Merge pull request #639 from asp8200/extend_output_from_snpeff

DRAFT: Extending output from snpEff

Author: FriederikeHanssen

conf/modules.config

@@ -1147,10 +1147,12 @@ process{
             ext.args          = '-nodownload -canon -v'
             if (!params.snpeff_cache) container = { params.snpeff_genome ? "nfcore/snpeff:${params.snpeff_version}.${params.snpeff_genome}" : "nfcore/snpeff:${params.snpeff_version}.${params.genome}" }
             publishDir       = [
-                mode: params.publish_dir_mode,
-                path: { "${params.outdir}/reports/SnpEff/${meta.id}/${meta.variantcaller}" },
-                pattern: "*csv",
-                saveAs: { params.tools.contains('snpeff') ? it : null }
+                [
+                    mode: params.publish_dir_mode,
+                    path: { "${params.outdir}/reports/snpeff/${meta.id}/${meta.variantcaller}" },
+                    pattern: "*{csv,html,genes.txt}",
+                    saveAs: { params.tools.contains('snpeff') ? it : null }
+                ]
             ]
         }
     }

modules.json

@@ -214,7 +214,7 @@
                 "git_sha": "6b64f9cb6c3dd3577931cc3cd032d6fb730000ce"
             },
             "snpeff": {
-                "git_sha": "d8bef6057bc2cf657d33ed496426be8416edd780"
+                "git_sha": "ffe037504897df081a7497fa5f495d8e23e93e24"
             },
             "strelka/germline": {
                 "git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d"

modules/nf-core/modules/snpeff/main.nf

@@ -6,7 +6,9 @@
   files:
     - path: results/annotation/test/test_snpEff.ann.vcf.gz
     - path: results/annotation/test/test_snpEff.ann.vcf.gz.tbi
-    - path: results/reports/SnpEff/test/test_snpEff.csv
+    - path: results/reports/snpeff/test/test_snpEff.csv
+    - path: results/reports/snpeff/test/snpEff_summary.html
+    - path: results/reports/snpeff/test/test_snpEff.genes.txt
     - path: results/multiqc
 - name: Run VEP
   command: nextflow run main.nf -profile test,annotation,docker --tools vep --skip_tools multiqc

modules/nf-core/modules/snpeff/meta.yml

@@ -1095,7 +1095,7 @@ def extract_csv(csv_file) {
                 System.exit(1)
             }
         } else if ((sample_count_tumor == sample_count_all) && params.tools) {  // In this case, the sample-sheet contains no normal/germline-samples
-            def tools_requiring_normal_samples = ['ascat', 'deepvariant', 'haplotypecaller']
+            def tools_requiring_normal_samples = ['ascat', 'deepvariant', 'haplotypecaller', 'msisensorpro']
             def requested_tools_requiring_normal_samples = []
             tools_requiring_normal_samples.each{ tool_requiring_normal_samples ->
                 if (params.tools.contains(tool_requiring_normal_samples)) requested_tools_requiring_normal_samples.add(tool_requiring_normal_samples)