Merge pull request #383 from WrightonLabCSU/bugfix/define_distill_sql…

…_script_default

Give default to ch_distill_sql_script since it is used always in annotations

README.md

@@ -250,12 +250,12 @@ Additionally, `--merge-annotations` and `--rename` can be run idenpendently of a
 
 1) **Rename fasta headers based on input sample file names:**
 
-`nextflow run DRAM --rename --input_fasta_dir <path/to/fasta/directory/>`
+`nextflow run DRAM --rename --input_fasta <path/to/fasta/directory/>`
 
 
 2) **Call genes using input fastas (use --rename to rename FASTA headers):**
 
-`nextflow run DRAM --call --rename --input_fasta_dir <path/to/fasta/directory/>`
+`nextflow run DRAM --call --rename --input_fasta <path/to/fasta/directory/>`
 
     
 3) **Annotate called genes using input called genes and the KOFAM database:**
@@ -285,7 +285,7 @@ Additionally, `--merge-annotations` and `--rename` can be run idenpendently of a
 
 8) **Call and Annotate genes using input fastas and KOFAM database. Distill using the default topic and the AG ecosystem:**
 
-`nextflow run DRAM --input_fasta_dir <path/to/fasta/directory/> --outdir <path/to/output/directory/> --call --annotate --distill_topic default --distill_ecosystem ag --threads <threads> --use_kofam`
+`nextflow run DRAM --input_fasta <path/to/fasta/directory/> --outdir <path/to/output/directory/> --call --annotate --distill_topic default --distill_ecosystem ag --threads <threads> --use_kofam`
 
 
 9) **"Real-world" example using the test data provided in this repository:**
@@ -334,7 +334,7 @@ DRAM
         nextflow run DRAM --rename --call --annotate --use_<database(s) --distill_topic <distillate(s)>
 
         Call genes using input fastas (use --rename to rename FASTA headers):
-            nextflow run DRAM --call --rename --input_fasta_dir <path/to/fasta/directory/>
+            nextflow run DRAM --call --rename --input_fasta <path/to/fasta/directory/>
 
         Annotate called genes using input fastas:
             nextflow run DRAM --annotate --input_genes <path/to/called/genes/directory>
@@ -465,7 +465,7 @@ DRAM
     Usage:
 
         Call genes using input fastas:
-            nextflow run DRAM --call --input_fasta_dir <path/to/fasta/directory/> --outdir <path/to/output/directory/> --threads <threads>
+            nextflow run DRAM --call --input_fasta <path/to/fasta/directory/> --outdir <path/to/output/directory/> --threads <threads>
     
     REQUIRED DRAM profile options:
         -profile                STRING  <conda, conda_slurm, singularity, singularity_conda>
@@ -587,7 +587,7 @@ DRAM
     
     Example:
         Call and Annotate genes using input fastas and KOFAM database. Distill using carbon topic and AG ecosystem:
-            nextflow run DRAM --input_fasta_dir <path/to/fasta/directory/> --outdir <path/to/output/directory/> --call --annotate --distill_topic carbon --distill_ecosystem ag --threads <threads> --use_kofam
+            nextflow run DRAM --input_fasta <path/to/fasta/directory/> --outdir <path/to/output/directory/> --call --annotate --distill_topic carbon --distill_ecosystem ag --threads <threads> --use_kofam
     
     REQUIRED DRAM profile options:
         -profile                STRING  <conda, conda_slurm, singularity, singularity_conda>

main.nf

@@ -1,6 +1,6 @@
 /*
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-    DRAM: DRAM (Distilled and Refined Annotation of Metabolism Version 2) is a tool for annotating metagenomic assembled genomes.
+    DRAM: DRAM (Distilled and Refined Annotation of Metabolism) is a tool for annotating metagenomic assembled genomes.
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 
     Homepage of project
@@ -458,6 +458,20 @@ if( params.use_dbset == "adjectives_set" ){
 //  channels for the various annotation databases
     def annotate_list = ""
 
+/*
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+    Defaults for all processes
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+*/
+
+ch_distill_sql_script = file(params.distill_sql_script)
+
+/*
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+    specific process stuff
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+*/
+
 if( params.annotate ){
     //This is just temporary - want these in the containers eventually
     ch_combine_annot_script = file(params.combine_annotations_script)
@@ -685,7 +699,6 @@ if (params.distill_topic != "" || params.distill_ecosystem != "" || params.disti
     distill_flag = "on"
     // Set channels for supporting python scripts - will be moved to container eventually
     ch_distill_xlsx_script = file(params.distill_xlsx_script)
-    ch_distill_sql_script = file(params.distill_sql_script)
 
     // Ensure rRNA and tRNA channels are populated if the user is not calling genes
     if( params.call == 0 ){
@@ -742,8 +755,7 @@ if( params.trees ) {
 
     ch_count_annots_script = file(params.count_annots_script)
     ch_distill_xlsx_script = file(params.distill_xlsx_script)
-    ch_distill_sql_script = file(params.distill_sql_script)
-
+
     //Add in option for --add_trees <list of paths to trees refpkg directories>
     if( params.add_trees ){
         ch_add_trees = file(params.add_trees).exists() ? file(params.add_trees) : error("Error: If using --add_trees, you must supply a path to a directory containing each tree subdirectory. Additional trees directory not found at ${params.add_trees}")

modules/utils/help.nf

@@ -47,7 +47,7 @@ Usage:
     nextflow run $workflow.manifest.name --rename --call --annotate --use_<database(s) --distill_topic <distillate(s)>
 
     Call genes using input fastas (use --rename to rename FASTA headers):
-        nextflow run $workflow.manifest.name --call --rename --input_fasta_dir <path/to/fasta/directory/>
+        nextflow run $workflow.manifest.name --call --rename --input_fasta <path/to/fasta/directory/>
 
     Annotate called genes using input fastas:
         nextflow run $workflow.manifest.name --annotate --input_genes <path/to/called/genes/directory>
@@ -276,7 +276,7 @@ Call description: The purpose of $workflow.manifest.name --call is to call genes
 Usage:
 
     Call genes using input fastas:
-        nextflow run $workflow.manifest.name --call --input_fasta_dir <path/to/fasta/directory/> --outdir <path/to/output/directory/> --threads <threads>
+        nextflow run $workflow.manifest.name --call --input_fasta <path/to/fasta/directory/> --outdir <path/to/output/directory/> --threads <threads>
 """
 
 ANNOTATE_DESCRIPTION = """
@@ -303,7 +303,7 @@ Usage:
 
 Example:
     Call and Annotate genes using input fastas and KOFAM database. Distill using carbon topic and AG ecosystem:
-        nextflow run $workflow.manifest.name --input_fasta_dir <path/to/fasta/directory/> --outdir <path/to/output/directory/> --call --annotate --distill_topic carbon --distill_ecosystem ag --threads <threads> --use_kofam
+        nextflow run $workflow.manifest.name --input_fasta <path/to/fasta/directory/> --outdir <path/to/output/directory/> --call --annotate --distill_topic carbon --distill_ecosystem ag --threads <threads> --use_kofam
 """
 
 PRODUCT_DESCRIPTION = """