Add funcscan code

nf-core · Oct 10, 2024 · a744175 · a744175
1 parent 2bd8352
commit a744175
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Showing 3 changed files with 46 additions and 18 deletions.
diff --git a/docs/output.md b/docs/output.md
@@ -760,12 +760,14 @@ Summary tool-specific plots and tables of following tools are currently displaye
 The pipeline can also generate input files for the following downstream
 pipelines:
 
+- [nf-core/funcscan](https://nf-co.re/funcscan)
 - [nf-core/taxprofiler](https://nf-co.re/taxprofiler)
 
 <details markdown="1">
 <summary>Output files</summary>
 
 - `downstream_samplesheets/`
+  - `funcscan.csv`: Filled out nf-core/funcscan `--input` csv with absolute paths to the assembly FASTA files produced by MAG (MEGAHIT, SPAdes, SPAdesHybrid)
   - `taxprofiler.csv`: Partially filled out nf-core/taxprofiler preprocessed short reads csv with paths to database directories or `.fast1.gz` relative to the results directory
 
 </details>

diff --git a/subworkflows/local/generate_downstream_samplesheets/main.nf b/subworkflows/local/generate_downstream_samplesheets/main.nf
@@ -37,6 +37,19 @@ workflow GENERATE_DOWNSTREAM_SAMPLESHEETS {
             .tap{ ch_header }
     }
 
+    if ( params.generate_pipeline_samplesheets == 'funcscan' ) {
+        format = 'csv'
+        format_sep = ','
+        ch_list_for_samplesheet = ch_assemblies
+                                    .map {
+                                        meta, filename ->
+                                            def sample = meta.id
+                                            def fasta  = file(params.outdir).toString() + '/Assembly/' + meta.assembler + '/' + filename.getName()
+                                        [ sample: sample, fasta: fasta ]
+                                    }
+                                    .tap{ ch_header }
+    }
+
     // Constructs the header string and then the strings of each row, and
     // finally concatenates for saving.
     ch_header

diff --git a/workflows/mag.nf b/workflows/mag.nf
@@ -13,18 +13,19 @@ include { methodsDescriptionText } from '../subworkflows/local/utils_nfcore_mag_
 //
 // SUBWORKFLOW: Consisting of a mix of local and nf-core/modules
 //
-include { BINNING_PREPARATION              } from '../subworkflows/local/binning_preparation'
-include { BINNING                          } from '../subworkflows/local/binning'
-include { BINNING_REFINEMENT               } from '../subworkflows/local/binning_refinement'
-include { BUSCO_QC                         } from '../subworkflows/local/busco_qc'
-include { VIRUS_IDENTIFICATION             } from '../subworkflows/local/virus_identification'
-include { CHECKM_QC                        } from '../subworkflows/local/checkm_qc'
-include { GUNC_QC                          } from '../subworkflows/local/gunc_qc'
-include { GTDBTK                           } from '../subworkflows/local/gtdbtk'
-include { ANCIENT_DNA_ASSEMBLY_VALIDATION  } from '../subworkflows/local/ancient_dna'
-include { DOMAIN_CLASSIFICATION            } from '../subworkflows/local/domain_classification'
-include { DEPTHS                           } from '../subworkflows/local/depths'
-include { GENERATE_DOWNSTREAM_SAMPLESHEETS } from '../subworkflows/local/generate_downstream_samplesheets/main.nf'
+include { BINNING_PREPARATION                                                              } from '../subworkflows/local/binning_preparation'
+include { BINNING                                                                          } from '../subworkflows/local/binning'
+include { BINNING_REFINEMENT                                                               } from '../subworkflows/local/binning_refinement'
+include { BUSCO_QC                                                                         } from '../subworkflows/local/busco_qc'
+include { VIRUS_IDENTIFICATION                                                             } from '../subworkflows/local/virus_identification'
+include { CHECKM_QC                                                                        } from '../subworkflows/local/checkm_qc'
+include { GUNC_QC                                                                          } from '../subworkflows/local/gunc_qc'
+include { GTDBTK                                                                           } from '../subworkflows/local/gtdbtk'
+include { ANCIENT_DNA_ASSEMBLY_VALIDATION                                                  } from '../subworkflows/local/ancient_dna'
+include { DOMAIN_CLASSIFICATION                                                            } from '../subworkflows/local/domain_classification'
+include { DEPTHS                                                                           } from '../subworkflows/local/depths'
+include { GENERATE_DOWNSTREAM_SAMPLESHEETS as GENERATE_DOWNSTREAM_SAMPLESHEETS_FUNCSCAN    } from '../subworkflows/local/generate_downstream_samplesheets/main.nf'
+include { GENERATE_DOWNSTREAM_SAMPLESHEETS as GENERATE_DOWNSTREAM_SAMPLESHEETS_TAXPROFILER } from '../subworkflows/local/generate_downstream_samplesheets/main.nf'
 
 //
 // MODULE: Installed directly from nf-core/modules
@@ -1006,13 +1007,25 @@ workflow MAG {
     //
     // Samplesheet generation
     //
-    ch_input_for_samplesheet = Channel
-                            .empty()
-                            .mix( ch_short_reads_assembly )
+    // if ( params.generate_pipeline_samplesheets.contains("taxprofiler") ) {
+        ch_input_for_samplesheet = Channel
+                                .empty()
+                                .mix( ch_short_reads_assembly )
 
-    if ( params.generate_downstream_samplesheets ) {
-        GENERATE_DOWNSTREAM_SAMPLESHEETS ( ch_input_for_samplesheet )
-    }
+        if ( params.generate_downstream_samplesheets ) {
+            GENERATE_DOWNSTREAM_SAMPLESHEETS_TAXPROFILER ( ch_input_for_samplesheet )
+        }
+    // }
+
+    // if ( params.generate_pipeline_samplesheets.contains("funcscan") ) {
+        ch_input_for_samplesheet = Channel
+                                .empty()
+                                .mix( ch_assemblies )
+
+        if ( params.generate_downstream_samplesheets ) {
+            GENERATE_DOWNSTREAM_SAMPLESHEETS_FUNCSCAN ( ch_input_for_samplesheet )
+        }
+    // }
 
     //
     // Collate and save software versions