Refactor module arguments to pipeline arguments

CHANGELOG.md

@@ -27,10 +27,11 @@ Initial release of Joon-Klaps/viralgenie, created with the [nf-core](https://nf-
 - include empty samples in multiqc sample overview ([#162](https://github.com/Joon-Klaps/viralgenie/pull/162))
 - Include samtools stats pre dedup & post dedup in overview tables ([#163](https://github.com/Joon-Klaps/viralgenie/pull/163))
 - adding prokka for gene detection & annotation ([#165](https://github.com/Joon-Klaps/viralgenie/pull/165))
+- Refactor module arguments to pipeline arguments ([#166](https://github.com/Joon-Klaps/viralgenie/pull/166))
 
 ### `Fixed`
 
-- OOM with longer contigs for lowcov_to_reference, uses more RAM now ([#125](https://github.com/Joon-Klaps/viralgenie/pull/125))
+- OOM with longer contigs for nocov_to_reference, uses more RAM now ([#125](https://github.com/Joon-Klaps/viralgenie/pull/125))
 - fixing null output from global prefix ([#147](https://github.com/Joon-Klaps/viralgenie/pull/147))
 - Fix empty filtered clusters ([#148](https://github.com/Joon-Klaps/viralgenie/pull/148))
 - Fixing missing columns from general stats & add general stats sample filtering ([#149](https://github.com/Joon-Klaps/viralgenie/pull/149))

README.md

@@ -58,7 +58,7 @@
     - [`Mash`](https://github.com/marbl/Mash)
 10. [Optional] Remove clusters with low read coverage. `bin/extract_clusters.py`
 11. Scaffolding of contigs to centroid ([`Minimap2`](https://github.com/lh3/minimap2), [`iVar-consensus`](https://andersen-lab.github.io/ivar/html/manualpage.html))
-12. [Optional] Annotate 0-depth regions with external reference `bin/lowcov_to_reference.py`.
+12. [Optional] Annotate 0-depth regions with external reference `bin/nocov_to_reference.py`.
 13. [Optional] Select best reference from `--mapping_constraints`:
     - [`Mash sketch`](https://github.com/marbl/Mash)
     - [`Mash screen`](https://github.com/marbl/Mash)
@@ -67,7 +67,7 @@
 16. Variant calling and filtering ([`BCFTools`](http://samtools.github.io/bcftools/bcftools.html),[`iVar`](https://andersen-lab.github.io/ivar/html/manualpage.html))
 17. Create consensus genome ([`BCFTools`](http://samtools.github.io/bcftools/bcftools.html),[`iVar`](https://andersen-lab.github.io/ivar/html/manualpage.html))
 18. Repeat step 12-15 multiple times for the denovo contig route
-19. Consensus evaluation and annotation ([`QUAST`](http://quast.sourceforge.net/quast),[`CheckV`](https://bitbucket.org/berkeleylab/checkv/src/master/),[`blastn`](https://blast.ncbi.nlm.nih.gov/Blast.cgi), [`mmseqs-search`](https://github.com/soedinglab/MMseqs2/wiki#batch-sequence-searching-using-mmseqs-search), [`MAFFT` - alignment of contigs vs iterations & consensus](https://mafft.cbrc.jp/alignment/software/))
+19. Consensus evaluation and annotation ([`QUAST`](http://quast.sourceforge.net/quast),[`CheckV`](https://bitbucket.org/berkeleylab/checkv/src/master/),[`blastn`](https://blast.ncbi.nlm.nih.gov/Blast.cgi),[`prokka`](http://github.com/tseemann/prokka) [`mmseqs-search`](https://github.com/soedinglab/MMseqs2/wiki#batch-sequence-searching-using-mmseqs-search), [`MAFFT` - alignment of contigs vs iterations & consensus](https://mafft.cbrc.jp/alignment/software/))
 20. Result summary visualisation for raw read, alignment, assembly, variant calling and consensus calling results ([`MultiQC`](http://multiqc.info/))
 
 ## Usage

bin/extract_preclust.py

@@ -862,8 +862,10 @@ def parse_args(argv=None):
     parser.add_argument(
         "-u",
         "--keep-unclassified",
-        action="store_true",
-        default= False,
+        nargs="?",  # Makes the argument optional
+        const=True,  # Value when flag is present but no value provided
+        default=False,
+        type=lambda x: (str(x).lower() == 'true') if x is not None else True,
         help="Keep unclassified reads in the output.",
     )