toying more with sylph-tax, rejigging main workflow.nf

Author: number-25

modules/local/sylph/tax/main.nf

@@ -25,6 +25,7 @@ process SYLPH_TAX {
 
     sylph-tax taxprof \\
         $sylph_profile \\
+        --taxonomy-dir !PWD \\
         -t $database_name \\
         -o ${prefix}_sylph_tax.sylphmpa
 

workflows/directrna.nf

@@ -333,57 +333,32 @@ workflow DIRECTRNA{
     // TRANSCRIPT RECONSTRUCTION
     //
     // FLAIR
-    if (!params.bam_input) {
+    if (!params.transcriptome_mapping) {
         if (!params.skip_flair) {
-            if (!params.transcriptome_mapping) {
-                if (!params.skip_flair_correct) {
-                    BAM_TO_BED12( ch_bam, ch_bam_index_path )
-                    ch_mapped_bed = BAM_TO_BED12.out.bed
-                    FLAIR_CORRECT( ch_mapped_bed, ch_genome_fasta, ch_annotation_gtf )
-                    ch_flair_corrected_bed = FLAIR_CORRECT.out.flair_corrected_bed
-                    BEDTOOLS_JACCARD_FLAIR( ch_flair_corrected_bed, ch_mapped_bed, 'flair' )
-                }
+            if (!params.skip_flair_correct) {
+                BAM_TO_BED12( ch_bam, ch_bam_index_path )
+                ch_mapped_bed = BAM_TO_BED12.out.bed
+                FLAIR_CORRECT( ch_mapped_bed, ch_genome_fasta, ch_annotation_gtf )
+                ch_flair_corrected_bed = FLAIR_CORRECT.out.flair_corrected_bed
+                BEDTOOLS_JACCARD_FLAIR( ch_flair_corrected_bed, ch_mapped_bed, 'flair' )
+            }
             if (!params.skip_flair_collapse) {
-                    if (!params.skip_flair_correct) {
-                        FLAIR_COLLAPSE( ch_sample, ch_flair_corrected_bed, ch_annotation_gtf, ch_genome_fasta )
-                        ch_flair_collapsed_bed = FLAIR_COLLAPSE.out.collapsed_isoforms_bed
-                        ch_flair_collapsed_gtf = FLAIR_COLLAPSE.out.collapsed_isoforms_gtf
-                        ch_flair_collapsed_fa = FLAIR_COLLAPSE.out.collapsed_isoforms_fa
-                    } else {
-                        BAM_TO_BED12( ch_bam, ch_bam_index_path )
-                        ch_mapped_bed = BAM_TO_BED12.out.bed
-                        FLAIR_COLLAPSE( ch_sample, ch_mapped_bed, ch_annotation_gtf, ch_genome_fasta )
-                        ch_flair_collapsed_bed = FLAIR_COLLAPSE.out.collapsed_isoforms_bed
-                        ch_flair_collapsed_gtf = FLAIR_COLLAPSE.out.collapsed_isoforms_gtf
-                        ch_flair_collapsed_fa = FLAIR_COLLAPSE.out.collapsed_isoforms_fa
-                    }
-                }
-            } else {
                 if (!params.skip_flair_correct) {
+                    FLAIR_COLLAPSE( ch_sample, ch_flair_corrected_bed, ch_annotation_gtf, ch_genome_fasta )
+                    ch_flair_collapsed_bed = FLAIR_COLLAPSE.out.collapsed_isoforms_bed
+                    ch_flair_collapsed_gtf = FLAIR_COLLAPSE.out.collapsed_isoforms_gtf
+                    ch_flair_collapsed_fa = FLAIR_COLLAPSE.out.collapsed_isoforms_fa
+                } else {
                     BAM_TO_BED12( ch_bam, ch_bam_index_path )
                     ch_mapped_bed = BAM_TO_BED12.out.bed
-                    FLAIR_CORRECT( ch_mapped_bed, ch_transcriptome_fasta, ch_annotation_gtf )
-                    ch_flair_corrected_bed = FLAIR_CORRECT.out.flair_corrected_bed
-                    BEDTOOLS_JACCARD_FLAIR( ch_flair_corrected_bed, ch_mapped_bed, 'flair' )
-                }
-                if (!params.skip_flair_collapse) {
-                    if (!params.skip_flair_correct) {
-                        FLAIR_COLLAPSE( ch_sample, ch_flair_corrected_bed, ch_annotation_gtf, ch_transcriptome_fasta )
-                        ch_flair_collapsed_bed = FLAIR_COLLAPSE.out.collapsed_isoforms_bed
-                        ch_flair_collapsed_gtf = FLAIR_COLLAPSE.out.collapsed_isoforms_gtf
-                        ch_flair_collapsed_fa = FLAIR_COLLAPSE.out.collapsed_isoforms_fa
-                    } else {
-                        BAM_TO_BED12( ch_bam, ch_bam_index_path )
-                        ch_mapped_bed = BAM_TO_BED12.out.bed
-                        FLAIR_COLLAPSE( ch_sample, ch_mapped_bed, ch_annotation_gtf, ch_transcriptome_fasta )
-                        ch_flair_collapsed_bed = FLAIR_COLLAPSE.out.collapsed_isoforms_bed
-                        ch_flair_collapsed_gtf = FLAIR_COLLAPSE.out.collapsed_isoforms_gtf
-                        ch_flair_collapsed_fa = FLAIR_COLLAPSE.out.collapsed_isoforms_fa
-                    }
+                    FLAIR_COLLAPSE( ch_sample, ch_mapped_bed, ch_annotation_gtf, ch_genome_fasta )
+                    ch_flair_collapsed_bed = FLAIR_COLLAPSE.out.collapsed_isoforms_bed
+                    ch_flair_collapsed_gtf = FLAIR_COLLAPSE.out.collapsed_isoforms_gtf
+                    ch_flair_collapsed_fa = FLAIR_COLLAPSE.out.collapsed_isoforms_fa
                 }
             }
         }
-        }
+    }
 
     // BAMBU
     if (!params.skip_bambu) {
@@ -455,7 +430,7 @@ workflow DIRECTRNA{
     // gffcompare
     if (!params.skip_gffcompare) {
         if (!params.skip_flair) {
-            if (!params.bam_input) {
+            if (!params.transcriptome_mapping) {
             GFFCOMPARE_FLAIR( ch_genome_fasta_with_index, ch_flair_collapsed_gtf, ch_annotation_gtf, 'flair' )
             ch_flair_gffcompare_stats = GFFCOMPARE_FLAIR.out.gffcompare_stats.collect{it[1]}.flatten()
             ch_multiqc_files = ch_multiqc_files.mix(ch_flair_gffcompare_stats.ifEmpty([]))
@@ -522,7 +497,7 @@ workflow DIRECTRNA{
     if (!params.skip_transcript_quantification) {
         if (!params.skip_oarfish) {
             if (!params.skip_flair) {
-                if (!params.bam_input) {
+                if (!params.transcriptome_mapping) {
                 OARFISH_FLAIR( ch_flair_collapsed_fa, ch_transcriptome_minimap2_index, ch_sequencing_type, 'flair' )
                 }
             }