Merge pull request #109 from Joon-Klaps/102-autodetect-paired-end

102 autodetect paired end

Author: Joon-Klaps

assets/samplesheets/samplesheet.csv

@@ -1,3 +1,3 @@
-sample,single_end,fastq_1,fastq_2
-SRR11140744,False,https://raw.githubusercontent.com/nf-core/test-datasets/viralrecon/illumina/sispa/SRR11140744_R1.fastq.gz,https://raw.githubusercontent.com/nf-core/test-datasets/viralrecon/illumina/sispa/SRR11140744_R2.fastq.gz
-SRR11140748,False,https://raw.githubusercontent.com/nf-core/test-datasets/viralrecon/illumina/sispa/SRR11140748_R1.fastq.gz,https://raw.githubusercontent.com/nf-core/test-datasets/viralrecon/illumina/sispa/SRR11140748_R2.fastq.gz
+sample,fastq_1,fastq_2
+SRR11140744,https://raw.githubusercontent.com/nf-core/test-datasets/viralrecon/illumina/sispa/SRR11140744_R1.fastq.gz,https://raw.githubusercontent.com/nf-core/test-datasets/viralrecon/illumina/sispa/SRR11140744_R2.fastq.gz
+SRR11140748,https://raw.githubusercontent.com/nf-core/test-datasets/viralrecon/illumina/sispa/SRR11140748_R1.fastq.gz,https://raw.githubusercontent.com/nf-core/test-datasets/viralrecon/illumina/sispa/SRR11140748_R2.fastq.gz

assets/schemas/input.json

@@ -13,11 +13,6 @@
                 "errorMessage": "Sample name must be provided and cannot contain spaces or special characters",
                 "meta": ["id", "sample"]
             },
-            "single_end": {
-                "type": "boolean",
-                "errorMessage": "Single end must be a boolean value (true/false)",
-                "meta": ["single_end"]
-            },
             "fastq_1": {
                 "type": "string",
                 "pattern": "^\\S+\\.f(ast)?q\\.gz$",

subworkflows/local/fasta_blast_refsel.nf

@@ -28,10 +28,10 @@ workflow FASTA_BLAST_REFSEL {
         .set { ch_blast_txt }
 
     // Throw an warning if no hits are found
-    ch_blast_txt
-        .hits
-        .collect()
-        .ifEmpty{ log.warn "No blast hits were found in any samples of the given BLAST database. Consider updating the search parameters or the database: \n ${params.reference_pool} "}
+    // ch_blast_txt
+    //     .hits
+    //     .collect()
+    //     .ifEmpty{ log.warn "No blast hits were found in any samples of the given BLAST database. Consider updating the search parameters or the database: \n ${params.reference_pool} "}
 
     // Make a table of samples that did not have any blast hits
     ch_no_blast_hits = Channel.empty()

workflows/viralgenie.nf

@@ -129,8 +129,14 @@ workflow VIRALGENIE {
         'input'
         ).map{
             meta, read1, read2 ->
-            [meta + [sample: meta.id] , [read1, read2]]
+            single_end = read1 && !read2
+            if (single_end) {
+                return [meta + [sample: meta.id, single_end: single_end] , [read1]]
             }
+            else {
+                return [meta + [sample: meta.id, single_end: single_end] , [read1, read2]]
+            }
+        }
 
     // Prepare Databases
     ch_db = Channel.empty()
@@ -176,19 +182,15 @@ workflow VIRALGENIE {
     ch_ref_pool     = Channel.empty()
     ch_blast_refdb  = Channel.empty()
     ch_blast_annodb = Channel.empty()
-    if ( !params.skip_consensus_qc || (!params.skip_assembly && !params.skip_polishing) ){
-        ch_blastdb_in = Channel.empty()
 
+    if ( (!params.skip_assembly && !params.skip_polishing) || (!params.skip_consensus_qc && !params.skip_blast_qc)){
+        ch_blastdb_in = Channel.empty()
         // see issue #56
         SEQKIT_REPLACE (ch_ref_pool_raw)
         ch_versions   = ch_versions.mix(SEQKIT_REPLACE.out.versions)
         ch_ref_pool   = SEQKIT_REPLACE.out.fastx
         ch_blastdb_in = ch_blastdb_in.mix(ch_ref_pool)
 
-        // if ( !params.skip_annotation){
-        //     ch_blastdb_in = ch_blastdb_in.mix(ch_annotation_db)
-        // }
-
         BLAST_MAKEBLASTDB ( ch_blastdb_in )
         BLAST_MAKEBLASTDB
             .out
@@ -201,7 +203,6 @@ workflow VIRALGENIE {
             }.
             set{ch_blastdb_out}
         ch_blast_refdb  = ch_blastdb_out.reference.collect{it[1]}.ifEmpty([]).map{it -> [[id: 'reference'], it]}
-        // ch_blast_annodb = ch_blastdb_out.annotation.collect{it[1]}.ifEmpty([]).map{it -> [[id: 'annotation'], it]}
         ch_versions     = ch_versions.mix(BLAST_MAKEBLASTDB.out.versions)
     }
 
@@ -271,6 +272,7 @@ workflow VIRALGENIE {
 
         ch_multiqc_files = ch_multiqc_files.mix(no_contigs.ifEmpty([]))
 
+
         if (!params.skip_polishing){
             // blast contigs against reference & identify clusters of (contigs & references)
             ch_contigs