Merge branch 'dev' into fusion_report_optional_cosmic

nf-core · Nov 29, 2024 · c5ed11b · c5ed11b
2 parents cb6671b + 228f5f4
commit c5ed11b
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Showing 11 changed files with 169 additions and 7 deletions.
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -13,12 +13,15 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - Add nf-test to local module: `ENSEMBL_DOWNLOAD` [#539](https://github.com/nf-core/rnafusion/pull/539)
 - Add nf-test to local module: `HGNC_DOWNLOAD` [#540](https://github.com/nf-core/rnafusion/pull/540)
 - Option to avoid using COSMIC (for example in the case of clinical use) [547](https://github.com/nf-core/rnafusion/pull/547)
+- Add nf-test to nf-core module: `PICARD_COLLECTRNASEQMETRICS` and update module [#551](https://github.com/nf-core/rnafusion/pull/551)
+- Add `--skip_vcf` boolean parameter to skip vcf file generation [#554](https://github.com/nf-core/rnafusion/pull/554)
 
 ### Changed
 
 - Updated modules and migrated non-specific modules to nf-core/modules [#484](https://github.com/nf-core/rnafusion/pull/484)
 - Updated to nf-core/tools 3.0.2 [#504](https://github.com/nf-core/rnafusion/pull/504)
 - Remove local module `RRNA_TRANSCRIPTS` (replaced by nf-core module) [#541](https://github.com/nf-core/rnafusion/pull/541)
+- Allow fastq files without a dot before .fn(.gz)/.fastq(.gz) files [#548](https://github.com/nf-core/rnafusion/pull/548)
 
 ### Fixed
 

diff --git a/assets/schema_input.json b/assets/schema_input.json
@@ -17,14 +17,14 @@
                 "type": "string",
                 "format": "file-path",
                 "exists": true,
-                "pattern": "^\\S+\\.f(ast)?q\\.gz$",
+                "pattern": "^\\S+f(ast)?q\\.gz$",
                 "errorMessage": "FastQ file for reads 1 must be provided, cannot contain spaces and must have extension '.fq.gz' or '.fastq.gz'"
             },
             "fastq_2": {
                 "type": "string",
                 "format": "file-path",
                 "exists": true,
-                "pattern": "^\\S+\\.f(ast)?q\\.gz$",
+                "pattern": "^\\S+f(ast)?q\\.gz$",
                 "errorMessage": "FastQ file for reads 2 cannot contain spaces and must have extension '.fq.gz' or '.fastq.gz'"
             },
             "strandedness": {

diff --git a/conf/modules.config b/conf/modules.config
@@ -356,6 +356,6 @@ process {
     }
 
     withName: 'VCF_COLLECT' {
-        ext.when = {!params.fusioninspector_only}
+        ext.when = { {!params.fusioninspector_only} && {!params.skip_vcf} }
     }
 }
diff --git a/modules.json b/modules.json
@@ -77,7 +77,7 @@
                     },
                     "picard/collectrnaseqmetrics": {
                         "branch": "master",
-                        "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
+                        "git_sha": "49f4e50534fe4b64101e62ea41d5dc43b1324358",
                         "installed_by": ["modules"]
                     },
                     "picard/collectwgsmetrics": {

diff --git a/modules/nf-core/picard/collectrnaseqmetrics/environment.yml b/modules/nf-core/picard/collectrnaseqmetrics/environment.yml
diff --git a/modules/nf-core/picard/collectrnaseqmetrics/main.nf b/modules/nf-core/picard/collectrnaseqmetrics/main.nf
diff --git a/modules/nf-core/picard/collectrnaseqmetrics/tests/main.nf.test b/modules/nf-core/picard/collectrnaseqmetrics/tests/main.nf.test
diff --git a/modules/nf-core/picard/collectrnaseqmetrics/tests/main.nf.test.snap b/modules/nf-core/picard/collectrnaseqmetrics/tests/main.nf.test.snap
diff --git a/modules/nf-core/picard/collectrnaseqmetrics/tests/nextflow.config b/modules/nf-core/picard/collectrnaseqmetrics/tests/nextflow.config
diff --git a/nextflow.config b/nextflow.config
@@ -71,6 +71,7 @@ params {
     // Skip steps
     skip_qc                    = false
     skip_vis                   = false
+    skip_vcf                   = false
 
     // Path to references
     no_cosmic                     = false

diff --git a/nextflow_schema.json b/nextflow_schema.json
@@ -18,6 +18,10 @@
                 "skip_vis": {
                     "type": "boolean",
                     "description": "Skip visualisation steps"
+                },
+                "skip_vcf": {
+                    "type": "boolean",
+                    "description": "Skip vcf generation step"
                 }
             },
             "fa_icon": "fas fa-fast-forward"