nf-core · dialvarezs · Aug 21, 2025 · Aug 16, 2025 · Aug 16, 2025 · Aug 16, 2025
@@ -25,6 +25,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - [#827](https://github.com/nf-core/mag/pull/827) - Updated to nf-core 3.3.2`TEMPLATE` (by @dialvarezs)
 - [#841](https://github.com/nf-core/mag/pull/841) - MultiQC config updated to support CheckM, CheckM2, and GTDB-Tk (by @harper357)
 - [#844](https://github.com/nf-core/mag/pull/843) - Change loading mechanism of internal PhiX/Lambda databases to improve Dev UX when schema building (by @jfy133)
+- [#851](https://github.com/nf-core/mag/pull/851) - Improve structure of local modules and subworkflows (by @dialvarezs)
 
 ### `Fixed`
 
@@ -48,8 +49,9 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ### `Deprecated`
 
-[#799](https://github.comf/nf-core/mag/pull/799) - Removed `--cat_official_taxonomy` in favour of `--cat_allow_unofficial_lineages` to control CAT's use of unofficial lineages (added by @dialvarezs)
-[#825](https://github.com/nf-core/mag/pull/825) - Removed `--centrifuge_db`, `--kraken2_db`, `--krona_db` and `--skip_krona` parameters following the removal of taxonomic profiling functionality. See nf-core/taxprofiler for replacement (added by @dialvarezs).
+- [#799](https://github.comf/nf-core/mag/pull/799) - Removed `--cat_official_taxonomy` in favour of `--cat_allow_unofficial_lineages` to control CAT's use of unofficial lineages (added by @dialvarezs)
+- [#825](https://github.com/nf-core/mag/pull/825) - Removed `--centrifuge_db`, `--kraken2_db`, `--krona_db` and `--skip_krona` parameters following the removal of taxonomic profiling functionality. See nf-core/taxprofiler for replacement (added by @dialvarezs)
+- [#851](https://github.com/nf-core/mag/pull/851) - Remove `POOL_READ_*` local modules in favor of nf-core cat/fastq (by @dialvarezs)
 
 ## v4.0.0 - [2025-05-22]
 

@@ -38,7 +38,7 @@
                     },
                     "cat/fastq": {
                         "branch": "master",
-                        "git_sha": "05954dab2ff481bcb999f24455da29a5828af08d",
+                        "git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46",
                         "installed_by": ["modules"]
                     },
                     "catpack/addnames": {

@@ -1,18 +1,18 @@
 process SAMTOOLS_UNMAPPED {
-    tag "$meta.id"
+    tag "${meta.id}"
     label 'process_low'
 
-    conda "bioconda::samtools=1.21"
-    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/9e/9edc2564215d5cd137a8b25ca8a311600987186d406b092022444adf3c4447f7/data' :
-        'community.wave.seqera.io/library/htslib_samtools:1.21--6cb89bfd40cbaabf' }"
+    conda "${moduleDir}/environment.yml"
+    container "${workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container
+        ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/9e/9edc2564215d5cd137a8b25ca8a311600987186d406b092022444adf3c4447f7/data'
+        : 'community.wave.seqera.io/library/htslib_samtools:1.21--6cb89bfd40cbaabf'}"
 
     input:
     tuple val(meta), path(input), path(index)
 
     output:
     tuple val(meta), path("*hostremoved.fastq.gz"), emit: fastq
-    path  "versions.yml",                        emit: versions
+    path "versions.yml"                           , emit: versions
 
     when:
     task.ext.when == null || task.ext.when
@@ -26,16 +26,16 @@ process SAMTOOLS_UNMAPPED {
     """
     samtools \\
         view \\
-        --threads ${task.cpus-1} \\
-        $args \\
-        $input \\
+        --threads ${task.cpus - 1} \\
+        ${args} \\
+        ${input} \\
         | \\
     samtools \\
         fastq \\
-        $args2 \\
-        --threads ${task.cpus-1} \\
+        ${args2} \\
+        --threads ${task.cpus - 1} \\
         -0 ${prefix}.fastq.gz \\
-        $mapped
+        ${mapped}
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
@@ -44,7 +44,6 @@ process SAMTOOLS_UNMAPPED {
     """
 
     stub:
-    def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
     """
     touch ${prefix}.fastq.gz

@@ -1,19 +1,19 @@
-include { BCFTOOLS_CONSENSUS }                                                           from '../../modules/nf-core/bcftools/consensus/main'
-include { BCFTOOLS_INDEX as BCFTOOLS_INDEX_PRE ; BCFTOOLS_INDEX as BCFTOOLS_INDEX_POST } from '../../modules/nf-core/bcftools/index/main'
-include { BCFTOOLS_VIEW }                                                                from '../../modules/nf-core/bcftools/view/main'
-include { FREEBAYES }                                                                    from '../../modules/nf-core/freebayes/main'
-include { PYDAMAGE_ANALYZE }                                                             from '../../modules/nf-core/pydamage/analyze/main'
-include { PYDAMAGE_FILTER }                                                              from '../../modules/nf-core/pydamage/filter/main'
-include { SAMTOOLS_FAIDX as FAIDX}                                                       from '../../modules/nf-core/samtools/faidx/main'
+include { BCFTOOLS_CONSENSUS }                                                           from '../../../modules/nf-core/bcftools/consensus/main'
+include { BCFTOOLS_INDEX as BCFTOOLS_INDEX_PRE ; BCFTOOLS_INDEX as BCFTOOLS_INDEX_POST } from '../../../modules/nf-core/bcftools/index/main'
+include { BCFTOOLS_VIEW }                                                                from '../../../modules/nf-core/bcftools/view/main'
+include { FREEBAYES }                                                                    from '../../../modules/nf-core/freebayes/main'
+include { PYDAMAGE_ANALYZE }                                                             from '../../../modules/nf-core/pydamage/analyze/main'
+include { PYDAMAGE_FILTER }                                                              from '../../../modules/nf-core/pydamage/filter/main'
+include { SAMTOOLS_FAIDX as FAIDX}                                                       from '../../../modules/nf-core/samtools/faidx/main'
 
