Only create profiler input channels when profiler activate

subworkflows/local/profiling.nf

@@ -48,7 +48,7 @@ workflow PROFILING {
             }
 
     /*
-        PREPARE PROFILER INPUT CHANNELS
+        PREPARE PROFILER INPUT CHANNELS & RUN PROFILING
     */
 
     // Each tool as a slightly different input structure and generally separate
@@ -56,6 +56,9 @@ workflow PROFILING {
     // for each tool and make liberal use of multiMap to keep reads/databases
     // channel element order in sync with each other
 
+    if ( params.run_malt ) {
+
+
         // MALT: We groupTuple to have all samples in one channel for MALT as database
         // loading takes a long time, so we only want to run it once per database
         // TODO document somewhere we only accept illumina short reads for MALT?
@@ -72,58 +75,7 @@ workflow PROFILING {
                                     it ->
                                         reads: [ it[0], it[1].flatten() ]
                                         db: it[2]
-                            }
 
-    // All subsequent tools can easily run on a per-sample basis
-
-    ch_input_for_kraken2 =  ch_input_for_profiling.kraken2
-                            .multiMap {
-                                it ->
-                                    reads: [ it[0] + it[2], it[1] ]
-                                    db: it[3]
-                            }
-
-    ch_input_for_centrifuge =  ch_input_for_profiling.centrifuge
-                            .filter{
-                                if (it[0].is_fasta) log.warn "[nf-core/taxprofiler] Centrifuge currently does not accept FASTA files as input. Skipping Centrifuge for sample ${it[0].id}."
-                                !it[0].is_fasta
-                            }
-                            .multiMap {
-                                it ->
-                                    reads: [ it[0] + it[2], it[1] ]
-                                    db: it[3]
-                            }
-
-    ch_input_for_metaphlan3 = ch_input_for_profiling.metaphlan3
-                            .filter{
-                                if (it[0].is_fasta) log.warn "[nf-core/taxprofiler] MetaPhlAn3 currently does not accept FASTA files as input. Skipping MetaPhlAn3 for sample ${it[0].id}."
-                                !it[0].is_fasta
-                            }
-                            .multiMap {
-                                it ->
-                                    reads: [it[0] + it[2], it[1]]
-                                    db: it[3]
-                            }
-
-    ch_input_for_kaiju = ch_input_for_profiling.kaiju
-                            .multiMap {
-                                it ->
-                                    reads: [it[0] + it[2], it[1]]
-                                    db: it[3]
-                            }
-
-    ch_input_for_diamond = ch_input_for_profiling.diamond
-                            .multiMap {
-                                it ->
-                                    reads: [it[0] + it[2], it[1]]
-                                    db: it[3]
-                            }
-
-    /*
-        RUN PROFILING
-    */
-
-    if ( params.run_malt ) {
         MALT_RUN ( ch_input_for_malt.reads, params.malt_mode, ch_input_for_malt.db )
 
         ch_maltrun_for_megan = MALT_RUN.out.rma6
@@ -143,40 +95,94 @@ workflow PROFILING {
         ch_multiqc_files   = ch_multiqc_files.mix( MALT_RUN.out.log.collect{it[1]}.ifEmpty([])  )
         ch_versions        = ch_versions.mix( MALT_RUN.out.versions.first(), MEGAN_RMA2INFO.out.versions.first() )
         ch_raw_profiles    = ch_raw_profiles.mix( MEGAN_RMA2INFO.out.txt )
+
     }
 
     if ( params.run_kraken2 ) {
+
+        ch_input_for_kraken2 =  ch_input_for_profiling.kraken2
+                                .multiMap {
+                                    it ->
+                                        reads: [ it[0] + it[2], it[1] ]
+                                        db: it[3]
+                                }
+
         KRAKEN2_KRAKEN2 ( ch_input_for_kraken2.reads, ch_input_for_kraken2.db  )
         ch_multiqc_files   = ch_multiqc_files.mix( KRAKEN2_KRAKEN2.out.txt.collect{it[1]}.ifEmpty([])  )
         ch_versions        = ch_versions.mix( KRAKEN2_KRAKEN2.out.versions.first() )
         ch_raw_profiles    = ch_raw_profiles.mix( KRAKEN2_KRAKEN2.out.txt )
+
     }
 
