nf-core · pinin4fjords · Jan 21, 2026 · Jan 21, 2026 · Jan 21, 2026 · Jan 21, 2026
diff --git a/.github/workflows/nextflow-lint.yml b/.github/workflows/nextflow-lint.yml
@@ -0,0 +1,17 @@
+name: Nextflow strict syntax lint
+on:
+  pull_request:
+  push:
+    branches: [master, dev]
+
+jobs:
+  lint:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Install Nextflow
+        uses: nf-core/setup-nextflow@v2
+
+      - name: Nextflow strict syntax lint
+        run: nextflow lint -o concise .
diff --git a/.nf-core.yml b/.nf-core.yml
@@ -1,5 +1,6 @@
 lint:
   actions_nf_test: false
+  nf_test_content: false
   files_exist:
     - conf/modules.config
   files_unchanged:

diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -22,6 +22,7 @@ Special thanks to the following for their contributions to the release:
 - [PR #1667](https://github.com/nf-core/rnaseq/pull/1667) - Enhance RSEM output exports and remove unnecessary star_rsem check
 - [PR #1669](https://github.com/nf-core/rnaseq/pull/1669) - Enable SeqKit stats MultiQC module for RiboDetector rRNA removal
 - [PR #1672](https://github.com/nf-core/rnaseq/pull/1672) - Document star_rsem STAR aligner settings and customization
+- [PR #1677](https://github.com/nf-core/rnaseq/pull/1677) - Apply Nextflow 25 strict syntax fixes
 
 ### Parameters
 

diff --git a/docs/output.md b/docs/output.md
@@ -335,8 +335,10 @@ The STAR section of the MultiQC report shows a bar plot with alignment rates: go
   - `*.transcript.bam`: If `--save_align_intermeds` is specified the BAM file from STAR alignment containing read alignments to the transcriptome will be placed in this directory. These files can be reused as `transcriptome_bam` input in future pipeline runs.
 - `star_rsem/<SAMPLE>.stat/`
   - `*.cnt`, `*.model`, `*.theta`: RSEM counts and statistics for each sample.
-  - `star_rsem/log/`
-  - `*.log`: STAR alignment report containing the mapping results summary.
+- `star_rsem/log/`
+  - `*.SJ.out.tab`: File containing filtered splice junctions detected after mapping the reads.
+  - `*.Log.final.out`: STAR alignment report containing the mapping results summary.
+  - `*.Log.out` and `*.Log.progress.out`: STAR log files containing detailed information about the run. Typically only useful for debugging purposes.
 
 </details>
 

diff --git a/main.nf b/main.nf
@@ -54,7 +54,7 @@ workflow NFCORE_RNASEQ {
 
     main:
 
-    ch_versions = Channel.empty()
+    ch_versions = channel.empty()
 
     //
     // SUBWORKFLOW: Prepare reference genome files
@@ -94,17 +94,17 @@ workflow NFCORE_RNASEQ {
         PREPARE_GENOME
             .out
             .fai
-            .map { checkMaxContigSize(it) }
+            .map { fai -> checkMaxContigSize(fai) }
     }
 
     //
     // WORKFLOW: Run nf-core/rnaseq workflow
     //
-    ch_samplesheet = Channel.value(file(params.input, checkIfExists: true))
+    ch_samplesheet = channel.value(file(params.input, checkIfExists: true))
 
     // Bowtie2 rRNA index is built on-demand inside the fastq_remove_rrna subworkflow
     // rather than in PREPARE_GENOME, to avoid duplicating the rRNA FASTA preparation logic
-    ch_bowtie2_index = Channel.empty()
+    ch_bowtie2_index = channel.empty()
 
