--fasta no longer required and --input not required with --build_refe…

…rences

conf/genomes.config

@@ -36,7 +36,6 @@ params {
             squid_ref                     = "${params.genomes_base}/squid"
             starfusion_ref                = "${params.genomes_base}/starfusion"
             starindex_ref                 = "${params.genomes_base}/star"
-
         }
     }
 }

main.nf

@@ -17,7 +17,6 @@ nextflow.enable.dsl = 2
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 */
 
-params.fasta             = WorkflowMain.getGenomeAttribute(params, 'fasta')
 params.genomes_base      = WorkflowMain.getGenomeAttribute(params, 'genomes_base')
 
 

modules.json

@@ -53,4 +53,4 @@
             }
         }
     }
-}
+}

nextflow.config

@@ -10,8 +10,8 @@
 params {
 
     // Input options
-    input                      = null
-    fasta                      = null
+    input                      = "fake_input_to_build_refs.csv"
+    fasta                      = "${params.ensembl_ref}/Homo_sapiens.GRCh38.${params.ensembl_version}.all.fa"
     build_references           = false
     cosmic_username            = null
     cosmic_passwd              = null
@@ -23,7 +23,7 @@ params {
 
     // Genome
     genome                     = 'GRCh38'
-    genomes_base               = null
+    genomes_base               = "${params.outdir}/references"
     ensembl_version            = 105
     read_length                = 100
     genomes                    = [:]
@@ -37,7 +37,6 @@ params {
     // Enable or disable tools
     all                        = false
     arriba                     = false
-    ericscript                 = false
     fusioncatcher              = false
     pizzly                     = false
     squid                      = false
@@ -52,7 +51,6 @@ params {
     // Path to references
     arriba_ref                    = "${params.genomes_base}/arriba"
     ensembl_ref                   = "${params.genomes_base}/ensembl"
-    ericscript_ref                = "${params.genomes_base}/ericscript/homo_sapiens"
     fusioncatcher_ref             = "${params.genomes_base}/fusioncatcher/human_v102"
     pizzly_ref                    = "${params.genomes_base}/pizzly"
     squid_ref                     = "${params.genomes_base}/squid"
@@ -69,18 +67,19 @@ params {
     fusioncatcher_fusions         = null
 
     // Boilerplate options
-    outdir                     = null
-    tracedir                   = "${params.outdir}/pipeline_info"
-    publish_dir_mode           = 'copy'
-    email                      = null
-    email_on_fail              = null
-    plaintext_email            = false
-    monochrome_logs            = false
-    help                       = false
-    validate_params            = true
-    show_hidden_params         = false
-    schema_ignore_params       = 'genomes'
-    enable_conda               = false
+    outdir                            = './results'
+    tracedir                          = "${params.outdir}/pipeline_info"
+    publish_dir_mode                  = 'copy'
+    email                             = null
+    email_on_fail                     = null
+    plaintext_email                   = false
+    monochrome_logs                   = false
+    help                              = false
+    validate_params                   = true
+    show_hidden_params                = false
+    schema_ignore_params              = 'genomes'
+    enable_conda                      = false
+    singularity_pull_docker_container = false
 
     // Config options
     custom_config_version      = 'master'

nextflow_schema.json

@@ -103,16 +103,6 @@
                     "fa_icon": "far fa-file-code",
                     "description": "Path to ensembl references"
                 },
-                "ericscript": {
-                    "type": "boolean",
-                    "fa_icon": "far fa-file-code",
-                    "description": "Build or run ericscript references/analyses"
-                },
-                "ericscript_ref": {
-                    "type": "string",
-                    "fa_icon": "far fa-file-code",
-                    "description": "Path to ericscript references"
-                },
                 "fusioncatcher": {
                     "type": "boolean",
                     "fa_icon": "far fa-file-code",
@@ -394,6 +384,12 @@
                     "hidden": true,
                     "fa_icon": "fas fa-bacon"
                 },
+                "singularity_pull_docker_container": {
+                    "type": "boolean",
+                    "description": "Use to pull docker containers to run with singularity",
+                    "hidden": true,
+                    "fa_icon": "fas fa-bacon"
+                },
                 "seq_center": {
                     "type": "boolean",
                     "description": "Sequencing center",

workflows/rnafusion.nf

@@ -9,23 +9,9 @@ def summary_params = NfcoreSchema.paramsSummaryMap(workflow, params)
 // Validate input parameters
 WorkflowRnafusion.initialise(params, log)
 
-// TODO nf-core: Add all file path parameters for the pipeline to the list below
-// Check input path parameters to see if they exist
-
-
-def checkPathParamList = [
-    params.input, params.multiqc_config,
-    params.fasta, params.genomes_base,
-    params.ensembl_ref,
-    params.fusioncatcher_ref, params.starfusion_ref,
-    params.arriba_ref, params.starindex_ref,
-    params.ensembl_version
-]
-
-
 // Check mandatory parameters
-if (params.input) { ch_input = file(params.input) } else { exit 1, 'Input samplesheet not specified!' }
 
+if (file(params.input).exists() || params.build_references) { ch_input = file(params.input) } else { exit 1, 'Input samplesheet does not exist or was not specified!' }
 
 /*
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~