fixing up channel logic, doing more tests

Author: number-25

conf/test_full.config

@@ -22,6 +22,7 @@ params {
     //input                           = "test/samplesheets/samplesheet_test_local_bam.csv"
     sequencing_type                 = "ont-drna" // sequencing molecule [ont-drna OR ont-cdna]
     bam_input                       = false
+    transcriptome_mapping           = false
     // Genome references
     // These channel names have to match those in the full workflow also
     genome_fasta                    = "assets/fulltest_data/hg38.analysisSet.fa.gz"
@@ -34,7 +35,6 @@ params {
     annotation_gtf                  = "assets/fulltest_data/Homo_sapiens.GRCh38.112_chr.gtf.gz"
     skip_prepare_reference          = false
     skip_mapping                    = false
-    transcriptome_mapping           = true
     skip_bam_to_bigwig              = false
     skip_qc                         = false
     skip_bam_qc                     = false

workflows/directrna.nf

@@ -261,7 +261,7 @@ workflow DIRECTRNA{
         ch_transcriptome_minimap2_index )
         ch_bam = MAPPING.out.bam.view()
         ch_bam_index = MAPPING.out.bai
-        ch_bam_index_path = MAPPING.out.bai.flatten().last().view()
+        ch_bam_index_path = MAPPING.out.bai.flatten().last()
         ch_mixed_bam = ch_bam.combine(ch_bam_index_path)
         SAMTOOLS_FASTA( ch_bam )
         ch_unmapped_reads = SAMTOOLS_FASTA.out.fasta
@@ -270,10 +270,11 @@ workflow DIRECTRNA{
         ch_bam = ch_sample
         ch_bam.view()
         SAMTOOLS_INDEX( ch_sample )
-        ch_bam_index = SAMTOOLS_INDEX.out.bai.flatten().last()
+        ch_bam_index_path = SAMTOOLS_INDEX.out.bai.flatten().last().view()
+        //ch_bam_index_path = ch_bam_index
         SAMTOOLS_FASTA( ch_sample )
         ch_unmapped_reads = SAMTOOLS_FASTA.out.fasta
-        ch_mixed_bam = ch_bam.combine(ch_bam_index).view()
+        ch_mixed_bam = ch_bam.combine(ch_bam_index_path).view()
     }
 
     // BAM TO BIGWIG for visualisation

workflows/nextflow.config

@@ -5,6 +5,7 @@ includeConfig "../modules/local/sequali/sequali/nextflow.config"
 includeConfig "../modules/local/minimap2/align/nextflow.config"
 includeConfig "../modules/local/samtools/sort/nextflow.config"
 includeConfig "../modules/local/samtools/index/nextflow.config"
+includeConfig "../modules/local/samtools/fasta/nextflow.config"
 includeConfig "../modules/local/bedtools/bam_to_bedgraph/nextflow.config"
 includeConfig "../modules/local/bedtools/bam_to_bedgraph/nextflow.config"
 includeConfig "../modules/local/ucsc/bedgraphtobigwig/nextflow.config"
@@ -31,7 +32,10 @@ includeConfig "../modules/local/unzip/unzip/nextflow.config"
 includeConfig "../modules/nf-core/gunzip/nextflow.config"
 includeConfig "../modules/nf-core/custom/getchromsizes/nextflow.config"
 includeConfig "../modules/local/isoquant/gtf2db/nextflow.config"
-
+includeConfig "../modules/local/sylph/get_tax_database/nextflow.config"
+includeConfig "../modules/local/sylph/prepare_reference/nextflow.config"
+includeConfig "../modules/local/sylph/profile/nextflow.config"
+includeConfig "../modules/local/sylph/tax/nextflow.config"
 
 //TODO
 // don't forget prepare reference and other subworkflows