documentation and indication of user-specified paths for binds

LANL-Bioinformatics · Aug 26, 2024 · 450d9e1 · 450d9e1
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diff --git a/contigsTaxonomyAssignment/contigsTaxonomyAssignment.nf b/contigsTaxonomyAssignment/contigsTaxonomyAssignment.nf
@@ -1,3 +1,8 @@
+//André Watson
+//Aug 2024
+//apwat @ lanl.gov
+
+//base process. Takes a FASTA file containing contigs and performs taxonomic analysis with MICCR (https://github.com/chienchi/miccr).
 process contigTaxonomy {
     publishDir(
         path: "$params.outDir/AssemblyBasedAnalysis/Taxonomy",
@@ -21,6 +26,7 @@ process contigTaxonomy {
     """
 }
 
+//adds multi-level taxonomic classification to results file. Takes in a .ctg.tsv file produced by MICCR.
 process addLineage {
     publishDir(
         path: "$params.outDir/AssemblyBasedAnalysis/Taxonomy",
@@ -40,6 +46,8 @@ process addLineage {
     """
 }
 
+//creates taxonomy classification graphs. Takes lineage file, .lca_ctg.tsv file produced by MICCR, 
+//and a coverage table (see https://github.com/chienchi/miccr/blob/master/utils/README.md), or from workflow runReadsToContig 
 process plotAndTable {
     publishDir(
         path: "$params.outDir/AssemblyBasedAnalysis/Taxonomy",

diff --git a/contigsTaxonomyAssignment/nextflow.config b/contigsTaxonomyAssignment/nextflow.config
@@ -1,7 +1,7 @@
 
 singularity {
     enabled=true
-    runOptions="--compat --home /media/volume/sdd/nextflow --bind /media/volume/sdd/nextflow/database/miccrDB:/venv/database/miccrDB"
+    runOptions="--compat --home /path/to/home --bind /path/to/miccrDB:/venv/database/miccrDB"
 }
 process.container = 'apwat/contigs_taxonomy:1.10'
 params {

diff --git a/contigsTaxonomyAssignment/test_files/parameters/contigTaxonomyBasic.json b/contigsTaxonomyAssignment/test_files/parameters/contigTaxonomyBasic.json
@@ -3,6 +3,6 @@
     "contigFile":"test_files/Final_contigs.fasta",
     "outDir": "contigTaxonomyOut",
     "projName": "contigTaxTest",
-    "dbPath": "/venv/database/miccrDB/NCBI-Bacteria-Virus.fna.mmi",
+    "dbPath": "/path/to/miccrDB/NCBI-Bacteria-Virus.fna.mmi",
     "coverageTable": "test_files/basic_coverage.table"
 }