Merge branch 'master' of github.com:sequana/demultiplex

sequana · Nov 19, 2021 · c982243 · c982243
2 parents 8bd2db6 + 70e02b1
commit c982243
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diff --git a/README.rst b/README.rst
@@ -114,6 +114,7 @@ Changelog
 Version   Description
 ========= =======================================================================
 1.1.2     * add the --mars-seq option that fills the config automatically
+          * fix the none_and_force merging strategy option
 1.1.1     * fix a regression bug
 1.1.0     * Uses new sequana-wrappers repository
 1.0.5     * Fix regression bug to cope with new snakemake API

diff --git a/doc/wiki/different_L1L2_merge_nomerge/L1L2_fastq_merging.png b/doc/wiki/different_L1L2_merge_nomerge/L1L2_fastq_merging.png
diff --git a/doc/wiki/different_L1L2_merge_nomerge/L1L2_fastqc_nomerging.png b/doc/wiki/different_L1L2_merge_nomerge/L1L2_fastqc_nomerging.png
diff --git a/doc/wiki/different_L1L2_merge_nomerge/L1L2_undetermined.png b/doc/wiki/different_L1L2_merge_nomerge/L1L2_undetermined.png
diff --git a/doc/wiki/different_L1L2_merge_nomerge/README.md b/doc/wiki/different_L1L2_merge_nomerge/README.md
@@ -0,0 +1,3 @@
+In this example, we had a NextSeq run with two lanes. The Lanes should be merged in theory. 
+We got a relatively good quality. However, the ratio of determined/undetermined in one of the lane was suspicious. 
+We decided to remove the merging. It appeare that one of the lane was faulty.
diff --git a/sequana_pipelines/demultiplex/main.py b/sequana_pipelines/demultiplex/main.py
@@ -155,7 +155,7 @@ def main(args=None):
         with open(runparam, "r") as fin:
             data = fin.read()
             if "NextSeq" in data and options.merging_strategy != "merge":
-                if otions.merging_strategy == "none_and_force":
+                if options.merging_strategy == "none_and_force":
                     msg = "This is a NextSeq. You set the --merging-strategy to"
                     msg += " none_and_force. So, we proceed with no merging strategy"
                     logger.warning(msg)