     RNASEQ (
         ch_samplesheet,

diff --git a/modules.json b/modules.json
@@ -7,7 +7,7 @@
                 "nf-core": {
                     "bbmap/bbsplit": {
                         "branch": "master",
-                        "git_sha": "2ddc92b750c7553f7a7becb4982851cef3ab848e",
+                        "git_sha": "6d1d4b987af3ee5852d852abf99f8883028cea9c",
                         "installed_by": ["fastq_qc_trim_filter_setstrandedness", "modules"]
                     },
                     "bedtools/genomecov": {
@@ -27,17 +27,17 @@
                     },
                     "bracken/bracken": {
                         "branch": "master",
-                        "git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46",
+                        "git_sha": "004e773fc35ebd24063ca4cbef057c94a24208aa",
                         "installed_by": ["modules"]
                     },
                     "cat/fastq": {
                         "branch": "master",
-                        "git_sha": "f4743b089085121497b7c1c81a28810ce2740dde",
+                        "git_sha": "cf735af4433f2dc8e410f67012dff824ef9990eb",
                         "installed_by": ["fastq_qc_trim_filter_setstrandedness", "modules"]
                     },
                     "custom/catadditionalfasta": {
                         "branch": "master",
-                        "git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46",
+                        "git_sha": "96c57dfd98a0641886a67bd449fe33ee2ec0e374",
                         "installed_by": ["modules"]
                     },
                     "custom/tx2gene": {
@@ -52,7 +52,7 @@
                     },
                     "fastp": {
                         "branch": "master",
-                        "git_sha": "d9ec4ef289ad39b8a662a7a12be50409b11df84b",
+                        "git_sha": "b8f1de0ac853ae5b56c63450d47438f899c553d0",
                         "installed_by": ["fastq_fastqc_umitools_fastp", "modules"]
                     },
                     "fastqc": {
@@ -72,12 +72,12 @@
                     },
                     "gffread": {
                         "branch": "master",
-                        "git_sha": "e753770db613ce014b3c4bc94f6cba443427b726",
+                        "git_sha": "51f2b493a7ff28b40a9f99faca64245521f2bb24",
                         "installed_by": ["modules"]
                     },
                     "gunzip": {
                         "branch": "master",
-                        "git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46",
+                        "git_sha": "96c57dfd98a0641886a67bd449fe33ee2ec0e374",
                         "installed_by": ["modules"]
                     },
                     "hisat2/align": {
@@ -93,7 +93,7 @@
                     },
                     "hisat2/extractsplicesites": {
                         "branch": "master",
-                        "git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46",
+                        "git_sha": "004e773fc35ebd24063ca4cbef057c94a24208aa",
                         "installed_by": ["modules"]
                     },
                     "kallisto/index": {
@@ -108,7 +108,7 @@
                     },
                     "kraken2/kraken2": {
                         "branch": "master",
-                        "git_sha": "1a9dc0fd9f8f61099b3c912df1ab97fac72a1f86",
+                        "git_sha": "71a39f3598935d64ffd65f0960e4d2d4a42ab778",
                         "installed_by": ["modules"]
                     },
                     "multiqc": {
@@ -144,7 +144,7 @@
                     },
                     "rsem/preparereference": {
                         "branch": "master",
-                        "git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46",
+                        "git_sha": "004e773fc35ebd24063ca4cbef057c94a24208aa",
                         "installed_by": ["modules"]
                     },
                     "rseqc/bamstat": {
@@ -174,7 +174,7 @@
                     },
                     "rseqc/readdistribution": {
                         "branch": "master",
-                        "git_sha": "0145202ae8a9f39a4e7c533f667c38989af799b2",
+                        "git_sha": "eed5d14302a6c9070dcc25feeab707a27a4b3254",
                         "installed_by": ["bam_rseqc"]
                     },
                     "rseqc/readduplication": {
@@ -184,7 +184,7 @@
                     },
                     "rseqc/tin": {
                         "branch": "master",
-                        "git_sha": "0145202ae8a9f39a4e7c533f667c38989af799b2",
+                        "git_sha": "eed5d14302a6c9070dcc25feeab707a27a4b3254",
                         "installed_by": ["bam_rseqc"]
                     },
                     "salmon/index": {
@@ -194,7 +194,7 @@
                     },
                     "salmon/quant": {
                         "branch": "master",
-                        "git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46",
+                        "git_sha": "9ebc300e05af07c770b86ff089581a2d41346c8b",
                         "installed_by": ["fastq_subsample_fq_salmon", "modules", "quantify_pseudo_alignment"]
                     },
                     "samtools/faidx": {
@@ -244,17 +244,17 @@
                     },
                     "sentieon/rsemcalculateexpression": {
                         "branch": "master",
-                        "git_sha": "e753770db613ce014b3c4bc94f6cba443427b726",
+                        "git_sha": "a3588330b09a84d3b7254ec0bdc27a746a403dad",
                         "installed_by": ["modules"]
                     },
                     "sentieon/rsempreparereference": {
                         "branch": "master",
-                        "git_sha": "256557155b2439c5d551f1a668bf6a7ff6b10f93",
+                        "git_sha": "a3588330b09a84d3b7254ec0bdc27a746a403dad",
                         "installed_by": ["modules"]
                     },
                     "sentieon/staralign": {
                         "branch": "master",
-                        "git_sha": "e753770db613ce014b3c4bc94f6cba443427b726",
+                        "git_sha": "a3588330b09a84d3b7254ec0bdc27a746a403dad",
                         "installed_by": ["modules"]
                     },
                     "seqkit/replace": {
@@ -269,7 +269,7 @@
                     },
                     "sortmerna": {
                         "branch": "master",
-                        "git_sha": "ddb0d667cf6cdee3bab9497241de4bbf6b88d8cc",
+                        "git_sha": "6d1d4b987af3ee5852d852abf99f8883028cea9c",
                         "installed_by": ["fastq_qc_trim_filter_setstrandedness", "fastq_remove_rrna", "modules"]
                     },
                     "star/align": {
@@ -299,7 +299,7 @@
