Make ancient DNA damage correction optional

CHANGELOG.md

@@ -10,6 +10,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - [#395](https://github.com/nf-core/mag/pull/395) - Add support for fast domain-level classification of bins using Tiara, to allow bins to be separated into eukaryotic and prokaryotic-specific processes.
 - [#422](https://github.com/nf-core/mag/pull/422) - Adds support for normalization of read depth with BBNorm (added by @erikrikarddaniel and @fabianegli)
 - [#439](https://github.com/nf-core/mag/pull/439) - Adds ability to enter the pipeline at the binning stage by providing a CSV of pre-computed assemblies (by @prototaxites)
+- [#459](https://github.com/nf-core/mag/pull/459) - Adds ability to skip damage correction step in the ancient DNA workflow and just run pyDamage (by @jfy133)
 
 ### `Changed`
 

conf/modules.config

@@ -521,7 +521,7 @@ process {
     withName: PYDAMAGE_ANALYZE {
         ext.prefix = { "${meta.assembler}-${meta.id}" }
         publishDir = [
-            path: {"${params.outdir}/Ancient_DNA/pydamage/analyze/" },
+            path: {"${params.outdir}/Ancient_DNA/pydamage/analyze/${meta.assembler}-${meta.id}" },
             mode: params.publish_dir_mode
         ]
     }
@@ -530,7 +530,7 @@ process {
         ext.prefix = { "${meta.assembler}-${meta.id}" }
         ext.args   = "-t ${params.pydamage_accuracy}"
         publishDir = [
-            path: {"${params.outdir}/Ancient_DNA/pydamage/filter/" },
+            path: {"${params.outdir}/Ancient_DNA/pydamage/filter/${meta.assembler}-${meta.id}" },
             mode: params.publish_dir_mode
         ]
     }

docs/output.md

@@ -641,7 +641,7 @@ Optional, only running when parameter `-profile ancient_dna` is specified.
 
 ### `variant_calling`
 
-Because of aDNA damage, _de novo_ assemblers sometimes struggle to call a correct consensus on the contig sequence. To avoid this situation, the consensus is re-called with a variant calling software using the reads aligned back to the contigs
+Because of aDNA damage, _de novo_ assemblers sometimes struggle to call a correct consensus on the contig sequence. To avoid this situation, the consensus is optionally re-called with a variant calling software using the reads aligned back to the contigs when `--run_ancient_damagecorrection` is supplied.
 
 <details markdown="1">
 <summary>Output files</summary>

modules.json

@@ -176,14 +176,15 @@
                         "git_sha": "371eff7748d769c2ddc8bd593773523a364a52fe",
                         "installed_by": ["modules"]
                     },
-                    "tiara/tiara": {
-                        "branch": "master",
-                        "git_sha": "d91e3d3d4806179065b087b91ff36c11976bf233"
-                    },
                     "seqtk/mergepe": {
                         "branch": "master",
                         "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
                         "installed_by": ["modules"]
+                    },
+                    "tiara/tiara": {
+                        "branch": "master",
+                        "git_sha": "d91e3d3d4806179065b087b91ff36c11976bf233",
+                        "installed_by": ["modules"]
                     }
                 }
             },

nextflow.config

@@ -61,13 +61,14 @@ params {
 
     // ancient DNA assembly validation options
     ancient_dna                          = false
+    pydamage_accuracy                    = 0.5
+    skip_ancient_damagecorrection         = false
     freebayes_ploidy                     = 1
     freebayes_min_basequality            = 20
     freebayes_minallelefreq              = 0.33
     bcftools_view_high_variant_quality   = 30
     bcftools_view_medium_variant_quality = 20
     bcftools_view_minimal_allelesupport  = 3
-    pydamage_accuracy                    = 0.5
 
