install subworkflows from nf-side

main.nf

@@ -46,6 +46,8 @@ workflow {
         args,
         params.outdir,
         params.input,
+        params.references_basepath,
+        ['${params.igenomes_base}', 's3://ngi-igenomes/igenomes/'],
     )
 
     // WORKFLOW: Run main workflow
@@ -193,6 +195,7 @@ output {
         }
     }
 }
+
 /*
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
     NAMED WORKFLOWS FOR PIPELINE
@@ -213,7 +216,7 @@ workflow NFCORE_REFERENCES {
         channel
             .map { meta, reference_ -> [meta + [reference: type], reference_] }
             .branch { _meta, reference_ ->
-                to_extract: reference_.toString().endsWith('.gz') || reference_.toString().endsWith('.zip')
+                to_extract: (reference_.toString().endsWith('.gz') || reference_.toString().endsWith('.zip'))
                 not_extracted: true
             }
     }

modules.json

@@ -12,17 +12,17 @@
                     },
                     "custom/catadditionalfasta": {
                         "branch": "master",
-                        "git_sha": "a1abf90966a2a4016d3c3e41e228bfcbd4811ccc",
+                        "git_sha": "05954dab2ff481bcb999f24455da29a5828af08d",
                         "installed_by": ["modules"]
                     },
                     "gunzip": {
                         "branch": "master",
-                        "git_sha": "81880787133db07d9b4c1febd152c090eb8325dc",
+                        "git_sha": "05954dab2ff481bcb999f24455da29a5828af08d",
                         "installed_by": ["archive_extract"]
                     },
                     "multiqc": {
                         "branch": "master",
-                        "git_sha": "81880787133db07d9b4c1febd152c090eb8325dc",
+                        "git_sha": "7b50cb7be890e4b28cffb82e438cc6a8d7805d3f",
                         "installed_by": ["modules"]
                     },
                     "sortmerna": {
@@ -32,12 +32,12 @@
                     },
                     "untar": {
                         "branch": "master",
-                        "git_sha": "81880787133db07d9b4c1febd152c090eb8325dc",
+                        "git_sha": "05954dab2ff481bcb999f24455da29a5828af08d",
                         "installed_by": ["archive_extract"]
                     },
                     "unzip": {
                         "branch": "master",
-                        "git_sha": "81880787133db07d9b4c1febd152c090eb8325dc",
+                        "git_sha": "05954dab2ff481bcb999f24455da29a5828af08d",
                         "installed_by": ["archive_extract"]
                     }
                 }
@@ -63,10 +63,120 @@
                         "branch": "master",
                         "git_sha": "2fd2cd6d0e7b273747f32e465fdc6bcc3ae0814e",
                         "installed_by": ["subworkflows"]
+                    }
+                }
+            }
+        },
+        "https://github.com/nf-side/modules.git": {
+            "modules": {
+                "nf-side": {
+                    "bowtie/build": {
+                        "branch": "main",
+                        "git_sha": "4d329b41d14a20dec31cae811f39e1a52b435220",
+                        "installed_by": ["prepare_genome_rnaseq"]
+                    },
+                    "bowtie2/build": {
+                        "branch": "main",
+                        "git_sha": "4d329b41d14a20dec31cae811f39e1a52b435220",
+                        "installed_by": ["prepare_genome_rnaseq"]
+                    },
+                    "bwa/index": {
+                        "branch": "main",
+                        "git_sha": "4d329b41d14a20dec31cae811f39e1a52b435220",
+                        "installed_by": ["prepare_genome_dnaseq"]
+                    },
+                    "bwamem2/index": {
+                        "branch": "main",
+                        "git_sha": "4d329b41d14a20dec31cae811f39e1a52b435220",
+                        "installed_by": ["prepare_genome_dnaseq"]
+                    },
+                    "dragmap/hashtable": {
+                        "branch": "main",
+                        "git_sha": "45771824ae473165222af14becffa213448a5edc",
+                        "installed_by": ["prepare_genome_dnaseq"]
+                    },
+                    "gatk4/createsequencedictionary": {
+                        "branch": "main",
+                        "git_sha": "4d329b41d14a20dec31cae811f39e1a52b435220",
+                        "installed_by": ["prepare_genome_dnaseq"]
+                    },
+                    "gawk": {
+                        "branch": "main",
+                        "git_sha": "4d329b41d14a20dec31cae811f39e1a52b435220",
+                        "installed_by": ["prepare_genome_dnaseq"]
+                    },
+                    "gffread": {
+                        "branch": "main",
+                        "git_sha": "4d329b41d14a20dec31cae811f39e1a52b435220",
+                        "installed_by": ["prepare_genome_rnaseq"]
+                    },
+                    "hisat2/build": {
+                        "branch": "main",
+                        "git_sha": "4d329b41d14a20dec31cae811f39e1a52b435220",
+                        "installed_by": ["prepare_genome_rnaseq"]
+                    },
+                    "hisat2/extractsplicesites": {
+                        "branch": "main",
+                        "git_sha": "4d329b41d14a20dec31cae811f39e1a52b435220",
+                        "installed_by": ["prepare_genome_rnaseq"]
+                    },
+                    "kallisto/index": {
+                        "branch": "main",
+                        "git_sha": "4d329b41d14a20dec31cae811f39e1a52b435220",
+                        "installed_by": ["prepare_genome_rnaseq"]
+                    },
+                    "msisensorpro/scan": {
+                        "branch": "main",
+                        "git_sha": "8c1309daf37cd08ec9f98298521abd1f2745288a",
+                        "installed_by": ["prepare_genome_dnaseq"]
+                    },
+                    "rsem/preparereference": {
+                        "branch": "main",
+                        "git_sha": "4d329b41d14a20dec31cae811f39e1a52b435220",
+                        "installed_by": ["prepare_genome_rnaseq"]
+                    },
+                    "salmon/index": {
+                        "branch": "main",
+                        "git_sha": "4d329b41d14a20dec31cae811f39e1a52b435220",
+                        "installed_by": ["prepare_genome_rnaseq"]
+                    },
+                    "samtools/faidx": {
+                        "branch": "main",
+                        "git_sha": "4d329b41d14a20dec31cae811f39e1a52b435220",
+                        "installed_by": ["prepare_genome_dnaseq", "prepare_genome_rnaseq"]
+                    },
+                    "star/genomegenerate": {
+                        "branch": "main",
+                        "git_sha": "4d329b41d14a20dec31cae811f39e1a52b435220",
+                        "installed_by": ["prepare_genome_rnaseq"]
+                    },
+                    "tabix/bgziptabix": {
+                        "branch": "main",
+                        "git_sha": "4d329b41d14a20dec31cae811f39e1a52b435220",
+                        "installed_by": ["prepare_genome_dnaseq"]
+                    },
+                    "tabix/tabix": {
+                        "branch": "main",
+                        "git_sha": "4d329b41d14a20dec31cae811f39e1a52b435220",
+                        "installed_by": ["prepare_genome_dnaseq"]
+                    }
+                }
+            },
+            "subworkflows": {
+                "nf-side": {
+                    "prepare_genome_dnaseq": {
+                        "branch": "main",
+                        "git_sha": "bc3122bf8ada968de886888792978a4d3058d9ab",
+                        "installed_by": ["subworkflows"]
+                    },
+                    "prepare_genome_rnaseq": {
+                        "branch": "main",
+                        "git_sha": "bc3122bf8ada968de886888792978a4d3058d9ab",
+                        "installed_by": ["subworkflows"]
                     },
                     "utils_references": {
-                        "branch": "master",
-                        "git_sha": "c18de39a419659720e2482df14df21affdc30f47",
+                        "branch": "main",
+                        "git_sha": "a11fa6f50d4247444be6904e83a627d0fc032b9f",
                         "installed_by": ["subworkflows"]
                     }
                 }