     if ( params.run_centrifuge ) {
+
+        ch_input_for_centrifuge =  ch_input_for_profiling.centrifuge
+                                .filter{
+                                    if (it[0].is_fasta) log.warn "[nf-core/taxprofiler] Centrifuge currently does not accept FASTA files as input. Skipping Centrifuge for sample ${it[0].id}."
+                                    !it[0].is_fasta
+                                }
+                                .multiMap {
+                                    it ->
+                                        reads: [ it[0] + it[2], it[1] ]
+                                        db: it[3]
+                                }
+
         CENTRIFUGE_CENTRIFUGE ( ch_input_for_centrifuge.reads, ch_input_for_centrifuge.db, params.centrifuge_save_unaligned, params.centrifuge_save_aligned, params.centrifuge_sam_format  )
         CENTRIFUGE_KREPORT (CENTRIFUGE_CENTRIFUGE.out.results, ch_input_for_centrifuge.db)
         ch_versions        = ch_versions.mix( CENTRIFUGE_CENTRIFUGE.out.versions.first() )
         ch_raw_profiles    = ch_raw_profiles.mix( CENTRIFUGE_KREPORT.out.kreport )
+
     }
 
     if ( params.run_metaphlan3 ) {
+
+        ch_input_for_metaphlan3 = ch_input_for_profiling.metaphlan3
+                            .filter{
+                                if (it[0].is_fasta) log.warn "[nf-core/taxprofiler] MetaPhlAn3 currently does not accept FASTA files as input. Skipping MetaPhlAn3 for sample ${it[0].id}."
+                                !it[0].is_fasta
+                            }
+                            .multiMap {
+                                it ->
+                                    reads: [it[0] + it[2], it[1]]
+                                    db: it[3]
+                            }
+
         METAPHLAN3 ( ch_input_for_metaphlan3.reads, ch_input_for_metaphlan3.db )
         ch_versions        = ch_versions.mix( METAPHLAN3.out.versions.first() )
         ch_raw_profiles    = ch_raw_profiles.mix( METAPHLAN3.out.biom )
+
     }
 
     if ( params.run_kaiju ) {
+
+        ch_input_for_kaiju = ch_input_for_profiling.kaiju
+                            .multiMap {
+                                it ->
+                                    reads: [it[0] + it[2], it[1]]
+                                    db: it[3]
+                            }
+
         KAIJU_KAIJU ( ch_input_for_kaiju.reads, ch_input_for_kaiju.db)
         KAIJU_KAIJU2TABLE (KAIJU_KAIJU.out.results, ch_input_for_kaiju.db, params.kaiju_taxon_name)
         ch_multiqc_files = ch_multiqc_files.mix( KAIJU_KAIJU2TABLE.out.summary.collect{it[1]}.ifEmpty([])  )
         ch_versions = ch_versions.mix( KAIJU_KAIJU.out.versions.first() )
         ch_raw_profiles = ch_raw_profiles.mix( KAIJU_KAIJU2TABLE.out.summary )
+
     }
 
     if ( params.run_diamond ) {
+
+        ch_input_for_diamond = ch_input_for_profiling.diamond
+                                .multiMap {
+                                    it ->
+                                        reads: [it[0] + it[2], it[1]]
+                                        db: it[3]
+                                }
+
         DIAMOND_BLASTX ( ch_input_for_diamond.reads, ch_input_for_diamond.db, params.diamond_output_format )
         ch_versions        = ch_versions.mix( DIAMOND_BLASTX.out.versions.first() )
         ch_raw_profiles    = ch_raw_profiles.mix( DIAMOND_BLASTX.out.output )
+
     }
 
     emit: