added docu on bed input

rki-mf1 · Sep 15, 2022 · 6916906 · 6916906
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -10,6 +10,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 ### Added
 
 - '--bamclipper_additional_parameters' option to adjust BAMClipper parameters
+- documentation on how names in the input BED file have to be to automatically generate a BEDPE file
 
 ## [0.2.7] 2022-08-23
 

diff --git a/CoVpipe2.nf b/CoVpipe2.nf
@@ -402,7 +402,8 @@ def helpMSG() {
                                  ${c_dim}TAB-delimited text file containing at least 6 fields, see here:
                                  https://bedtools.readthedocs.io/en/latest/content/general-usage.html#bedpe-format${c_reset}
     OR
-    --primer_bed             Provide the path to the primer BED file. [default: $params.primer_bed]
+    --primer_bed             Provide the path to the primer BED file. A BEDPE file will be generated automatically.
+                                 The name of each entry has to match this pattern: primerID[_LEFT|_RIGHT]_ampliconID [default: $params.primer_bed]
     OR
     --primer_version         Provide a primer version. Currently supported ARTIC versions: V1, V2, V3, V4, V4.1 [default: $params.primer_version]
 

diff --git a/README.md b/README.md
@@ -181,7 +181,8 @@ Robert Koch Institute, MF1 Bioinformatics
                                  TAB-delimited text file containing at least 6 fields, see here:
                                  https://bedtools.readthedocs.io/en/latest/content/general-usage.html#bedpe-format
     OR
-    --primer_bed             Provide the path to the primer BED file. [default: false]
+    --primer_bed             Provide the path to the primer BED file. A BEDPE file will be generated automatically.
+                                 The name of each entry has to match this pattern: primerID[_LEFT|_RIGHT]_ampliconID [default: false]
     OR
     --primer_version         Provide a primer version. Currently supported ARTIC versions: V1, V2, V3, V4, V4.1 [default: false]