 workflow ANCIENT_DNA_ASSEMBLY_VALIDATION {
     take:
-        input //channel: [val(meta), path(contigs), path(bam), path(bam_index)]
+        ch_input //channel: [val(meta), path(contigs), path(bam), path(bam_index)]
     main:
         ch_versions = Channel.empty()
 
         PYDAMAGE_ANALYZE(
-            input.map {
+            ch_input.map {
                 meta, _contigs, bam, bai -> [
                     meta, bam[0], bai[0]
                 ]
@@ -28,8 +28,8 @@ workflow ANCIENT_DNA_ASSEMBLY_VALIDATION {
         }
 
         if ( !params.skip_ancient_damagecorrection ) {
-            FAIDX(input.map { item -> [ item[0], item[1] ] }, [[],[]], false )
-            freebayes_input = input.join(FAIDX.out.fai)  // [val(meta), path(contigs), path(bam), path(bam_index), path(fai)]
+            FAIDX(ch_input.map { item -> [ item[0], item[1] ] }, [[],[]], false )
+            freebayes_input = ch_input.join(FAIDX.out.fai)  // [val(meta), path(contigs), path(bam), path(bam_index), path(fai)]
                                 .multiMap{
                                     meta, contigs, bam, bai, fai ->
                                         reads: [ meta, bam, bai, [], [], [] ]
@@ -48,7 +48,7 @@ workflow ANCIENT_DNA_ASSEMBLY_VALIDATION {
             BCFTOOLS_INDEX_POST(BCFTOOLS_VIEW.out.vcf)
             BCFTOOLS_CONSENSUS(BCFTOOLS_VIEW.out.vcf
                                     .join(BCFTOOLS_INDEX_POST.out.tbi)
-                                    .join(input.map { item -> [ item[0], item[1] ] }))
+                                    .join(ch_input.map { item -> [ item[0], item[1] ] }))
 
             ch_corrected_contigs = BCFTOOLS_CONSENSUS.out.fasta
 
@@ -60,7 +60,7 @@ workflow ANCIENT_DNA_ASSEMBLY_VALIDATION {
 
 
     emit:
-        contigs_recalled          = ch_corrected_contigs // channel: [ val(meta), path(fasta) ]
+        contigs_recalled          = ch_corrected_contigs         // channel: [ val(meta), path(fasta) ]
         pydamage_results          = PYDAMAGE_ANALYZE.out.csv     // channel: [ val(meta), path(csv) ]
         pydamage_filtered_results = PYDAMAGE_FILTER.out.csv      // channel: [ val(meta), path(csv) ]
         versions                  = ch_versions                  // channel: [ versions.yml ]

@@ -0,0 +1,80 @@
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/subworkflows/yaml-schema.json
+name: "ancient_dna_assembly_validation"
+description: Ancient DNA analysis workflow for metagenomic samples
+keywords:
+  - ancient DNA
+  - aDNA
+  - metagenomics
+  - authentication
+  - damage patterns
+components:
+  - bcftools/consensus
+  - bcftools/view
+  - freebayes
+  - pydamage/analyze
+  - pydamage/filter
+  - samtools/faidx
+input:
+  - ch_input:
+      description: Assembled contigs with alignment data
+      structure:
+        - meta:
+            type: map
+            description: Metadata map
+        - contigs:
+            type: file
+            description: Assembled contigs in FASTA format
+            pattern: "*.{fasta,fa}"
+        - bam:
+            type: file
+            description: BAM alignment files
+            pattern: "*.bam"
+        - bam_index:
+            type: file
+            description: BAM index files
+            pattern: "*.bai"
+output:
+  - contigs_recalled:
+      description: Damage-corrected contigs
+      structure:
+        - meta:
+            type: map
+            description: Metadata map
+        - fasta:
+            type: file
+            description: Corrected contigs in FASTA format
+            pattern: "*.{fasta,fa}"
+  - pydamage_results:
+      description: PyDamage analysis results
+      structure:
+        - meta:
+            type: map
+            description: Metadata map
+        - csv:
+            type: file
+            description: Damage pattern analysis in CSV format
+            pattern: "*.csv"
+  - pydamage_filtered_results:
+      description: Filtered PyDamage results
+      structure:
+        - meta:
+            type: map
+            description: Metadata map
+        - csv:
+            type: file
+            description: Filtered damage pattern results in CSV format
+            pattern: "*.csv"
+  - versions:
+      type: file
+      description: File containing software versions
+      pattern: "versions.yml"
+authors:
+  - "@maxibor"
+  - "@@alexhbnr"
+  - "@jfy133"
+maintainers:
+  - "@jfy133"
+  - "@prototaxites"
+  - "@dialvarezs"
+  - "@d4straub"
+  - "@muabnezor"