ignore md line length rule

.pre-commit-config.yaml

@@ -24,6 +24,7 @@ repos:
     rev: master
     hooks:
       - id: markdownlint
+        args: ['--help']
         name: markdownlint
         language: node
         types: [markdown]

README.md

@@ -20,7 +20,7 @@ conda env create -f phylo-env.yaml --name phylo-env
 conda activate phylo-env
 ```
 
-## Reproduce from previously generated database
+## Run full pipeline to reproduce previous analysis
 
 ```bash
 nextflow run pipeline.nf \
@@ -30,49 +30,50 @@ nextflow run pipeline.nf \
 
 ## Step By Step (From Scratch)
 
-### Build, Update, Join NCBImeta database
+### Build NCBImeta metadata database
 
 ```bash
 nextflow run pipeline.nf \
   --ncbimeta_create ncbimeta.yaml \
   --outdir results \
-  --ncbimeta_update ncbimeta.yaml \
-  --skip_assembly_download \
+  --skip_ncbimeta_update \
   --skip_reference_download
 ```
 
 ### Customize and Curate the Annotations
 
-1. Create a metadata TSV file with just the metadata columns of interest (ie. for NextStrain visualization)
+Curate metadata with a DB Browser (SQLite), example:
+* ex. Add "REMOVE: Not Yersinia pestis" to the column BioSampleComment.
+* ex. Add collection data, geographic location, host etc. from literature.
+
+### Update and Join Database Tables
 
 ```bash
-scripts/sqlite_NextStrain_tsv.py   \
-  --database test/ncbimeta_db/update/latest/output/database/yersinia_pestis_db.sqlite   \
-  --query "SELECT BioSampleAccession,AssemblyFTPGenbank,SRARunAccession,BioSampleStrain,BioSampleCollectionDate,BioSampleHost,BioSampleGeographicLocation,BioSampleBiovar,PubmedArticleTitle,PubmedAuthorsLastName,AssemblyContigCount,AssemblyTotalLength,NucleotideGenes,NucleotideGenesTotal,NucleotidePseudoGenes,NucleotidePseudoGenesTotal,NucleotiderRNAs,AssemblySubmissionDate,SRARunPublishDate,BioSampleComment FROM Master"   \
-  --no-data-char ? \
-  --output ncbimeta_default_annot.txt
+nextflow run pipeline.nf \
+  --ncbimeta_update ncbimeta.yaml \
+  --outdir results \
+  --skip_sqlite_import \
+  --skip_reference_download
 ```
 
-2. Curate/Add metadata with a text-editor, example:
-Add "REMOVE: Not Yersinia pestis" to the BioSampleComment column to any rows that are the wrong organism.
-Edit the collection data, geographic location, host etc. based on associated publication.
+### Export metadata for downstream visualization
 
-3. Replace ? with empty "" for NCBImeta annotation script
+NextStrain metadata file preparation
 
 ```bash
-sed 's/?//g' ncbimeta_default_annot.txt > ncbimeta_annot.txt
+scripts/sqlite_NextStrain_tsv.py   \
+  --database test/ncbimeta_db/update/latest/output/database/yersinia_pestis_db.sqlite   \
+  --query "SELECT BioSampleAccession,AssemblyFTPGenbank,SRARunAccession,BioSampleStrain,BioSampleCollectionDate,BioSampleHost,BioSampleGeographicLocation,BioSampleBiovar,PubmedArticleTitle,PubmedAuthorsLastName,AssemblyContigCount,AssemblyTotalLength,NucleotideGenes,NucleotideGenesTotal,NucleotidePseudoGenes,NucleotidePseudoGenesTotal,NucleotiderRNAs,AssemblySubmissionDate,SRARunPublishDate,BioSampleComment FROM Master"   \
+  --no-data-char ? \
+  --output nextstrain_annot.txt
 ```
 
-### Update Database With Annotations
-
-Remember that this drops/deletes the Master tables every time it's rerun:
-
+### Run the sqlite import command to see what samples will be run
 ```bash
 nextflow run pipeline.nf \
-  --ncbimeta_update ncbimeta.yaml \
-  --ncbimeta_annot ncbimeta_annot.txt \
+  --sqlite results/ncbimeta_db/update/latest/output/database/yersinia_pestis_db.sqlite \
   --outdir results \
-  --skip_sqlite_import \
+  --skip_assembly_download \
   --skip_reference_download \
   -resume
 ```