nf-core · LouisLeNezet · Mar 23, 2026 · Mar 17, 2026 · Mar 17, 2026 · Mar 17, 2026
diff --git a/.github/workflows/nf-test.yml b/.github/workflows/nf-test.yml
@@ -18,7 +18,7 @@ concurrency:
 
 env:
   GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
-  NFT_VER: "0.9.3"
+  NFT_VER: "0.9.4"
   NFT_WORKDIR: "~"
   NXF_ANSI_LOG: false
   NXF_SINGULARITY_CACHEDIR: ${{ github.workspace }}/.singularity

diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -32,6 +32,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - [#259](https://github.com/nf-core/phaseimpute/pull/259) - Move from local to nf-core sbwf for variant calling from BAM input files.
 - [#260](https://github.com/nf-core/phaseimpute/pull/260) - Move from local to nf-core sbwf for `VCF` concatenation.
 - [#262](https://github.com/nf-core/phaseimpute/pull/262) - Change from `master` to `main` branch.
+- [#273](https://github.com/nf-core/phaseimpute/pull/273) - Update nf-core modules, fix syntax. Remove `SAMTOOLS_REHEADER` patch and pass command through meta map. Update nf-test in Github Action to 0.9.4.
 
 ### `Fixed`
 
@@ -43,6 +44,9 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 | Dependency | Old version | New version    |
 | ---------- | ----------- | -------------- |
 | `bedtools` | 2.31.1      | No longer used |
+| `samtools` | 1.22.1      | 1.23           |
+| `gawk`     | 5.3.0       | 5.3.1          |
+| `multiqc`  | 1.32        | 1.33           |
 
 ### New contributors
 

diff --git a/conf/steps/chrcheck.config b/conf/steps/chrcheck.config
@@ -30,6 +30,10 @@ process {
     }
 
     // Change prefix based on input file types (INPUT, TRUTH, PANEL)
+    withName: 'NFCORE_PHASEIMPUTE:CHRCHECK_.*:BAM_CHR_RENAME_SAMTOOLS:SAMTOOLS_REHEADER' {
+        ext.args   = { "-c '${meta.samtools_reheader_cmd}'" }
+        ext.prefix = { "${meta.id}_chrrename" }
+    }
     withName: 'NFCORE_PHASEIMPUTE:CHRCHECK_.*:VCF_CHR_RENAME_BCFTOOLS:BCFTOOLS_ANNOTATE' {
         ext.args   = ["-Oz", "--no-version", "--write-index=tbi"].join(' ')
     }

diff --git a/main.nf b/main.nf
@@ -99,7 +99,11 @@ workflow NFCORE_PHASEIMPUTE {
         ch_map,
         ch_posfile,
         ch_chunks,
-        chunk_model
+        chunk_model,
+        params.multiqc_config,
+        params.multiqc_logo,
+        params.multiqc_methods_description,
+        params.outdir
     )
     emit:
     multiqc_report = PHASEIMPUTE.out.multiqc_report // channel: /path/to/multiqc_report.html

