Revert "fix vcf_collect when a tool is absent"

This reverts commit f5a1c41.
nf-core · Dec 20, 2023 · 0ccea2e · 0ccea2e
1 parent f5a1c41
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -3,18 +3,6 @@
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/)
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
-## v3.0.2 - [date]
-
-### Added
-
-### Changed
-
-### Fixed
-
-- fix VCF_COLLECT handling when a tool is absent from FUSIONREPORT report
-
-### Removed
-
 ## v3.0.1 - [2023-11-29]
 
 ### Added

diff --git a/assets/multiqc_config.yml b/assets/multiqc_config.yml
@@ -1,7 +1,7 @@
 report_comment: >
-  This report has been generated by the <a href="https://github.com/nf-core/rnafusion/releases/tag/dev" target="_blank">nf-core/rnafusion</a>
+  This report has been generated by the <a href="https://github.com/nf-core/rnafusion/releases/tag/3.0.1" target="_blank">nf-core/rnafusion</a>
   analysis pipeline. For information about how to interpret these results, please see the
-  <a href="https://nf-co.re/rnafusion/dev/docs/output" target="_blank">documentation</a>.
+  <a href="https://nf-co.re/rnafusion/3.0.1/docs/output" target="_blank">documentation</a>.
 
 report_section_order:
   nf-core-rnafusion-methods-description:

diff --git a/bin/vcf_collect.py b/bin/vcf_collect.py
@@ -346,11 +346,8 @@ def read_build_fusionreport(fusionreport_file: str) -> pd.DataFrame:
 
 def read_fusionreport_csv(file: str) -> pd.DataFrame:
     df = pd.read_csv(file)
-    columns_to_iterate = ["starfusion", "arriba", "fusioncatcher"]
-    for column in columns_to_iterate:
-        if column not in df.columns:
-            df[column] = ""
     df[["starfusion", "arriba", "fusioncatcher"]] = df[["starfusion", "arriba", "fusioncatcher"]].astype("str")
+    columns_to_iterate = ["starfusion", "arriba", "fusioncatcher"]
     for index, row in df.iterrows():
         for column in columns_to_iterate:
             cell_value = row[column]

diff --git a/nextflow.config b/nextflow.config
@@ -290,7 +290,7 @@ manifest {
     description     = """Nextflow rnafusion analysis pipeline, part of the nf-core community."""
     mainScript      = 'main.nf'
     nextflowVersion = '!>=23.04.0'
-    version = '3.0.2dev'
+    version = '3.0.1'
     doi             = ''
 }