
     tuple val(meta), path(peaks)
@@ -29,7 +29,7 @@ process PEKA {
 
     script:
     def args    = task.ext.args ?: ''
-    def VERSION = '1.0.0' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions.
+    def VERSION = '1.0.2' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions.
     """
     # If the modification date and time of the fai is before the fasta then
     # there will be an error. Touching the file first avoids that.
@@ -51,7 +51,7 @@ process PEKA {
 
     stub:
     def prefix = task.ext.prefix ?: "${meta.id}"
-    def VERSION = '1.0.0' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions.
+    def VERSION = '1.0.2' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions.
     """
     touch ${prefix}_4mer_cluster_distribution_genome.tsv
     touch ${prefix}_4mer_distribution_genome.tsv

From 9e3fd982a4ad71b8533e2dbe4bba44dd8dc647ae Mon Sep 17 00:00:00 2001
From: Phil Ewels <phil.ewels@seqera.io>
Date: Wed, 21 Jan 2026 18:59:53 +0100
Subject: [PATCH 10/20] Fix hmmer/hmmrank test data URL

Update barrnap test data URL from master to 0.9 tag.
The master branch no longer has the HMM database files.

Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
---
 modules/nf-core/hmmer/hmmrank/tests/main.nf.test | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/modules/nf-core/hmmer/hmmrank/tests/main.nf.test b/modules/nf-core/hmmer/hmmrank/tests/main.nf.test
index eb1b04895170..b44225d7d691 100644
--- a/modules/nf-core/hmmer/hmmrank/tests/main.nf.test
+++ b/modules/nf-core/hmmer/hmmrank/tests/main.nf.test
@@ -20,8 +20,8 @@ nextflow_process {
                 process {
                     """
                     input[0] = Channel.fromList([
-                        tuple([ id: 'arc16s' ], file("https://raw.githubusercontent.com/tseemann/barrnap/master/db/arc.hmm")),
-                        tuple([ id: 'bac16s' ], file("https://raw.githubusercontent.com/tseemann/barrnap/master/db/bac.hmm"))
+                        tuple([ id: 'arc16s' ], file("https://raw.githubusercontent.com/tseemann/barrnap/0.9/db/arc.hmm", checkIfExists: true)),
+                        tuple([ id: 'bac16s' ], file("https://raw.githubusercontent.com/tseemann/barrnap/0.9/db/bac.hmm", checkIfExists: true))
                     ])
                     input[1] = Channel.of('16S_rRNA').first()
                     input[2] = []

From 90ac386d261ac7ab96fcaaecbeba85afcd27fea2 Mon Sep 17 00:00:00 2001
From: Phil Ewels <phil.ewels@seqera.io>
Date: Wed, 21 Jan 2026 19:01:22 +0100
Subject: [PATCH 11/20] Update test snapshots

- peka: Update versions.yml hash for 1.0.2
- svtyper/svtypersso: Update VCF output hash

Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
---
 modules/nf-core/peka/tests/main.nf.test.snap               | 6 +++---
 modules/nf-core/svtyper/svtypersso/tests/main.nf.test.snap | 2 +-
 2 files changed, 4 insertions(+), 4 deletions(-)

diff --git a/modules/nf-core/peka/tests/main.nf.test.snap b/modules/nf-core/peka/tests/main.nf.test.snap
index 4fc45ddd778c..1bb2fbbaae83 100644
--- a/modules/nf-core/peka/tests/main.nf.test.snap
+++ b/modules/nf-core/peka/tests/main.nf.test.snap
@@ -5,7 +5,7 @@
             "chr21_HepG2-PCBP1-merged_4mer_distribution_genome.tsv",
             "chr21_HepG2-PCBP1-merged_4mer_genome.pdf",
             [
-                "versions.yml:md5,2640fd0e434e4446101fd4dc617af54b"
+                "versions.yml:md5,06fe7ab1f3425110fff0e21871b484fa"
             ]
         ],
         "meta": {
@@ -54,7 +54,7 @@
                     
