Add quantification command expander to Run Pipeline tab, revert Analysis tab change

Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>

Author: garrettc00per

RNA-seq Processor.app/Contents/Resources/app/app.py

@@ -1213,6 +1213,21 @@ def update_progress(msg):
                 est_minutes = 1
             st.info(f"⏱️ Estimated processing time: **~{est_minutes} minutes** for {n_samples} samples at {threads} threads")
 
+            with st.expander("View quantification command"):
+                st.code(
+                    f"salmon quant \\\n"
+                    f"  --index <index_dir> \\\n"
+                    f"  --libType A \\\n"
+                    f"  --mates1 <R1.fastq.gz> \\\n"
+                    f"  --mates2 <R2.fastq.gz> \\\n"
+                    f"  --output <output_dir> \\\n"
+                    f"  --threads {threads} \\\n"
+                    f"  --validateMappings \\\n"
+                    f"  --gcBias \\\n"
+                    f"  --seqBias",
+                    language="bash"
+                )
+
             # Run button
             if st.button("🚀 Start Quantification", type="primary", disabled=st.session_state.pipeline_running):
                 st.session_state.pipeline_running = True
@@ -1772,15 +1787,6 @@ def run_pipeline_thread():
         3. Run analysis
         """)
 
-        st.info(
-            "**What's running under the hood:** Salmon (quasi-mapping) quantifies reads at the "
-            "transcript level. tximport summarizes to gene-level counts using the "
-            "`lengthScaledTPM` method. DESeq2 normalizes counts (median-of-ratios), applies "
-            "variance stabilizing transformation (VST) for PCA, and runs Wald tests for "
-            "differential expression. GSEA is performed with fgsea using pre-ranked gene lists "
-            "(ranked by log2 fold change)."
-        )
-
         with st.expander("View analysis code (analysis.R)"):
             r_script = Path(__file__).parent / "analysis.R"
             if r_script.exists():

app.py

@@ -1285,6 +1285,21 @@ def update_progress(msg):
                 est_minutes = 1
             st.info(f"⏱️ Estimated processing time: **~{est_minutes} minutes** for {n_samples} samples at {threads} threads")
 
+            with st.expander("View quantification command"):
+                st.code(
+                    f"salmon quant \\\n"
+                    f"  --index <index_dir> \\\n"
+                    f"  --libType A \\\n"
+                    f"  --mates1 <R1.fastq.gz> \\\n"
+                    f"  --mates2 <R2.fastq.gz> \\\n"
+                    f"  --output <output_dir> \\\n"
+                    f"  --threads {threads} \\\n"
+                    f"  --validateMappings \\\n"
+                    f"  --gcBias \\\n"
+                    f"  --seqBias",
+                    language="bash"
+                )
+
             # Run button
             if st.button("🚀 Start Quantification", type="primary", disabled=st.session_state.pipeline_running):
                 st.session_state.pipeline_running = True
@@ -1875,15 +1890,6 @@ def run_pipeline_thread():
         3. Run analysis
         """)
 
-        st.info(
-            "**What's running under the hood:** Salmon (quasi-mapping) quantifies reads at the "
-            "transcript level. tximport summarizes to gene-level counts using the "
-            "`lengthScaledTPM` method. DESeq2 normalizes counts (median-of-ratios), applies "
-            "variance stabilizing transformation (VST) for PCA, and runs Wald tests for "
-            "differential expression. GSEA is performed with fgsea using pre-ranked gene lists "
-            "(ranked by log2 fold change)."
-        )
-
         with st.expander("View analysis code (analysis.R)"):
             r_script = Path(__file__).parent / "analysis.R"
             if r_script.exists():