fixing bam inputs

Author: number-25

modules/local/flair/bam_to_bed12/main.nf

@@ -8,7 +8,8 @@ process BAM_TO_BED12 {
 
     input:
     tuple val(meta), path(mapped_bam)
-    tuple val(meta), path(mapped_bam_index)
+    path(mapped_bam_index)
+    //tuple val(meta), path(mapped_bam_index)
 
     output:
     tuple val(meta), path("*.bed"), emit: bed

workflows/directrna.nf

@@ -264,7 +264,7 @@ workflow DIRECTRNA{
     } else {
         ch_bam = ch_sample
         SAMTOOLS_INDEX( ch_bam )
-        ch_bam_index = SAMTOOLS_INDEX.out.bai
+        ch_bam_index = SAMTOOLS_INDEX.out.bai.flatten().last()
         ch_mixed_bam = ch_bam.combine(ch_bam_index)
     }
 
@@ -320,27 +320,29 @@ workflow DIRECTRNA{
     // TRANSCRIPT RECONSTRUCTION
     //
     // FLAIR
-    if (!params.skip_flair) {
-        if (!params.skip_flair_correct) {
-            BAM_TO_BED12( ch_bam, ch_bam_index )
-            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.bam_input) {
+        if (!params.skip_flair) {
             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 )
                 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
+                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 )
+                    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
+                }
             }
         }
     }
@@ -391,9 +393,11 @@ workflow DIRECTRNA{
     // gffcompare
     if (!params.skip_gffcompare) {
         if (!params.skip_flair) {
+            if (!params.bam_input) {
             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([]))
+            }
         }
         if (!params.skip_bambu) {
             GFFCOMPARE_BAMBU( ch_genome_fasta_with_index, ch_bambu_supported_gtf, ch_annotation_gtf, 'bambu' )
@@ -438,7 +442,9 @@ workflow DIRECTRNA{
     if (!params.skip_transcript_quantification) {
         if (!params.skip_oarfish) {
             if (!params.skip_flair) {
+                if (!params.bam_input) {
                 OARFISH_FLAIR( ch_flair_collapsed_fa, ch_transcriptome_minimap2_index, ch_sequencing_type, 'flair' )
+                }
             }
             if (!params.skip_bambu) {
                 OARFISH_BAMBU( ch_bambu_transcripts, ch_transcriptome_minimap2_index, ch_sequencing_type, 'bambu' )