Merge pull request #366 from kedhammar/10x-comments

Add 10X steps to comments-to-running-notes config
NationalGenomicsInfrastructure · Sep 25, 2024 · b3ee9b3 · b3ee9b3
2 parents e1656a1 + b591a97
commit b3ee9b3
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Showing 2 changed files with 29 additions and 16 deletions.
diff --git a/VERSIONLOG.md b/VERSIONLOG.md
@@ -1,5 +1,9 @@
 # Scilifelab_epps Version Log
 
+## 20240925.1
+
+Add 10X steps to comments-to-running-notes config.
+
 ## 20240924.1
 
 Fix bug with data type in frag_an_driver_gen

diff --git a/scripts/comments_to_running_notes.py b/scripts/comments_to_running_notes.py
@@ -14,6 +14,15 @@
 
 def categorization(process_name):
     decision = {
+        "10X Chromium Generic: cDNA QC": "Workset",
+        "10X Chromium Generic: Finish GEM Processing": "Workset",
+        "10X Chromium Generic: Finish Library Processing": "Workset",
+        "10X Chromium Generic: GEM Cleanup": "Workset",
+        "10X Chromium Generic: GEM Generation": "Workset",
+        "10X Chromium Generic: Library Construction": "Workset",
+        "10X Chromium Generic: Library Purification": "Workset",
+        "10X Chromium Generic: Pre-GEM Processing": "Workset",
+        "10X Chromium Generic: Pre-Library Processing": "Workset",
         "Adapter ligation and reverse transcription": "Workset",
         "Aggregate QC (DNA) 4.0": "Workset",
         "Aggregate QC (Library Validation) 4.0": "Workset",
@@ -24,9 +33,9 @@ def categorization(process_name):
         "Aliquot Samples for Qubit/Bioanalyzer": "Workset",
         "Amplification and Purification": "Workset",
         "Amplify Adapter-Ligated Library (SS XT) 4.0": "",
-        "Amplify Captured Libraries to Add Index Tags (SS XT) 4.0": "",
-        "Amplify by PCR and Add Index Tags": "Workset",
         "Amplify by PCR and Add Index Tags (TruSeq small RNA) 1.0": "Workset",
+        "Amplify by PCR and Add Index Tags": "Workset",
+        "Amplify Captured Libraries to Add Index Tags (SS XT) 4.0": "",
         "AMPure Size Selection": "Workset",
         "Applications Generic Process": "Workset",
         "Applications Indexing": "Workset",
@@ -38,20 +47,20 @@ def categorization(process_name):
         "Bioanalyzer QC (DNA) 4.0": "Workset",
         "Bioanalyzer QC (Library Validation) 4.0": "Workset",
         "Bioanalyzer QC (RNA) 4.0": "Workset",
-        "cDNA QC": "",
         "CA Purification": "Workset",
         "CaliperGX QC (DNA)": "",
         "CaliperGX QC (RNA)": "",
         "Capture And Wash (SS XT) 4.0": "Workset",
+        "cDNA QC": "",
         "Chromatin capture, digestion, end ligation and crosslink reversal (HiC) 1.0": "",
         "Circularization": "Workset",
         "Cluster Generation (HiSeq X) 1.0": "Flowcell",
         "Cluster Generation (Illumina SBS) 4.0": "Flowcell",
         "Crosslinking & Digestion": "",
         "Customer Gel QC": "Workset",
         "Denature, Dilute and Load Sample (MiSeq) 4.0": "Flowcell",
-        "End Repair, A-Tailing and Adapter Ligation (SS XT) 4.0": "Workset",
         "End repair, A-tailing and adapter ligation (Nextera) 4.0": "Workset",
+        "End Repair, A-Tailing and Adapter Ligation (SS XT) 4.0": "Workset",
         "End repair, A-tailing and adapter ligation (TruSeq RNA) 4.0": "Workset",
         "End repair, adapter ligation, ligation capture and Index PCR (HiC)": "",
         "End repair, size selection, A-tailing and adapter ligation (TruSeq PCR-free DNA) 4.0": "Workset",
@@ -64,23 +73,23 @@ def categorization(process_name):
         "Fragmentation & cDNA synthesis (TruSeq RNA) 4.0": "Workset",
         "g-Tube Fragmentation": "Workset",
         "Generic QC": "",
-        "HT-End repair, A-tailing and adapter ligation (TruSeq RNA) 4.0": "Workset",
         "HiC Intermediate QC": "",
+        "HT-End repair, A-tailing and adapter ligation (TruSeq RNA) 4.0": "Workset",
         "Hybridize Library  (SS XT) 4.0": "",
-        "Illumina DNA PCR-free Library Construction": "Workset",
         "Illumina DNA No-QC Library Construction": "Workset",