nextflow.config

@@ -11,6 +11,7 @@ params {
     // Input options
     input                       = null
     tools                       = null
+    references_basepath         = null
 
     // Asset creation options
     kallisto_make_unique        = false
@@ -268,7 +269,7 @@ manifest {
 
 // Nextflow plugins
 plugins {
-    id 'nf-schema@2.2.1' // Validation of pipeline parameters and creation of an asset channel from a asset yaml file
+    id 'nf-schema@2.4.1' // Validation of pipeline parameters and creation of an asset channel from a asset yaml file
 }
 
 validation {

nextflow_schema.json

@@ -16,7 +16,7 @@
                     "type": "string",
                     "format": "file-path",
                     "exists": true,
-                    "schema": "subworkflows/nf-core/utils_references/schema_references.json",
+                    "schema": "subworkflows/nf-side/utils_references/schema_references.json",
                     "mimetype": "text/csv",
                     "pattern": "^\\S+\\.(yaml|yml)$",
                     "description": "Path to yaml file containing information about the genome(s) and files to use for building references.",
@@ -36,6 +36,11 @@
                     "help_text": "Multiple tools separated with commas.",
                     "pattern": "^((bowtie1|bowtie2|bwamem1|bwamem2|createsequencedictionary|dragmap|faidx|gffread|hisat2|hisat2_extractsplicesites|intervals|kallisto|msisensorpro|rsem|rsem_make_transcript_fasta|salmon|sizes|star|tabix)?,?)*(?<!,)$"
                 },
+                "references_basepath": {
+                    "type": "string",
+                    "description": "The basepath to replace in the asset yaml file.",
+                    "fa_icon": "fas fa-folder-open"
+                },
                 "email": {
                     "type": "string",
                     "description": "Email address for completion summary.",