Merge pull request #420 from nf-core/fix_ref_build

Fix ref build

CHANGELOG.md

@@ -10,10 +10,13 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 ### Changed
 
 - Removed `--fusioninspector_filter` and `--fusionreport_filter` in favor of `--tools_cutoff` (default = 1, no filters applied) [#389](https://github.com/nf-core/rnafusion/pull/389)
+- Now publishing convert2bed output to convert2bed to keep the output file for mosdepth [#420](https://github.com/nf-core/rnafusion/pull/420)
+- No more checks for existence of samplesheet, which made building references fail (building references uses a fake sample sheet if none is provided) [#420](https://github.com/nf-core/rnafusion/pull/420)
 
 ### Fixed
 
 - Fix channel i/o issue in StringTie workflow and add StringTie in github CI tests [#416](https://github.com/nf-core/rnafusion/pull/416)
+- Updated COSMIC database to fix 404 error while downloading fusionreport references [#420](https://github.com/nf-core/rnafusion/pull/420)
 
 ### Removed
 

conf/modules.config

@@ -45,6 +45,14 @@ process {
         ]
     }
 
+    withName: CONVERT2BED {
+        publishDir = [
+            path: { "${params.genomes_base}/convert2bed" },
+            mode: params.publish_dir_mode,
+            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
+        ]
+    }
+
     withName: CUSTOM_DUMPSOFTWAREVERSIONS {
         publishDir = [
             path: { "${params.outdir}/pipeline_info" },
@@ -178,11 +186,6 @@ process {
         ext.when         = { !params.skip_qc && !params.fusioninspector_only && (params.starfusion || params.all)}
     }
 
-    withName: REFORMAT {
-        ext.args = "forcetrimright=75"
-        ext.args2 = "forcetrimleft=75"
-    }
-
     withName: SAMPLESHEET_CHECK {
         publishDir = [
             path: { "${params.outdir}/pipeline_info" },

modules/local/fusionreport/detect/main.nf

@@ -4,7 +4,7 @@ process FUSIONREPORT {
 
     // Note: 2.7X indices incompatible with AWS iGenomes.
     conda "bioconda::star=2.7.9a"
-    container "docker.io/clinicalgenomics/fusion-report:2.1.5p4"
+    container "docker.io/clinicalgenomics/fusion-report:2.1.5p5"
 
 
     input:

modules/local/fusionreport/download/main.nf

@@ -4,7 +4,7 @@ process FUSIONREPORT_DOWNLOAD {
 
     // Note: 2.7X indices incompatible with AWS iGenomes.
     conda "bioconda::star=2.7.9a"
-    container "docker.io/clinicalgenomics/fusion-report:2.1.5p4"
+    container "docker.io/clinicalgenomics/fusion-report:2.1.5p5"
 
     input:
     val(username)

nextflow_schema.json

@@ -32,7 +32,6 @@
                 "input": {
                     "type": "string",
                     "format": "file-path",
-                    "exists": true,
                     "mimetype": "text/csv",
                     "pattern": "^\\S+\\.csv$",
                     "description": "Path to comma-separated file containing information about the samples in the experiment.",