Rip out 10x auto-detection. It was broken anyway as it was

using the old barcode sets
EdinburghGenomics · Dec 18, 2024 · 8e790f7 · 8e790f7
1 parent 6ce3d35
commit 8e790f7
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Showing 6 changed files with 6 additions and 392 deletions.
diff --git a/10x_barcodes/Chromium-i7-Multiplex-Kit-N-Set-A-sample-indexes-plate.csv b/10x_barcodes/Chromium-i7-Multiplex-Kit-N-Set-A-sample-indexes-plate.csv
diff --git a/10x_barcodes/chromium-shared-sample-indexes-plate.csv b/10x_barcodes/chromium-shared-sample-indexes-plate.csv
diff --git a/count_10x_barcodes.py b/count_10x_barcodes.py
diff --git a/driver.sh b/driver.sh
@@ -289,8 +289,6 @@ action_demultiplexed() {
 
     set +e
 
-    detect_and_keep_10x |& plog
-
     # In certain cases read1_qc can make a 1-tile report with a later timestamp than the full
     # bcl2fastq output and the reduced numbers end up in the final report. To be sure, touch all
     # the real Stats.json files so Snakemake sees they are new and picks them up.
@@ -680,18 +678,6 @@ send_summary_to_rt() {
            || echo "Error while summarizing lane contents." ) ) 2>&1
 }
 
-detect_and_keep_10x() {
-    # Attempt to avoid accidental deletion of 10x runs following the incident where
-    # they were left unprocessed and the run was deleted.
-    # Note this might resonably fail so set +e before running it, and redirect outputs
-    # to the plog.
-    if count_10x_barcodes.py "$DEMUX_OUTPUT_FOLDER"/demultiplexing/lane*/Stats/Stats.json ; then
-        echo "10X barcodes detected, so adding pipeline/keep file"
-        ( set -o noclobber ;
-          echo "10X barcodes detected by Illuminatus" > pipeline/keep )
-    fi
-}
-
 run_qc() {
     # At present, this is only ever called by action_demultiplexed.
     # If qc failed, the ticket subject will be 'failed' so reset it (but an RT error should not be fatal).

diff --git a/test/test_count_10x_barcodes.py b/test/test_count_10x_barcodes.py