                     },
                     "sylph/profile": {
                         "branch": "master",
-                        "git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46",
+                        "git_sha": "004e773fc35ebd24063ca4cbef057c94a24208aa",
                         "installed_by": ["modules"]
                     },
                     "sylphtax/taxprof": {
@@ -309,7 +309,7 @@
                     },
                     "trimgalore": {
                         "branch": "master",
-                        "git_sha": "1b32b48b7d2803ae78a1beb20b7e9657dbcda776",
+                        "git_sha": "eed5d14302a6c9070dcc25feeab707a27a4b3254",
                         "installed_by": ["fastq_fastqc_umitools_trimgalore"]
                     },
                     "tximeta/tximport": {
@@ -319,12 +319,12 @@
                     },
                     "ucsc/bedclip": {
                         "branch": "master",
-                        "git_sha": "e753770db613ce014b3c4bc94f6cba443427b726",
+                        "git_sha": "51f2b493a7ff28b40a9f99faca64245521f2bb24",
                         "installed_by": ["bedgraph_bedclip_bedgraphtobigwig"]
                     },
                     "ucsc/bedgraphtobigwig": {
                         "branch": "master",
-                        "git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46",
+                        "git_sha": "51f2b493a7ff28b40a9f99faca64245521f2bb24",
                         "installed_by": ["bedgraph_bedclip_bedgraphtobigwig"]
                     },
                     "umicollapse": {
@@ -361,22 +361,22 @@
                 "nf-core": {
                     "bam_dedup_stats_samtools_umicollapse": {
                         "branch": "master",
-                        "git_sha": "0b2435805036a16dcdcf21533632d956b8273ac4",
+                        "git_sha": "eed5d14302a6c9070dcc25feeab707a27a4b3254",
                         "installed_by": ["bam_dedup_umi", "subworkflows"]
                     },
                     "bam_dedup_stats_samtools_umitools": {
                         "branch": "master",
-                        "git_sha": "0b2435805036a16dcdcf21533632d956b8273ac4",
+                        "git_sha": "eed5d14302a6c9070dcc25feeab707a27a4b3254",
                         "installed_by": ["bam_dedup_umi", "subworkflows"]
                     },
                     "bam_dedup_umi": {
                         "branch": "master",
-                        "git_sha": "0b2435805036a16dcdcf21533632d956b8273ac4",
+                        "git_sha": "eed5d14302a6c9070dcc25feeab707a27a4b3254",
                         "installed_by": ["subworkflows"]
                     },
                     "bam_markduplicates_picard": {
                         "branch": "master",
-                        "git_sha": "0b2435805036a16dcdcf21533632d956b8273ac4",
+                        "git_sha": "eed5d14302a6c9070dcc25feeab707a27a4b3254",
                         "installed_by": ["subworkflows"]
                     },
                     "bam_rseqc": {
@@ -386,12 +386,12 @@
                     },
                     "bam_sort_stats_samtools": {
                         "branch": "master",
-                        "git_sha": "0b2435805036a16dcdcf21533632d956b8273ac4",
+                        "git_sha": "eed5d14302a6c9070dcc25feeab707a27a4b3254",
                         "installed_by": ["bam_dedup_umi", "fastq_align_hisat2"]
                     },
                     "bam_stats_samtools": {
                         "branch": "master",
-                        "git_sha": "0b2435805036a16dcdcf21533632d956b8273ac4",
+                        "git_sha": "eed5d14302a6c9070dcc25feeab707a27a4b3254",
                         "installed_by": [
                             "bam_dedup_stats_samtools_umicollapse",
                             "bam_dedup_stats_samtools_umitools",
@@ -401,42 +401,42 @@
                     },
                     "bedgraph_bedclip_bedgraphtobigwig": {
                         "branch": "master",
-                        "git_sha": "05954dab2ff481bcb999f24455da29a5828af08d",
+                        "git_sha": "51f2b493a7ff28b40a9f99faca64245521f2bb24",
                         "installed_by": ["subworkflows"]
                     },
                     "fastq_align_hisat2": {
                         "branch": "master",
-                        "git_sha": "20b042e352fc47ab6dab717a622253e96429e887",
+                        "git_sha": "eed5d14302a6c9070dcc25feeab707a27a4b3254",
                         "installed_by": ["subworkflows"]
                     },
                     "fastq_fastqc_umitools_fastp": {
                         "branch": "master",
-                        "git_sha": "0b2435805036a16dcdcf21533632d956b8273ac4",
+                        "git_sha": "eed5d14302a6c9070dcc25feeab707a27a4b3254",
                         "installed_by": ["fastq_qc_trim_filter_setstrandedness", "subworkflows"]
                     },
                     "fastq_fastqc_umitools_trimgalore": {
                         "branch": "master",
-                        "git_sha": "1b32b48b7d2803ae78a1beb20b7e9657dbcda776",
+                        "git_sha": "eed5d14302a6c9070dcc25feeab707a27a4b3254",
                         "installed_by": ["fastq_qc_trim_filter_setstrandedness", "subworkflows"]
                     },
                     "fastq_qc_trim_filter_setstrandedness": {
                         "branch": "master",
-                        "git_sha": "0745ffcda877676de0d0b21208377e841db6218f",
+                        "git_sha": "6d1d4b987af3ee5852d852abf99f8883028cea9c",
                         "installed_by": ["subworkflows"]
                     },
                     "fastq_remove_rrna": {
                         "branch": "master",
-                        "git_sha": "0745ffcda877676de0d0b21208377e841db6218f",
+                        "git_sha": "6d1d4b987af3ee5852d852abf99f8883028cea9c",
                         "installed_by": ["fastq_qc_trim_filter_setstrandedness"]
                     },
                     "fastq_subsample_fq_salmon": {
                         "branch": "master",
-                        "git_sha": "05954dab2ff481bcb999f24455da29a5828af08d",
+                        "git_sha": "9ebc300e05af07c770b86ff089581a2d41346c8b",
                         "installed_by": ["fastq_qc_trim_filter_setstrandedness", "subworkflows"]
                     },
                     "quantify_pseudo_alignment": {
                         "branch": "master",
-                        "git_sha": "e753770db613ce014b3c4bc94f6cba443427b726",
+                        "git_sha": "9ebc300e05af07c770b86ff089581a2d41346c8b",
                         "installed_by": ["subworkflows"]
                     },
                     "utils_nextflow_pipeline": {

