Merge pull request #264 from MaxUlysse/dsl2_preprocessing

Improvment on preprocessing
nf-core · Aug 6, 2020 · a7679b9 · a7679b9
2 parents 7c2150e + 25661e0
commit a7679b9
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Showing 6 changed files with 181 additions and 274 deletions.
diff --git a/conf/modules.config b/conf/modules.config
@@ -9,7 +9,7 @@ params {
         'fastqc' {
             args             = "--quiet"
             suffix           = ""
-            publish_dir      = "fastqc"
+            publish_dir      = "Reports/FastQC"
             publish_results  = "all"
         }
         'trimgalore' {
@@ -32,6 +32,18 @@ params {
             publish_dir      = ""
             publish_results  = "all"
         }
+        'samtools_index_mapped' {
+            args             = ""
+            suffix           = ""
+            publish_dir      = "Mapped"
+            publish_results  = "all"
+        }
+        'samtools_index_recal' {
+            args             = ""
+            suffix           = "recal"
+            publish_dir      = ""
+            publish_results  = "all"
+        }
         'gatk_markduplicates' {
             args             = "ASSUME_SORTED=true REMOVE_DUPLICATES=false VALIDATION_STRINGENCY=LENIENT TMP_DIR=tmp"
             suffix           = ".mLb.mkD"