nf-core · apsteinberg · Aug 21, 2024 · Aug 21, 2024 · Aug 21, 2024 · Aug 21, 2024
@@ -17,6 +17,44 @@ process {
         path: { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" },
         saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
     ]
+// BBSPLIT
+if (!params.skip_bbsplit && params.bbsplit_fasta_list) {
+    process {
+        withName: '.*:PREPARE_BBSPLIT:BBMAP_BBSPLIT' {
+            ext.args   = 'build=1'
+            publishDir = [
+                path: { params.save_reference ? "${params.outdir}/genome/index" : params.outdir },
+                mode: params.publish_dir_mode,
+                saveAs: { filename -> (filename != 'versions.yml' && params.save_reference) ? filename : null }
+            ]
+        }
+    }
+}
+
+//
+// Contaminant removal options
+//
+
+if (!params.skip_bbsplit) {
+    process {
+        withName: 'BBMAP_BBSPLIT' {
+            ext.args   = 'build=1 ambiguous2=all maxindel=150000'
+            publishDir = [
+                [
+                    path: { "${params.outdir}/bbsplit" },
+                    mode: params.publish_dir_mode,
+                    pattern: '*.txt'
+                ],
+                [
+                    path: { params.save_bbsplit_reads ? "${params.outdir}/bbsplit" : params.outdir },
+                    mode: params.publish_dir_mode,
+                    saveAs: { params.save_bbsplit_reads ? it : null }
+                ]
+            ]
+        }
+    }
+}
 
 // QC
     withName: 'FASTQC' {

@@ -60,7 +60,10 @@ params.vep_cache_version       = getGenomeAttribute('vep_cache_version')
 params.vep_genome              = getGenomeAttribute('vep_genome')
 params.vep_species             = getGenomeAttribute('vep_species')
 
-aligner = params.aligner
+aligner            = params.aligner
+skip_bbsplit       = params.skip_bbsplit
+bbsplit_fasta_list = params.bbsplit_fasta_list
+bbsplit_index      = params.bbsplit_index
 
 /*
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
@@ -145,7 +148,10 @@ workflow NFCORE_SAREK {
         germline_resource,
         known_indels,
         known_snps,
-        pon)
+        pon,
+        bbsplit_fasta_list,
+        bbsplit_index
+        )
 
     // Gather built indices or get them from the params
     // Built from the fasta file:
@@ -159,6 +165,8 @@ workflow NFCORE_SAREK {
                                     : PREPARE_GENOME.out.bwamem2
     dragmap     = params.dragmap    ? Channel.fromPath(params.dragmap).map{ it -> [ [id:'dragmap'], it ] }.collect()
                                     : PREPARE_GENOME.out.hashtable
+    // get index from bbsplit
+    bbsplit_index           = PREPARE_GENOME.out.bbsplit_index
 
     // Gather index for mapping given the chosen aligner
     index_alignment = (aligner == "bwa-mem" || aligner == "sentieon-bwamem") ? bwa :
@@ -305,7 +313,11 @@ workflow NFCORE_SAREK {
         vep_extra_files,
         vep_fasta,
         vep_genome,
-        vep_species
+        vep_species,
+        bbsplit_fasta_list,
+        bbsplit_index,
+        skip_bbsplit
+
     )
     emit:
     multiqc_report = SAREK.out.multiqc_report // channel: /path/to/multiqc_report.html

@@ -10,6 +10,11 @@
                         "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
                         "installed_by": ["modules"]
                     },
+                    "bbmap/bbsplit": {
+                        "branch": "master",
+                        "git_sha": "1ceaa8ba4d0fd886dbca0e545815d905b7407de7",
+                        "installed_by": ["modules"]
+                    },
 
9E88
                    "bcftools/annotate": {
                         "branch": "master",
                         "git_sha": "cb08035150685b11d890d90c9534d4f16869eaec",
@@ -315,6 +320,11 @@
                         "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
                         "installed_by": ["modules"]
                     },
+                    "gunzip": {
+                        "branch": "master",
+                        "git_sha": "81880787133db07d9b4c1febd152c090eb8325dc",
+                        "installed_by": ["modules"]
+                    },
                     "lofreq/callparallel": {
                         "branch": "master",
                         "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",