diff --git a/modules/local/multiqc_custom_biotype/nextflow.config b/modules/local/multiqc_custom_biotype/nextflow.config
@@ -1,13 +1,9 @@
-if (!params.skip_qc) {
-    if (!params.skip_biotype_qc && params.featurecounts_group_type) {
-        process {
-            withName: 'MULTIQC_CUSTOM_BIOTYPE' {
-                publishDir = [
-                    path: { "${params.outdir}/${params.aligner}/featurecounts" },
-                    mode: params.publish_dir_mode,
-                    saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
-                ]
-            }
-        }
+process {
+    withName: 'MULTIQC_CUSTOM_BIOTYPE' {
+        publishDir = [
+            path: { "${params.outdir}/${params.aligner}/featurecounts" },
+            mode: params.publish_dir_mode,
+            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
+        ]
     }
 }
diff --git a/modules/local/star_align_igenomes/main.nf b/modules/local/star_align_igenomes/main.nf
@@ -38,10 +38,10 @@ process STAR_ALIGN_IGENOMES {
     def prefix = task.ext.prefix ?: "${meta.id}"
     def reads1 = []
     def reads2 = []
-    meta.single_end ? [reads].flatten().each{reads1 << it} : reads.eachWithIndex{ v, ix -> ( ix & 1 ? reads2 : reads1) << v }
-    def ignore_gtf      = star_ignore_sjdbgtf ? '' : "--sjdbGTFfile $gtf"
-    def seq_platform    = seq_platform ? "'PL:$seq_platform'" : ""
-    def seq_center      = seq_center ? "--outSAMattrRGline ID:$prefix 'CN:$seq_center' 'SM:$prefix' $seq_platform " : "--outSAMattrRGline ID:$prefix 'SM:$prefix' $seq_platform "
+    meta.single_end ? [reads].flatten().each{ read -> reads1 << read } : reads.eachWithIndex{ v, ix -> ( ix & 1 ? reads2 : reads1) << v }
+    def ignore_gtf       = star_ignore_sjdbgtf ? '' : "--sjdbGTFfile $gtf"
+    def seq_platform_str = seq_platform ? "'PL:$seq_platform'" : ""
+    def seq_center_str   = seq_center ? "--outSAMattrRGline ID:$prefix 'CN:$seq_center' 'SM:$prefix' $seq_platform_str " : "--outSAMattrRGline ID:$prefix 'SM:$prefix' $seq_platform_str "
     def out_sam_type    = (args.contains('--outSAMtype')) ? '' : '--outSAMtype BAM Unsorted'
     def mv_unsorted_bam = (args.contains('--outSAMtype BAM Unsorted SortedByCoordinate')) ? "mv ${prefix}.Aligned.out.bam ${prefix}.Aligned.unsort.out.bam" : ''
     """
@@ -52,7 +52,7 @@ process STAR_ALIGN_IGENOMES {
         --outFileNamePrefix $prefix. \\
         $out_sam_type \\
         $ignore_gtf \\
-        $seq_center \\
+        $seq_center_str \\
         $args
 
     $mv_unsorted_bam