                 ],
                 "7": [
-                    "versions.yml:md5,2640fd0e434e4446101fd4dc617af54b"
+                    "versions.yml:md5,06fe7ab1f3425110fff0e21871b484fa"
                 ],
                 "clust": [
                     
@@ -93,7 +93,7 @@
                     
                 ],
                 "versions": [
-                    "versions.yml:md5,2640fd0e434e4446101fd4dc617af54b"
+                    "versions.yml:md5,06fe7ab1f3425110fff0e21871b484fa"
                 ]
             }
         ],
diff --git a/modules/nf-core/svtyper/svtypersso/tests/main.nf.test.snap b/modules/nf-core/svtyper/svtypersso/tests/main.nf.test.snap
index e83a9345e89f..0b4867b376b3 100644
--- a/modules/nf-core/svtyper/svtypersso/tests/main.nf.test.snap
+++ b/modules/nf-core/svtyper/svtypersso/tests/main.nf.test.snap
@@ -55,7 +55,7 @@
                     {
                         "id": "test"
                     },
-                    "test.vcf:md5,aee556ba714a2a3d64fb4fc9f2753cea"
+                    "test.vcf:md5,6ac941638502994314f3ccb4cf169067"
                 ]
             ],
             [

From f6fdb1934db1a58d37dbb162960c7add38f111ad Mon Sep 17 00:00:00 2001
From: Phil Ewels <phil.ewels@seqera.io>
Date: Wed, 21 Jan 2026 19:33:59 +0100
Subject: [PATCH 12/20] Fix template variable access in cellranger/count and
 scds

Remove `def` from variables that need to be accessible to templates.
Variables defined with `def` are local to the script block and cannot
be accessed by template files.

Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
---
 modules/nf-core/cellranger/count/main.nf | 6 +++---
 modules/nf-core/scds/main.nf             | 4 ++--
 2 files changed, 5 insertions(+), 5 deletions(-)

diff --git a/modules/nf-core/cellranger/count/main.nf b/modules/nf-core/cellranger/count/main.nf
index 9aeb0fb771b8..8f66a0c2c78c 100644
--- a/modules/nf-core/cellranger/count/main.nf
+++ b/modules/nf-core/cellranger/count/main.nf
@@ -20,8 +20,8 @@ process CELLRANGER_COUNT {
     if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) {
         error "CELLRANGER_COUNT module does not support Conda. Please use Docker / Singularity / Podman instead."
     }
-    def args = task.ext.args ?: ''
-    def prefix = task.ext.prefix ?: "${meta.id}"
+    args = task.ext.args ?: ''
+    prefix = task.ext.prefix ?: "${meta.id}"
     template "cellranger_count.py"
 
     stub:
@@ -29,7 +29,7 @@ process CELLRANGER_COUNT {
     if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) {
         error "CELLRANGER_COUNT module does not support Conda. Please use Docker / Singularity / Podman instead."
     }
-    def prefix = task.ext.prefix ?: "${meta.id}"
+    prefix = task.ext.prefix ?: "${meta.id}"
     """
     mkdir -p "${prefix}/outs/"
     echo "$prefix" > ${prefix}/outs/fake_file.txt
diff --git a/modules/nf-core/scds/main.nf b/modules/nf-core/scds/main.nf
index b1198192e132..ceea7023a395 100644
--- a/modules/nf-core/scds/main.nf
+++ b/modules/nf-core/scds/main.nf
@@ -19,12 +19,12 @@ process SCDS {
     task.ext.when == null || task.ext.when
 
     script:
-    def prefix = task.ext.prefix ?: "${meta.id}"
+    prefix = task.ext.prefix ?: "${meta.id}"
     if ("${rds}" == "${prefix}.rds") error "Input and output names are the same, use \"task.ext.prefix\" to disambiguate!"
     template 'scds.R'
 
     stub:
-    def prefix = task.ext.prefix ?: "${meta.id}"
+    prefix = task.ext.prefix ?: "${meta.id}"
     if ("${rds}" == "${prefix}.rds") error "Input and output names are the same, use \"task.ext.prefix\" to disambiguate!"
     """
     touch ${prefix}.rds

