small refactor + adding intervals

assets/genomes/test/pipelines/default_full.yml

@@ -0,0 +1,15 @@
+- genome: "GRCh38_chr21"
+  bed_intervals: "https://raw.githubusercontent.com/nf-core/test-datasets/references/references/GRCh38_chr21/GRCh38_chr21.bed"
+  fasta: "https://raw.githubusercontent.com/nf-core/test-datasets/references/references/GRCh38_chr21/GRCh38_chr21.fa"
+  fasta_dict: "https://raw.githubusercontent.com/nf-core/test-datasets/references/references/GRCh38_chr21/GRCh38_chr21.dict"
+  fasta_fai: "https://raw.githubusercontent.com/nf-core/test-datasets/references/references/GRCh38_chr21/GRCh38_chr21.fa.fai"
+  fasta_sizes: "https://raw.githubusercontent.com/nf-core/test-datasets/references/references/GRCh38_chr21/GRCh38_chr21.fa.sizes"
+  gff: "https://raw.githubusercontent.com/nf-core/test-datasets/references/references/GRCh38_chr21/genes_chr21.gff"
+  gtf: "https://raw.githubusercontent.com/nf-core/test-datasets/references/references/GRCh38_chr21/genes_chr21.gtf"
+  mito_name: "MT"
+  readme: "https://raw.githubusercontent.com/nf-core/test-datasets/references/references/GRCh38_chr21/README.md"
+  source: "nf-core/references"
+  species: "Homo_sapiens"
+  splice_sites: "https://raw.githubusercontent.com/nf-core/test-datasets/references/references/GRCh38_chr21/genes_chr21.splice_sites.txt"
+  transcript_fasta: "https://raw.githubusercontent.com/nf-core/test-datasets/references/references/GRCh38_chr21/genome.transcripts.fa"
+  # macs_gsize:   "1.2e7"

assets/schema_input.json

@@ -23,6 +23,11 @@
                 "errorMessage": "Species of the reference",
                 "meta": ["species"]
             },
+            "bed_intervals": {
+                "type": "string",
+                "pattern": "^\\S+\\.bed$",
+                "errorMessage": "TODO"
+            },
             "fasta": {
                 "type": "string",
                 "pattern": "^\\S+\\.f(ast|n)?a(\\.gz)?$",

conf/modules.config

@@ -18,6 +18,11 @@ process {
         saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
     ]
 
+    withName: 'BUILD_INTERVALS' {
+        ext.args   = { "-v FS='\t' -v OFS='\t' '{ print \$1, \"0\", \$2 }'" }
+        ext.suffix = { "bed" }
+    }
+
     withName: 'GFFREAD' {
         ext.args   = '--keep-exon-attrs -F -T'
     }

main.nf

@@ -44,6 +44,11 @@ workflow {
     )
 
     // WORKFLOW: Run main workflow
+    if (!params.tools) {
+        log.error("No tools specified")
+        error("EXIT: No tools specified")
+    }
+
     NFCORE_REFERENCES(PIPELINE_INITIALISATION.out.samplesheet, params.tools)
 
     ch_multiqc_files = Channel.empty()
@@ -104,5 +109,24 @@ workflow NFCORE_REFERENCES {
     REFERENCES(input, tools)
 
     emit:
-    versions = REFERENCES.out.versions
+    bowtie1               = REFERENCES.out.bowtie1
+    bowtie2               = REFERENCES.out.bowtie2
+    bwamem1               = REFERENCES.out.bwamem1
+    bwamem2               = REFERENCES.out.bwamem2
+    dict                  = REFERENCES.out.dict
+    dragmap               = REFERENCES.out.dragmap
+    faidx                 = REFERENCES.out.faidx
+    fasta                 = REFERENCES.out.fasta
+    gffread               = REFERENCES.out.gffread
+    hisat2                = REFERENCES.out.hisat2
+    hisat2_splice_sites   = REFERENCES.out.hisat2_splice_sites
+    intervals             = REFERENCES.out.intervals
+    kallisto              = REFERENCES.out.kallisto
+    msisensorpro          = REFERENCES.out.msisensorpro
+    rsem                  = REFERENCES.out.rsem
+    rsem_transcript_fasta = REFERENCES.out.rsem_transcript_fasta
+    salmon                = REFERENCES.out.salmon
+    sizes                 = REFERENCES.out.sizes
+    star                  = REFERENCES.out.star
+    versions              = REFERENCES.out.versions
 }

modules.json

@@ -46,6 +46,11 @@
                         "git_sha": "1999eff2c530b2b185a25cc42117a1686f09b685",
                         "installed_by": ["modules"]
                     },
+                    "gawk": {
+                        "branch": "master",
+                        "git_sha": "97321eded31a12598837a476d3615300af413bb7",
+                        "installed_by": ["modules"]
+                    },
                     "gffread": {
                         "branch": "master",
                         "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",