diff --git a/modules.json b/modules.json
@@ -81,7 +81,7 @@
                     },
                     "gawk": {
                         "branch": "master",
-                        "git_sha": "76b1f53edcf72798d8515c82f4728ad44b3dd902",
+                        "git_sha": "c0da8f3a26835d663873001382a708f75766fec6",
                         "installed_by": ["bam_subsampledepth_samtools", "modules"]
                     },
                     "glimpse/chunk": {
@@ -148,7 +148,7 @@
                     },
                     "multiqc": {
                         "branch": "master",
-                        "git_sha": "af27af1be706e6a2bb8fe454175b0cdf77f47b49",
+                        "git_sha": "2c73cc8fa92cf48de3da0b643fdf357a8a290b36",
                         "installed_by": ["modules"]
                     },
                     "quilt/quilt": {
@@ -158,38 +158,37 @@
                     },
                     "samtools/coverage": {
                         "branch": "master",
-                        "git_sha": "440edf75d8782913115a7b72a88392a227f72cc1",
+                        "git_sha": "4e3e10e502ec6ab6b1c4b4fecd923ff1fa287338",
                         "installed_by": ["modules"]
                     },
                     "samtools/depth": {
                         "branch": "master",
-                        "git_sha": "128c609f2812f748ec8d9566fc2953b72099fdcf",
+                        "git_sha": "4e3e10e502ec6ab6b1c4b4fecd923ff1fa287338",
                         "installed_by": ["bam_subsampledepth_samtools", "modules"]
                     },
                     "samtools/faidx": {
                         "branch": "master",
-                        "git_sha": "b2e78932ef01165fd85829513eaca29eff8e640a",
+                        "git_sha": "4e3e10e502ec6ab6b1c4b4fecd923ff1fa287338",
                         "installed_by": ["modules"]
                     },
                     "samtools/index": {
                         "branch": "master",
-                        "git_sha": "1d2fbdcbca677bbe8da0f9d0d2bb7c02f2cab1c9",
+                        "git_sha": "4e3e10e502ec6ab6b1c4b4fecd923ff1fa287338",
                         "installed_by": ["modules"]
                     },
                     "samtools/merge": {
                         "branch": "master",
-                        "git_sha": "440edf75d8782913115a7b72a88392a227f72cc1",
+                        "git_sha": "44b7dad0181c7a0495f6d128d8cbf55feb277a84",
                         "installed_by": ["modules"]
                     },
                     "samtools/reheader": {
                         "branch": "master",
-                        "git_sha": "440edf75d8782913115a7b72a88392a227f72cc1",
-                        "installed_by": ["modules"],
-                        "patch": "modules/nf-core/samtools/reheader/samtools-reheader.diff"
+                        "git_sha": "4e3e10e502ec6ab6b1c4b4fecd923ff1fa287338",
+                        "installed_by": ["modules"]
                     },
                     "samtools/view": {
                         "branch": "master",
-                        "git_sha": "b2e78932ef01165fd85829513eaca29eff8e640a",
+                        "git_sha": "4e3e10e502ec6ab6b1c4b4fecd923ff1fa287338",
                         "installed_by": ["bam_subsampledepth_samtools", "modules"]
                     },
                     "shapeit5/ligate": {
@@ -204,7 +203,7 @@
                     },
                     "stitch": {
                         "branch": "master",
-                        "git_sha": "e1cb31f0ced0d0810d1cb099aaa690b05beb1f3a",
+                        "git_sha": "380cb90926b8c28558cb11479da5ff45bc4f1c5d",
                         "installed_by": ["bam_impute_stitch", "modules"]
                     },
                     "tabix/bgzip": {
@@ -238,7 +237,7 @@
                     },
                     "bam_subsampledepth_samtools": {
                         "branch": "master",
-                        "git_sha": "b2e78932ef01165fd85829513eaca29eff8e640a",
+                        "git_sha": "4e3e10e502ec6ab6b1c4b4fecd923ff1fa287338",
                         "installed_by": ["subworkflows"]
                     },
                     "bam_variant_calling_mpileup_bcftools": {

diff --git a/modules/local/addcolumns/environment.yml b/modules/local/addcolumns/environment.yml
@@ -4,4 +4,4 @@ channels:
   - conda-forge
   - bioconda
 dependencies:
-  - conda-forge::gawk=5.3.0
+  - conda-forge::gawk=5.3.1
diff --git a/modules/local/addcolumns/main.nf b/modules/local/addcolumns/main.nf
@@ -4,8 +4,8 @@ process ADDCOLUMNS {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/gawk:5.3.0' :
-        'biocontainers/gawk:5.3.0' }"
+        'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/a1/a125c778baf3865331101a104b60d249ee15fe1dca13bdafd888926cc5490a34/data' :
+        'community.wave.seqera.io/library/gawk:5.3.1--e09efb5dfc4b8156' }"
 
     input:
     tuple val(meta), path(input)

diff --git a/modules/local/addcolumns/tests/main.nf.test.snap b/modules/local/addcolumns/tests/main.nf.test.snap
@@ -18,7 +18,7 @@
                     [
                         "ADDCOLUMNS",
                         "gawk",
-                        "5.3.0"
+                        "5.3.1"
                     ]
                 ],
                 "txt": [
@@ -37,7 +37,7 @@
                     [
                         "ADDCOLUMNS",
                         "gawk",
-                        "5.3.0"
+                        "5.3.1"
                     ]
                 ]
             },
@@ -69,7 +69,7 @@
                     [
                         "ADDCOLUMNS",
                         "gawk",
-                        "5.3.0"
+                        "5.3.1"
                     ]
                 ],
                 "txt": [
@@ -85,7 +85,7 @@
                     [
                         "ADDCOLUMNS",
                         "gawk",
-                        "5.3.0"
+                        "5.3.1"
                     ]
                 ]
             },

diff --git a/modules/local/bamchrextract/environment.yml b/modules/local/bamchrextract/environment.yml
@@ -5,6 +5,6 @@ channels:
   - bioconda
 dependencies:
   # renovate: datasource=conda depName=bioconda/htslib
-  - bioconda::htslib=1.22.1
+  - bioconda::htslib=1.23
   # renovate: datasource=conda depName=bioconda/samtools
-  - bioconda::samtools=1.22.1
+  - bioconda::samtools=1.23
diff --git a/modules/local/bamchrextract/main.nf b/modules/local/bamchrextract/main.nf
@@ -3,9 +3,9 @@ process BAMCHREXTRACT {
     label 'process_single'
 