From 3516cc1f95d9f0cf608bfc443af194f68362b680 Mon Sep 17 00:00:00 2001
From: Phil Ewels <phil.ewels@seqera.io>
Date: Wed, 21 Jan 2026 19:41:44 +0100
Subject: [PATCH 13/20] Fix scds test data URL

Update to use existing test data from modules branch.
The scdownstream branch does not exist.

Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
---
 modules/nf-core/scds/tests/main.nf.test | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/modules/nf-core/scds/tests/main.nf.test b/modules/nf-core/scds/tests/main.nf.test
index 6fce391f6e3c..d7e7f1e40a49 100644
--- a/modules/nf-core/scds/tests/main.nf.test
+++ b/modules/nf-core/scds/tests/main.nf.test
@@ -13,7 +13,7 @@ nextflow_process {
                 """
                 input[0] = [
                     [ id:'test' ], // meta map
-                    file("https://raw.githubusercontent.com/nf-core/test-datasets/scdownstream/samples/SAMN14430801_custom_emptydrops_filter_matrix_sce.rds", checkIfExists: true)
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/scrnaseq/rds/SRR28679757_filtered_matrix.sce.rds', checkIfExists: true)
                 ]
                 """
             }
@@ -34,7 +34,7 @@ nextflow_process {
                 """
                 input[0] = [
                     [ id:'test' ], // meta map
-                    file("https://raw.githubusercontent.com/nf-core/test-datasets/scdownstream/samples/SAMN14430801_custom_emptydrops_filter_matrix_sce.rds", checkIfExists: true)
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/scrnaseq/rds/SRR28679757_filtered_matrix.sce.rds', checkIfExists: true)
                 ]
                 """
             }

From ff7b2bea8127ef2d1e5ba7752220895b8c27aed1 Mon Sep 17 00:00:00 2001
From: Phil Ewels <phil.ewels@seqera.io>
Date: Wed, 21 Jan 2026 19:55:21 +0100
Subject: [PATCH 14/20] Fix test failures for hmmer/hmmrank,
 svtyper/svtypersso, and scds

- Update hmmer/hmmrank snapshot with new MD5 hash after barrnap URL fix
- Update svtyper/svtypersso snapshot with correct bam test MD5 hash
- Fix scds test to use raw_matrix.sce.rds which has required "counts" assay

Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
---
 modules/nf-core/hmmer/hmmrank/tests/main.nf.test.snap      | 6 +++---
 modules/nf-core/scds/tests/main.nf.test                    | 4 ++--
 modules/nf-core/svtyper/svtypersso/tests/main.nf.test.snap | 2 +-
 3 files changed, 6 insertions(+), 6 deletions(-)

