first draft push with TODOs

nextflow.config

@@ -194,6 +194,9 @@ params {
     validationShowHiddenParams       = false
     validate_params                  = true
 
+    // Generate downstream samplesheets
+    generate_samplesheet = false
+    downstream_pipeline  = 'taxprofiler'
 }
 
 // Load base.config by default for all pipelines

subworkflows/local/generate_downstream_samplesheets/main.nf

@@ -0,0 +1,46 @@
+//
+// Subworkflow with functionality specific to the nf-core/createtaxdb pipeline
+//
+
+workflow GENERATE_DOWNSTREAM_SAMPLESHEETS {
+    take:
+    ch_databases
+
+    main:
+    ch_header  = Channel.empty()
+    format     = 'csv' // most common format in nf-core
+    format_sep = ','
+
+    // TODO --
+    // Make your samplesheet channel construct here depending on your downstream
+    // pipelines
+    if ( params.downstream_pipeline == 'taxprofiler' ) {
+        format = 'csv'
+        format_sep = ','
+        ch_list_for_samplesheet = ch_databases
+                                    .map {
+                                        meta, db ->
+                                            def tool      = meta.tool
+                                            def db_name   = meta.id + '-' + meta.tool
+                                            def db_params = ""
+                                            def db_type   = ""
+                                            def db_path   = file(params.outdir).getParent() + '/' + meta.tool + '/' + db.getName()
+                                        [ tool: tool, db_name: db_name, db_params: db_params, db_type: db_type, db_path: db_path ]
+                                    }
+                                    .tap{ ch_header }
+    }
+    // -- FINISH TODO
+
+    // Constructs the header string and then the strings of each row, and
+    // finally concatenates for saving.
+    ch_header
+        .first()
+        .map{ it.keySet().join(format_sep) }
+        .concat( ch_list_for_samplesheet.map{ it.values().join(format_sep) })
+        .collectFile(
+            name:"${params.outdir}/downstream_samplesheet/${params.downstream_pipeline}.${format}",
+            newLine: true,
+            sort: false
+        )
+
+}

workflows/mag.nf

@@ -13,17 +13,18 @@ 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 { 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'
 
 //
 // MODULE: Installed directly from nf-core/modules
@@ -356,6 +357,8 @@ workflow MAG {
                         }
     }
 
+    // TODO remove ch_short_reads_assembly.view()
+
     /*
     ================================================================================
                                     Preprocessing and QC for long reads
@@ -1002,6 +1005,26 @@ workflow MAG {
         }
     }
 
+    //
+    // Samplesheet generation
+    //
+    ch_input_for_samplesheet = Channel
+                            .empty()
+                            // TODO
+                            // .mix(
+                            //         ch_centrifuge_output.map     {meta, db -> [ meta + [tool: "centrifuge"]     , db ]},
+                            //         ch_diamond_output.map        {meta, db -> [ meta + [tool: "diamond"]        , db ]},
+                            //         ch_kaiju_output.map          {meta, db -> [ meta + [tool: "kaiju"]          , db ]},
+                            //         ch_kraken2_bracken_output.map{meta, db -> [ meta + [tool: "kraken2_bracken"], db ]},
+                            //         ch_krakenuniq_output.map     {meta, db -> [ meta + [tool: "krakenuniq"]     , db ]},
+                            //         ch_malt_output.map           {meta, db -> [ meta + [tool: "malt"]           , db ]}
+                            //     )
+                            //     .view()
+
+    if ( params.generate_samplesheet ) {
+        GENERATE_DOWNSTREAM_SAMPLESHEETS ( ch_input_for_samplesheet )
+    }
+
     //
     // Collate and save software versions
     //