Merge branch 'dev' into anaconda_purge_2

docs/usage.md

@@ -78,7 +78,8 @@ The BlobToolKit pipeline can be run in many different ways. The default way requ
 
 It is a good idea to put a date suffix for each database location so you know at a glance whether you are using the latest version. We are using the `YYYY_MM` format as we do not expect the databases to be updated more frequently than once a month. However, feel free to use `DATE=YYYY_MM_DD` or a different format if you prefer.
 
-Note that all input databases may be optionall passed directly to the pipeline compressed as `.tar.gz`, and the pipeline will handle decompression.
+Note that all input databases may be optionally passed directly to the pipeline compressed as `.tar.gz`, and the pipeline will handle decompression.
+The instructions below show how to build each input database in _two_ forms: decompressed _and_ compressed. You may not need to do both. Select the one that is most appropriate for how you want to use the pipeline.
 
 #### 1. NCBI taxdump database
 

modules/local/generate_config.nf

@@ -11,9 +11,9 @@ process GENERATE_CONFIG {
     val busco_lin
     path lineage_tax_ids
     val reads
-    tuple val(meta2), path(blastp)
-    tuple val(meta3), path(blastx)
-    tuple val(meta4), path(blastn)
+    tuple val(meta2), path(blastp, stageAs: 'blastp/*')
+    tuple val(meta3), path(blastx, stageAs: 'blastx/*')
+    tuple val(meta4), path(blastn, stageAs: 'blastn/*')
     tuple val(meta5), path(taxdump)
 
     output:

subworkflows/local/input_check.nf

@@ -48,7 +48,7 @@ workflow INPUT_CHECK {
     ch_databases = UNTAR.out.untar.concat( ch_dbs_for_untar.skip )
         .map { meta, db -> [ meta + [id: db.baseName], db] }
         .map { db_meta, db_path ->
-            if (db_meta.type in ["blastp", "blastx"]) {
+            if (db_meta.type in ["blastp", "blastx"] && db_path.isDirectory()) {
                 [db_meta, file(db_path.toString() + "/${db_path.name}", checkIfExists: true)]
             } else {
                 [db_meta, db_path]