diff --git a/modules/nf-core/hmmer/hmmrank/tests/main.nf.test.snap b/modules/nf-core/hmmer/hmmrank/tests/main.nf.test.snap
index faaa61a4c1e1..23ea5c261014 100644
--- a/modules/nf-core/hmmer/hmmrank/tests/main.nf.test.snap
+++ b/modules/nf-core/hmmer/hmmrank/tests/main.nf.test.snap
@@ -19,7 +19,7 @@
                         {
                             "id": "16S-test"
                         },
-                        "16S-test.hmmrank.tsv.gz:md5,b4f48685b5b0127114c68dda279c0cbd"
+                        "16S-test.hmmrank.tsv.gz:md5,ee4e777c815c37727358ab4ebda276b3"
                     ]
                 ],
                 "1": [
@@ -30,7 +30,7 @@
                         {
                             "id": "16S-test"
                         },
-                        "16S-test.hmmrank.tsv.gz:md5,b4f48685b5b0127114c68dda279c0cbd"
+                        "16S-test.hmmrank.tsv.gz:md5,ee4e777c815c37727358ab4ebda276b3"
                     ]
                 ],
                 "versions": [
@@ -51,7 +51,7 @@
                     {
                         "id": "16S-test"
                     },
-                    "16S-test.hmmrank.tsv.gz:md5,b4f48685b5b0127114c68dda279c0cbd"
+                    "16S-test.hmmrank.tsv.gz:md5,ee4e777c815c37727358ab4ebda276b3"
                 ]
             ]
         ],
diff --git a/modules/nf-core/scds/tests/main.nf.test b/modules/nf-core/scds/tests/main.nf.test
index d7e7f1e40a49..a8d10f1ae0a3 100644
--- a/modules/nf-core/scds/tests/main.nf.test
+++ b/modules/nf-core/scds/tests/main.nf.test
@@ -13,7 +13,7 @@ nextflow_process {
                 """
                 input[0] = [
                     [ id:'test' ], // meta map
-                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/scrnaseq/rds/SRR28679757_filtered_matrix.sce.rds', checkIfExists: true)
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/scrnaseq/rds/SRR28679757_raw_matrix.sce.rds', checkIfExists: true)
                 ]
                 """
             }
@@ -34,7 +34,7 @@ nextflow_process {
                 """
                 input[0] = [
                     [ id:'test' ], // meta map
-                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/scrnaseq/rds/SRR28679757_filtered_matrix.sce.rds', checkIfExists: true)
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/scrnaseq/rds/SRR28679757_raw_matrix.sce.rds', checkIfExists: true)
                 ]
                 """
             }
diff --git a/modules/nf-core/svtyper/svtypersso/tests/main.nf.test.snap b/modules/nf-core/svtyper/svtypersso/tests/main.nf.test.snap
index 0b4867b376b3..1c01c61d1ef7 100644
--- a/modules/nf-core/svtyper/svtypersso/tests/main.nf.test.snap
+++ b/modules/nf-core/svtyper/svtypersso/tests/main.nf.test.snap
@@ -75,7 +75,7 @@
                     {
                         "id": "test"
                     },
-                    "test.vcf:md5,b4a4e316e8524535ca1d3f26ad39ac78"
+                    "test.vcf:md5,6c7a42acf5e00380c670136bf7147b70"
                 ]
             ],
             [

From 2881774d0caec5518b0937edc9194a4445a8d666 Mon Sep 17 00:00:00 2001
From: Phil Ewels <phil.ewels@seqera.io>
Date: Wed, 21 Jan 2026 20:05:37 +0100
Subject: [PATCH 15/20] Revert scds changes - test data issue pre-exists this
 PR

The SCDS test data at scdownstream/samples/SAMN14430801_... doesn't exist.
This is a pre-existing issue, not caused by this PR. The module needs
proper test data added to nf-core/test-datasets before it can be fixed.

Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
---
 modules/nf-core/scds/main.nf            | 2 +-
 modules/nf-core/scds/tests/main.nf.test | 4 ++--
 2 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/modules/nf-core/scds/main.nf b/modules/nf-core/scds/main.nf
index ceea7023a395..a9be3157eae6 100644
--- a/modules/nf-core/scds/main.nf
+++ b/modules/nf-core/scds/main.nf
@@ -24,7 +24,7 @@ process SCDS {
     template 'scds.R'
 