         "Illumina DNA No-QC Library Pooling": "Workset",
+        "Illumina DNA PCR-free Library Construction": "Workset",
         "Illumina Sequencing (HiSeq X) 1.0": "Flowcell",
         "Illumina Sequencing (Illumina SBS) 4.0": "Flowcell",
         "Illumina Sequencing (NextSeq) v1.0": "Flowcell",
         "Intermediate QC": "",
-        "Library Normalization": "",
         "Library Normalization (AVITI) v1.0": "",
         "Library Normalization (Illumina SBS) 4.0": "",
         "Library Normalization (MiSeq) 4.0": "",
         "Library Normalization (NextSeq) v1.0": "",
         "Library Normalization (NovaSeq) v2.0": "",
         "Library Normalization (NovaSeqXPlus) v1.0": "",
+        "Library Normalization": "",
         "Library Pooling (Finished Libraries) 4.0": "",
         "Library Pooling (Illumina SBS) 4.0": "",
         "Library Pooling (MiSeq) 4.0": "",
@@ -91,44 +100,44 @@ def categorization(process_name):
         "Ligate 5' adapters (TruSeq small RNA) 1.0": "Workset",
         "Linear DNA digestion, Circularized DNA shearing and Streptavidin Bead Binding": "Workset",
         "Load to Flowcell (NextSeq v1.0)": "",
-        "mRNA Purification, Fragmentation & cDNA synthesis (TruSeq RNA) 4.0": "Workset",
         "MinElute Purification": "",
         "MinION QC": "Workset",
         "MiSeq Run (MiSeq) 4.0": "Flowcell",
+        "mRNA Purification, Fragmentation & cDNA synthesis (TruSeq RNA) 4.0": "Workset",
         "NeoPrep Library QC v1.0": "Workset",
         "ONT Adapter ligation v2.0": "Workset",
         "ONT Barcoding": "Workset",
         "ONT End-Prep v2.0": "Workset",
         "ONT Finish Sequencing v2.1": "Flowcell",
         "ONT Pooling v2.0": "Workset",
-        "ONT Sequencing and Reloading v3.1": "Flowcell",
-        "ONT Start Sequencing v3.0": "Flowcell",
         "ONT QC Adapter Ligation v1.2": "",
         "ONT QC Analysis": "",
         "ONT QC Barcoding v1.2": "",
         "ONT QC End-prep v1.2": "",
         "ONT QC Pooling v1.2": "",
         "ONT QC Setup Workset/Plate": "",
         "ONT QC Start Sequencing": "Flowcell",
-        "Pre-Pooling": "",
+        "ONT Sequencing and Reloading v3.1": "Flowcell",
+        "ONT Start Sequencing v3.0": "Flowcell",
         "Pre-Pooling (AVITI) v1.0": "",
         "Pre-Pooling (Illumina SBS) 4.0": "",
         "Pre-Pooling (MiSeq) 4.0": "",
         "Pre-Pooling (NextSeq) v1.0": "",
         "Pre-Pooling (NovaSeq) v2.0": "",
         "Pre-Pooling (NovaSeqXPlus) v1.0": "",
+        "Pre-Pooling": "",
         "Project Summary 1.3": "",
         "PromethION Sequencing": "",
         "Proximity Ligation": "",
-        "Purification": "Workset",
         "Purification (ThruPlex)": "Workset",
+        "Purification": "Workset",
         "qPCR QC (Dilution Validation) 4.0": "",
         "qPCR QC (Library Validation) 4.0": "",
         "Quant-iT QC (DNA) 4.0": "Workset",
         "Quant-iT QC (Library Validation) 4.0": "Workset",
         "Quant-iT QC (RNA) 4.0": "Workset",
-        "Qubit QC (DNA) 4.0": "Workset",
         "Qubit QC (Dilution Validation) 4.0": "Workset",
+        "Qubit QC (DNA) 4.0": "Workset",
         "Qubit QC (Library Validation) 4.0": "Workset",
         "Qubit QC (RNA) 4.0": "Workset",
         "RAD-seq Library Indexing v1.0": "",
@@ -151,14 +160,14 @@ def categorization(process_name):
         "Sort NextSeq Samples (NextSeq) v1.0": "",
         "Sort NovaSeq Samples (NovaSeq) v2.0": "",
         "Sort NovaSeqXPlus Samples (NovaSeqXPlus) v1.0": "",
-        "Sort Samples for Norm/Pooling": "",
         "Sort Samples (ONT Pre-Prep)": "Workset",
         "Sort Samples (ONT Seq)": "Workset",
+        "Sort Samples for Norm/Pooling": "",
         "Tagmentation, Strand displacement and AMPure purification": "Workset",
-        "Tissue Extraction": "",
-        "Tissue QC": "",
         "ThruPlex library amplification": "Workset",
         "ThruPlex template preparation and synthesis": "Workset",
+        "Tissue Extraction": "",
+        "Tissue QC": "",
         "Volume Measurement QC": "Workset",
     }