getting closer to testing sylph out, need to index unmapped bam and convert it to fastq/a, then try again

Author: number-25

conf/test.config

@@ -75,7 +75,7 @@ params {
     extra_gffcompare_options        = null
     // CONTAMINATION / UNMAPPED READ PROFILING
     skip_sylph                      = true
-    sylph_database_url              = ''
+    sylph_database                  = ''
     sylph_database_name             = ''
     skip_sqanti_qc                  = true
     sqanti_qc_reference             = 'human'

conf/test_full.config

@@ -68,7 +68,7 @@ params {
     extra_gffcompare_options        = null
     // CONTAMINATION / UNMAPPED READ PROFILING
     skip_sylph                      = false
-    sylph_database_url              = "http://faust.compbio.cs.cmu.edu/sylph-stuff/gtdb-r226-c1000-dbv1.syldb"
+    sylph_database                  = "data/gtdb-r226-c1000-dbv1.syldb"
     sylph_database_name             = "GTDB_r226"
     skip_sqanti_all                 = true
     skip_sqanti_qc                  = true

conf/test_gzipped.config

@@ -74,7 +74,7 @@ params {
     extra_gffcompare_options        = null
     // CONTAMINATION / UNMAPPED READ PROFILING
     skip_sylph                      = true
-    sylph_database_url              = ""
+    sylph_database                  = ""
     sylph_database_name             = ""
     skip_sqanti_qc                  = true
     sqanti_qc_reference             = 'human'

modules/local/flair/bam_to_bed12/main.nf

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

nextflow.config

@@ -59,7 +59,7 @@ params {
     //extra_ngs_bits_options          = null
 
     // MAPPING
-    transcriptome_mapping           = false
+    transcriptome_mapping           = true
     // minimap2 options
     skip_mapping                    = false
     //extra_minimap2_options          = null
@@ -120,7 +120,7 @@ params {
 
     // CONTAMINATION / UNMAPPED READ PROFILING
     skip_sylph                      = false
-    sylph_database_url              = "http://faust.compbio.cs.cmu.edu/sylph-stuff/gtdb-r226-c1000-dbv1.syldb"
+    sylph_database                  = "data/gtdb-r226-c1000-dbv1.syldb"
     sylph_database_name             = "GTDB_r226"
 
     // Boilerplate options

nextflow_schema.json

@@ -385,10 +385,10 @@
                     "type": "boolean",
                     "description": "Skip OARFISH transcript quantification."
                 },
-                "sylph_database_url": {
+                "sylph_database": {
                     "type": "string",
-                    "default": "http://faust.compbio.cs.cmu.edu/sylph-stuff/gtdb-r226-c1000-dbv1.syldb",
-                    "description": "URL to sylph prebuild database used for downloads - from https://sylph-docs.github.io/pre%E2%80%90built-databases/ ."
+                    "default": "data/gtdb-r226-c1000-dbv1.syldb",
+                    "description": "Path to sylph prebuilt database used for downloads - from https://sylph-docs.github.io/pre%E2%80%90built-databases/ ."
                 },
                 "skip_sylph": {
                     "type": "boolean",