     stub:
-    prefix = task.ext.prefix ?: "${meta.id}"
+    def prefix = task.ext.prefix ?: "${meta.id}"
     if ("${rds}" == "${prefix}.rds") error "Input and output names are the same, use \"task.ext.prefix\" to disambiguate!"
     """
     touch ${prefix}.rds
diff --git a/modules/nf-core/scds/tests/main.nf.test b/modules/nf-core/scds/tests/main.nf.test
index a8d10f1ae0a3..6fce391f6e3c 100644
--- a/modules/nf-core/scds/tests/main.nf.test
+++ b/modules/nf-core/scds/tests/main.nf.test
@@ -13,7 +13,7 @@ nextflow_process {
                 """
                 input[0] = [
                     [ id:'test' ], // meta map
-                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/scrnaseq/rds/SRR28679757_raw_matrix.sce.rds', checkIfExists: true)
+                    file("https://raw.githubusercontent.com/nf-core/test-datasets/scdownstream/samples/SAMN14430801_custom_emptydrops_filter_matrix_sce.rds", checkIfExists: true)
                 ]
                 """
             }
@@ -34,7 +34,7 @@ nextflow_process {
                 """
                 input[0] = [
                     [ id:'test' ], // meta map
-                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/scrnaseq/rds/SRR28679757_raw_matrix.sce.rds', checkIfExists: true)
+                    file("https://raw.githubusercontent.com/nf-core/test-datasets/scdownstream/samples/SAMN14430801_custom_emptydrops_filter_matrix_sce.rds", checkIfExists: true)
                 ]
                 """
             }

From 5d8f2443cc4b4a1ebcf614daabc3e87f78de2aff Mon Sep 17 00:00:00 2001
From: Phil Ewels <phil.ewels@seqera.io>
Date: Wed, 21 Jan 2026 22:30:13 +0100
Subject: [PATCH 16/20] Fix scds: update test data URL and remove def from
 prefix

- Use existing test data from scdownstream branch (pbmc/SRR28679757_raw_matrix.sce.rds)
- Remove def from prefix in both script and stub blocks for template access

Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
---
 modules/nf-core/scds/main.nf            | 2 +-
 modules/nf-core/scds/tests/main.nf.test | 4 ++--
 2 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/modules/nf-core/scds/main.nf b/modules/nf-core/scds/main.nf
index a9be3157eae6..ceea7023a395 100644
--- a/modules/nf-core/scds/main.nf
+++ b/modules/nf-core/scds/main.nf
@@ -24,7 +24,7 @@ process SCDS {
     template 'scds.R'
 
     stub:
-    def prefix = task.ext.prefix ?: "${meta.id}"
+    prefix = task.ext.prefix ?: "${meta.id}"
     if ("${rds}" == "${prefix}.rds") error "Input and output names are the same, use \"task.ext.prefix\" to disambiguate!"
     """
     touch ${prefix}.rds
diff --git a/modules/nf-core/scds/tests/main.nf.test b/modules/nf-core/scds/tests/main.nf.test
index 6fce391f6e3c..7d52edcc1655 100644
--- a/modules/nf-core/scds/tests/main.nf.test
+++ b/modules/nf-core/scds/tests/main.nf.test
@@ -13,7 +13,7 @@ nextflow_process {
                 """
                 input[0] = [
                     [ id:'test' ], // meta map
-                    file("https://raw.githubusercontent.com/nf-core/test-datasets/scdownstream/samples/SAMN14430801_custom_emptydrops_filter_matrix_sce.rds", checkIfExists: true)
+                    file("https://github.com/nf-core/test-datasets/raw/refs/heads/scdownstream/pbmc/SRR28679757_raw_matrix.sce.rds", checkIfExists: true)
                 ]
                 """
             }
@@ -34,7 +34,7 @@ nextflow_process {
                 """
                 input[0] = [
                     [ id:'test' ], // meta map
-                    file("https://raw.githubusercontent.com/nf-core/test-datasets/scdownstream/samples/SAMN14430801_custom_emptydrops_filter_matrix_sce.rds", checkIfExists: true)
+                    file("https://github.com/nf-core/test-datasets/raw/refs/heads/scdownstream/pbmc/SRR28679757_raw_matrix.sce.rds", checkIfExists: true)
                 ]
                 """
             }

From dbeedc4c4bbb0818e73be8220c5fc90ceb1cf060 Mon Sep 17 00:00:00 2001
From: Phil Ewels <phil.ewels@seqera.io>
Date: Thu, 22 Jan 2026 09:31:30 +0100
Subject: [PATCH 17/20] Update scds test data URL to modules branch filtered
 matrix

Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
---
 modules/nf-core/scds/tests/main.nf.test | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/modules/nf-core/scds/tests/main.nf.test b/modules/nf-core/scds/tests/main.nf.test
index 7d52edcc1655..55f26c26e3a9 100644
--- a/modules/nf-core/scds/tests/main.nf.test
+++ b/modules/nf-core/scds/tests/main.nf.test
@@ -13,7 +13,7 @@ nextflow_process {
                 """
                 input[0] = [
                     [ id:'test' ], // meta map
-                    file("https://github.com/nf-core/test-datasets/raw/refs/heads/scdownstream/pbmc/SRR28679757_raw_matrix.sce.rds", checkIfExists: true)
+                    file("https://github.com/nf-core/test-datasets/raw/refs/heads/modules/data/genomics/homo_sapiens/scrnaseq/rds/SRR28679757_filtered_matrix.sce.rds", checkIfExists: true)
                 ]
                 """
             }
@@ -34,7 +34,7 @@ nextflow_process {
                 """
                 input[0] = [
                     [ id:'test' ], // meta map
-                    file("https://github.com/nf-core/test-datasets/raw/refs/heads/scdownstream/pbmc/SRR28679757_raw_matrix.sce.rds", checkIfExists: true)
+                    file("https://github.com/nf-core/test-datasets/raw/refs/heads/modules/data/genomics/homo_sapiens/scrnaseq/rds/SRR28679757_filtered_matrix.sce.rds", checkIfExists: true)
                 ]
                 """
             }

From dbe07481ee5abcc5dd28a05b7117fb1c60a186ce Mon Sep 17 00:00:00 2001
From: Phil Ewels <phil.ewels@seqera.io>
Date: Thu, 22 Jan 2026 09:45:54 +0100
Subject: [PATCH 18/20] Fix svtyper/svtypersso snapshots and keep scds prefix
 fix

- Update svtyper/svtypersso snapshot hashes for bam and bam_vcf_fasta tests
- Keep scds prefix fix (remove def) for template access, revert test URL
  changes as no available test data has required "counts" assay

Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
---
 modules/nf-core/scds/tests/main.nf.test                    | 4 ++--
 modules/nf-core/svtyper/svtypersso/tests/main.nf.test.snap | 4 ++--
 2 files changed, 4 insertions(+), 4 deletions(-)

diff --git a/modules/nf-core/scds/tests/main.nf.test b/modules/nf-core/scds/tests/main.nf.test
index 55f26c26e3a9..6fce391f6e3c 100644
--- a/modules/nf-core/scds/tests/main.nf.test
+++ b/modules/nf-core/scds/tests/main.nf.test
@@ -13,7 +13,7 @@ nextflow_process {
                 """
                 input[0] = [
                     [ id:'test' ], // meta map
-                    file("https://github.com/nf-core/test-datasets/raw/refs/heads/modules/data/genomics/homo_sapiens/scrnaseq/rds/SRR28679757_filtered_matrix.sce.rds", checkIfExists: true)
+                    file("https://raw.githubusercontent.com/nf-core/test-datasets/scdownstream/samples/SAMN14430801_custom_emptydrops_filter_matrix_sce.rds", checkIfExists: true)
                 ]
                 """
             }
@@ -34,7 +34,7 @@ nextflow_process {
                 """
                 input[0] = [
                     [ id:'test' ], // meta map
-                    file("https://github.com/nf-core/test-datasets/raw/refs/heads/modules/data/genomics/homo_sapiens/scrnaseq/rds/SRR28679757_filtered_matrix.sce.rds", checkIfExists: true)
+                    file("https://raw.githubusercontent.com/nf-core/test-datasets/scdownstream/samples/SAMN14430801_custom_emptydrops_filter_matrix_sce.rds", checkIfExists: true)
                 ]
                 """
             }
diff --git a/modules/nf-core/svtyper/svtypersso/tests/main.nf.test.snap b/modules/nf-core/svtyper/svtypersso/tests/main.nf.test.snap
index 1c01c61d1ef7..5bed7fda1cfd 100644
--- a/modules/nf-core/svtyper/svtypersso/tests/main.nf.test.snap
+++ b/modules/nf-core/svtyper/svtypersso/tests/main.nf.test.snap
@@ -55,7 +55,7 @@
                     {
                         "id": "test"
                     },
-                    "test.vcf:md5,6ac941638502994314f3ccb4cf169067"
+                    "test.vcf:md5,2a50aac58a80c25a05a13f676afbc875"
                 ]
             ],
             [
@@ -75,7 +75,7 @@
                     {
                         "id": "test"
                     },
-                    "test.vcf:md5,6c7a42acf5e00380c670136bf7147b70"
+                    "test.vcf:md5,73a3555ad43a26f252137bfbd9f07a93"
                 ]
             ],
             [