     // taxonomy options
     centrifuge_db                        = null

nextflow_schema.json

@@ -32,7 +32,7 @@
                     "format": "file-path",
                     "description": "Additional input CSV samplesheet containing information about pre-computed assemblies. When set, both read pre-processing and assembly are skipped and the pipeline begins at the binning stage.",
                     "help_text": "If you have pre-computed assemblies from another source, it is possible to jump straight to the binning stage of the pipeline by supplying these assemblies in a CSV file. This CSV file should have three columns and the following header: `id,group,assembler,fasta`. Short reads must still be supplied in to `--input` in CSV format. See [usage docs](https://nf-co.re/mag/usage#input-specifications) for further details.",
-                    "default": null,
+                    "default": "None",
                     "fa_icon": "fas fa-file-csv"
                 },
                 "outdir": {
@@ -740,7 +740,7 @@
                     "type": "number",
                     "default": 0.5,
                     "description": "Specify single-copy gene score threshold for bin refinement.",
-                    "help_text": "Score threshold for single-copy gene selection algorithm to keep selecting bins, with a value ranging from 0-1.\n\nFor description of scoring algorithm, see: Sieber, Christian M. K., et al. 2018. Nature Microbiology 3 (7): 836–43. https://doi.org/10.1038/s41564-018-0171-1.\n\n> Modifies DAS Tool parameter --score_threshold\n"
+                    "help_text": "Score threshold for single-copy gene selection algorithm to keep selecting bins, with a value ranging from 0-1.\n\nFor description of scoring algorithm, see: Sieber, Christian M. K., et al. 2018. Nature Microbiology 3 (7): 836\u201343. https://doi.org/10.1038/s41564-018-0171-1.\n\n> Modifies DAS Tool parameter --score_threshold\n"
                 },
                 "postbinning_input": {
                     "type": "string",
@@ -780,6 +780,15 @@
                     "type": "boolean",
                     "description": "Turn on/off the ancient DNA subworfklow"
                 },
+                "pydamage_accuracy": {
+                    "type": "number",
+                    "default": 0.5,
+                    "description": "PyDamage accuracy threshold"
+                },
+                "skip_ancient_damagecorrection": {
+                    "type": "boolean",
+                    "description": "deactivate damage correction of ancient contigs using variant and consensus calling"
+                },
                 "freebayes_ploidy": {
                     "type": "integer",
                     "default": 1,
@@ -809,11 +818,6 @@
                     "type": "integer",
                     "default": 3,
                     "description": "minimum number of bases supporting the alternative allele"
-                },
-                "pydamage_accuracy": {
-                    "type": "number",
-                    "default": 0.5,
-                    "description": "PyDamage accuracy threshold"
                 }
             }
         }

subworkflows/local/ancient_dna.nf

@@ -10,31 +10,44 @@ workflow ANCIENT_DNA_ASSEMBLY_VALIDATION {
     take:
         input //channel: [val(meta), path(contigs), path(bam), path(bam_index)]
     main:
+        ch_versions = Channel.empty()
+
         PYDAMAGE_ANALYZE(input.map {item -> [item[0], item[2], item[3]]})
         PYDAMAGE_FILTER(PYDAMAGE_ANALYZE.out.csv)
-        FAIDX(input.map { item -> [ item[0], item[1] ] })
-        freebayes_input = input.join(FAIDX.out.fai) // [val(meta), path(contigs), path(bam), path(bam_index), path(fai)]
-        FREEBAYES (freebayes_input.map { item -> [item[0], item[2], item[3], [], [], []] },
-                    freebayes_input.map { item -> item[1] },
-                    freebayes_input.map { item -> item[4] },
-                    [],
-                    [],
-                    [] )
-
-        BCFTOOLS_INDEX_PRE(FREEBAYES.out.vcf)
-        BCFTOOLS_VIEW(FREEBAYES.out.vcf.join(BCFTOOLS_INDEX_PRE.out.tbi), [], [], [])
-        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] ] }))
+        ch_versions = ch_versions.mix(PYDAMAGE_ANALYZE.out.versions.first())
+
+        if ( params.skip_ancient_damagecorrection ) {
+            ch_corrected_contigs = Channel.empty()
+        }
+
+        if ( !params.skip_ancient_damagecorrection ) {
+            FAIDX(input.map { item -> [ item[0], item[1] ] })
+            freebayes_input = input.join(FAIDX.out.fai) // [val(meta), path(contigs), path(bam), path(bam_index), path(fai)]
+            FREEBAYES (freebayes_input.map { item -> [item[0], item[2], item[3], [], [], []] },
+                        freebayes_input.map { item -> item[1] },
+                        freebayes_input.map { item -> item[4] },
+                        [],
+                        [],
+                        [] )
+
+            BCFTOOLS_INDEX_PRE(FREEBAYES.out.vcf)
+            BCFTOOLS_VIEW(FREEBAYES.out.vcf.join(BCFTOOLS_INDEX_PRE.out.tbi), [], [], [])
+            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] ] }))
+
+            ch_corrected_contigs = BCFTOOLS_CONSENSUS.out.fasta
+
+            ch_versions = ch_versions.mix(FAIDX.out.versions.first())
+            ch_versions = ch_versions.mix(FREEBAYES.out.versions.first())
+            ch_versions = ch_versions.mix(BCFTOOLS_CONSENSUS.out.versions.first())
+        }
+
+
 
-        ch_versions = Channel.empty()
-        ch_versions = PYDAMAGE_ANALYZE.out.versions.first()
-        ch_versions = ch_versions.mix(FAIDX.out.versions.first())
-        ch_versions = ch_versions.mix(FREEBAYES.out.versions.first())
-        ch_versions = ch_versions.mix(BCFTOOLS_CONSENSUS.out.versions.first())
     emit:
-        contigs_recalled          = BCFTOOLS_CONSENSUS.out.fasta // 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 ]

workflows/mag.nf

@@ -647,7 +647,7 @@ workflow MAG {
 
     if (!params.skip_binning){
 
-        if (params.ancient_dna) {
+        if (params.ancient_dna && params.run_ancient_damagecorrection) {
             BINNING (
                 BINNING_PREPARATION.out.grouped_mappings
                     .join(ANCIENT_DNA_ASSEMBLY_VALIDATION.out.contigs_recalled)