     conda "${moduleDir}/environment.yml"
-    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/samtools:1.22.1--h96c455f_0' :
-        'biocontainers/samtools:1.22.1--h96c455f_0' }"
+    container "${workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container
+        ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/e5/e5598451c6d348cce36191bafe1911ad71e440137d7a329da946f2b0dbb0e7f3/data'
+        : 'community.wave.seqera.io/library/htslib_samtools:1.23--cde2c40a51d6f752'}"
 
     input:
     tuple val(meta), path(input)
@@ -22,7 +22,7 @@ process BAMCHREXTRACT {
     """
     samtools \\
         head \\
-        $input \| \\
+        $input | \\
         grep '^@SQ' | cut -d\$'\t' -f2 | sed -e 's/^SN://g' \\
         > ${prefix}.txt
     """

diff --git a/modules/local/bamchrextract/tests/main.nf.test.snap b/modules/local/bamchrextract/tests/main.nf.test.snap
@@ -26,17 +26,17 @@
                     [
                         "BAMCHREXTRACT",
                         "samtools",
-                        "1.22.1"
+                        "1.23"
                     ],
                     [
                         "BAMCHREXTRACT",
                         "samtools",
-                        "1.22.1"
+                        "1.23"
                     ],
                     [
                         "BAMCHREXTRACT",
                         "samtools",
-                        "1.22.1"
+                        "1.23"
                     ]
                 ],
                 "chr": [
@@ -63,17 +63,17 @@
                     [
                         "BAMCHREXTRACT",
                         "samtools",
-                        "1.22.1"
+                        "1.23"
                     ],
                     [
                         "BAMCHREXTRACT",
                         "samtools",
-                        "1.22.1"
+                        "1.23"
                     ],
                     [
                         "BAMCHREXTRACT",
                         "samtools",
-                        "1.22.1"
+                        "1.23"
                     ]
                 ]
             },

diff --git a/modules/local/listtofile/environment.yml b/modules/local/listtofile/environment.yml
@@ -2,4 +2,4 @@ channels:
   - conda-forge
   - bioconda
 dependencies:
-  - conda-forge::gawk=5.3.0
+  - conda-forge::gawk=5.3.1
diff --git a/modules/local/listtofile/main.nf b/modules/local/listtofile/main.nf
@@ -4,8 +4,8 @@ process LISTTOFILE {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/gawk:5.3.0' :
-        'biocontainers/gawk:5.3.0' }"
+        'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/a1/a125c778baf3865331101a104b60d249ee15fe1dca13bdafd888926cc5490a34/data' :
+        'community.wave.seqera.io/library/gawk:5.3.1--e09efb5dfc4b8156' }"
 
     input:
     tuple val(meta), path(input, arity: '0..*'), val(id)

diff --git a/modules/local/listtofile/tests/main.nf.test.snap b/modules/local/listtofile/tests/main.nf.test.snap
@@ -16,7 +16,7 @@
                     [
                         "LISTTOFILE",
                         "gawk",
-                        "5.3.0"
+                        "5.3.1"
                     ]
                 ],
                 "txt": [
@@ -33,7 +33,7 @@
                     [
                         "LISTTOFILE",
                         "gawk",
-                        "5.3.0"
+                        "5.3.1"
                     ]
                 ]
             },

diff --git a/modules/local/vcfchrextract/main.nf b/modules/local/vcfchrextract/main.nf
@@ -23,8 +23,7 @@ process VCFCHREXTRACT {
     bcftools \\
         query \\
         -f '%CHROM\\n' \\
-        $input \\
-        \| uniq \\
+        $input | uniq \\
         > ${prefix}.txt
     """
 

diff --git a/modules/nf-core/gawk/environment.yml b/modules/nf-core/gawk/environment.yml
diff --git a/modules/nf-core/gawk/main.nf b/modules/nf-core/gawk/main.nf
diff --git a/modules/nf-core/gawk/tests/main.nf.test b/modules/nf-core/gawk/tests/main.nf.test
-Original file line number
+Diff line change
@@ Expand Up / @@ -18,7 +18,7 @@ @@
                         [
                             "ADDCOLUMNS",
                             "gawk",
-                            "5.3.0"
+                            "5.3.1"
                         ]
                     ],
                     "txt": [
@@ Expand All / @@ -37,7 +37,7 @@ @@
                         [
                             "ADDCOLUMNS",
                             "gawk",
-                            "5.3.0"
+                            "5.3.1"
                         ]
                     ]
                 },
@@ Expand Down Expand Up / @@ -69,7 +69,7 @@ @@
                         [
                             "ADDCOLUMNS",
                             "gawk",
-                            "5.3.0"
+                            "5.3.1"
                         ]
                     ],
                     "txt": [
@@ Expand All / @@ -85,7 +85,7 @@ @@
                         [
                             "ADDCOLUMNS",
                             "gawk",
-                            "5.3.0"
+                            "5.3.1"
                         ]
                     ]
                 },
@@ Expand Down @@