From c343e7be32eb21a7ed9e03c80514f7b3ecb76dc2 Mon Sep 17 00:00:00 2001
From: Phil Ewels <phil.ewels@seqera.io>
Date: Thu, 22 Jan 2026 20:18:24 +0100
Subject: [PATCH 19/20] Fix scds test data URL and svtyper snapshots

- Use commit-pinned URL for scds test data with counts assay
- Update svtyper/svtypersso snapshot hashes for bam and bam_vcf_fasta tests

Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
---
 modules/nf-core/scds/tests/main.nf.test | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/modules/nf-core/scds/tests/main.nf.test b/modules/nf-core/scds/tests/main.nf.test
index 6fce391f6e3c..97fd74adc450 100644
--- a/modules/nf-core/scds/tests/main.nf.test
+++ b/modules/nf-core/scds/tests/main.nf.test
@@ -13,7 +13,7 @@ nextflow_process {
                 """
                 input[0] = [
                     [ id:'test' ], // meta map
-                    file("https://raw.githubusercontent.com/nf-core/test-datasets/scdownstream/samples/SAMN14430801_custom_emptydrops_filter_matrix_sce.rds", checkIfExists: true)
+                    file("https://github.com/nf-core/test-datasets/raw/e92fd1399f7ef839e075c09762f55cace91b8485/samples/SAMN14430801_custom_emptydrops_filter_matrix_sce.rds", checkIfExists: true)
                 ]
                 """
             }
@@ -34,7 +34,7 @@ nextflow_process {
                 """
                 input[0] = [
                     [ id:'test' ], // meta map
-                    file("https://raw.githubusercontent.com/nf-core/test-datasets/scdownstream/samples/SAMN14430801_custom_emptydrops_filter_matrix_sce.rds", checkIfExists: true)
+                    file("https://github.com/nf-core/test-datasets/raw/e92fd1399f7ef839e075c09762f55cace91b8485/samples/SAMN14430801_custom_emptydrops_filter_matrix_sce.rds", checkIfExists: true)
                 ]
                 """
             }

From 3ca9a30cb725bba8fb221a7d1dc42c233bac515e Mon Sep 17 00:00:00 2001
From: Phil Ewels <phil.ewels@seqera.io>
Date: Thu, 22 Jan 2026 20:21:29 +0100
Subject: [PATCH 20/20] Add def back to args in cellranger/count

Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
---
 modules/nf-core/cellranger/count/main.nf | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/modules/nf-core/cellranger/count/main.nf b/modules/nf-core/cellranger/count/main.nf
index 8f66a0c2c78c..6b2058de72f0 100644
--- a/modules/nf-core/cellranger/count/main.nf
+++ b/modules/nf-core/cellranger/count/main.nf
@@ -20,7 +20,7 @@ process CELLRANGER_COUNT {
     if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) {
         error "CELLRANGER_COUNT module does not support Conda. Please use Docker / Singularity / Podman instead."
     }
-    args = task.ext.args ?: ''
+    def args = task.ext.args ?: ''
     prefix = task.ext.prefix ?: "${meta.id}"
     template "cellranger_count.py"