ci - auto build from bactopia

rpetit3 · actions-user · commit 859855f78402 · 2024-09-18T02:38:13.000Z
diff --git a/docs/bactopia-tools/abricate.md b/docs/bactopia-tools/abricate.md
@@ -10,8 +10,7 @@ for antimicrobial resistance and virulence genes.
 ## Example Usage
 ```
 bactopia --wf abricate \
-  --bactopia /path/to/your/bactopia/results \ 
-  --include includes.txt  
+  --bactopia /path/to/your/bactopia/results  
 ```
 
 ## Output Overview
diff --git a/docs/bactopia-tools/abritamr.md b/docs/bactopia-tools/abritamr.md
@@ -13,8 +13,7 @@ reporting presence of reportable AMR genes in Victoria Australia.
 ## Example Usage
 ```
 bactopia --wf abritamr \
-  --bactopia /path/to/your/bactopia/results \ 
-  --include includes.txt  
+  --bactopia /path/to/your/bactopia/results  
 ```
 
 ## Output Overview
diff --git a/docs/bactopia-tools/agrvate.md b/docs/bactopia-tools/agrvate.md
@@ -10,8 +10,7 @@ to rapidly identify the _agr_ locus type in _Staphylococcus aureus_ assemblies.
 ## Example Usage
 ```
 bactopia --wf agrvate \
-  --bactopia /path/to/your/bactopia/results \ 
-  --include includes.txt  
+  --bactopia /path/to/your/bactopia/results  
 ```
 
 ## Output Overview
diff --git a/docs/bactopia-tools/amrfinderplus.md b/docs/bactopia-tools/amrfinderplus.md
@@ -10,8 +10,7 @@ for antimicrobial resistance and virulence genes.
 ## Example Usage
 ```
 bactopia --wf amrfinderplus \
-  --bactopia /path/to/your/bactopia/results \ 
-  --include includes.txt  
+  --bactopia /path/to/your/bactopia/results  
 ```
 
 ## Output Overview
diff --git a/docs/bactopia-tools/ariba.md b/docs/bactopia-tools/ariba.md
@@ -10,8 +10,7 @@ to rapidly identify genes in a database by creating local assemblies.
 ## Example Usage
 ```
 bactopia --wf ariba \
-  --bactopia /path/to/your/bactopia/results \ 
-  --include includes.txt  
+  --bactopia /path/to/your/bactopia/results  
 ```
 
 ## Output Overview
diff --git a/docs/bactopia-tools/bakta.md b/docs/bactopia-tools/bakta.md
@@ -11,8 +11,7 @@ to provide extensive annotations including: tRNA, tmRNA, rRNA, ncRNA, CRISPR, CD
 ## Example Usage
 ```
 bactopia --wf bakta \
-  --bactopia /path/to/your/bactopia/results \ 
-  --include includes.txt  
+  --bactopia /path/to/your/bactopia/results  
 ```
 
 ## Output Overview
diff --git a/docs/bactopia-tools/blastn.md b/docs/bactopia-tools/blastn.md
@@ -11,8 +11,7 @@ to query nucleotide sequences against nucleotide databases (contigs or genes) fo
 ## Example Usage
 ```
 bactopia --wf blastn \
-  --bactopia /path/to/your/bactopia/results \ 
-  --include includes.txt  
+  --bactopia /path/to/your/bactopia/results  
 ```
 
 ## Output Overview
diff --git a/docs/bactopia-tools/blastp.md b/docs/bactopia-tools/blastp.md
@@ -11,8 +11,7 @@ to query protein sequences against protein databases for each sample.
 ## Example Usage
 ```
 bactopia --wf blastp \
-  --bactopia /path/to/your/bactopia/results \ 
-  --include includes.txt  
+  --bactopia /path/to/your/bactopia/results  
 ```
 
 ## Output Overview
diff --git a/docs/bactopia-tools/blastx.md b/docs/bactopia-tools/blastx.md
@@ -11,8 +11,7 @@ to query translated nucleotide sequences against protein databases for each samp
 ## Example Usage
 ```
 bactopia --wf blastx \
-  --bactopia /path/to/your/bactopia/results \ 
-  --include includes.txt  
+  --bactopia /path/to/your/bactopia/results  
 ```
 
 ## Output Overview
diff --git a/docs/bactopia-tools/bracken.md b/docs/bactopia-tools/bracken.md
@@ -12,8 +12,7 @@ automatically and generate [Krona](https://github.com/marbl/Krona) charts for bo
 ## Example Usage
 ```
 bactopia --wf bracken \
-  --bactopia /path/to/your/bactopia/results \ 
-  --include includes.txt  
+  --bactopia /path/to/your/bactopia/results  
 ```
 
 ## Output Overview
diff --git a/docs/bactopia-tools/btyper3.md b/docs/bactopia-tools/btyper3.md
@@ -11,8 +11,7 @@ Bacillus cereus group isolates from genome assemblies.
 ## Example Usage
 ```
 bactopia --wf btyper3 \
-  --bactopia /path/to/your/bactopia/results \ 
-  --include includes.txt  
+  --bactopia /path/to/your/bactopia/results  
 ```
 
 ## Output Overview
diff --git a/docs/bactopia-tools/busco.md b/docs/bactopia-tools/busco.md
@@ -10,8 +10,7 @@ to assess the completeness of your assembly.
 ## Example Usage
 ```
 bactopia --wf busco \
-  --bactopia /path/to/your/bactopia/results \ 
-  --include includes.txt  
+  --bactopia /path/to/your/bactopia/results  
 ```
 
 ## Output Overview
diff --git a/docs/bactopia-tools/checkm.md b/docs/bactopia-tools/checkm.md
@@ -10,8 +10,7 @@ genomes recovered from isolates, single cells, and metagenomes.
 ## Example Usage
 ```
 bactopia --wf checkm \
-  --bactopia /path/to/your/bactopia/results \ 
-  --include includes.txt  
+  --bactopia /path/to/your/bactopia/results  
 ```
 
 ## Output Overview
diff --git a/docs/bactopia-tools/ectyper.md b/docs/bactopia-tools/ectyper.md
@@ -11,8 +11,7 @@ tp provide basic species identification and the predicted _E. coli_ serotype (e.
 ## Example Usage
 ```
 bactopia --wf ectyper \
-  --bactopia /path/to/your/bactopia/results \ 
-  --include includes.txt  
+  --bactopia /path/to/your/bactopia/results  
 ```
 
 ## Output Overview
diff --git a/docs/bactopia-tools/eggnog.md b/docs/bactopia-tools/eggnog.md
@@ -11,8 +11,7 @@ from the eggNOG database to more precisely functionally annotate than traditiona
 ## Example Usage
 ```
 bactopia --wf eggnog \
-  --bactopia /path/to/your/bactopia/results \ 
-  --include includes.txt  
+  --bactopia /path/to/your/bactopia/results  
 ```
 
 ## Output Overview
diff --git a/docs/bactopia-tools/emmtyper.md b/docs/bactopia-tools/emmtyper.md
@@ -10,8 +10,7 @@ emm-typing of _Streptococcus pyogenes_ using a de novo or complete assembly.
 ## Example Usage
 ```
 bactopia --wf emmtyper \
-  --bactopia /path/to/your/bactopia/results \ 
-  --include includes.txt  
+  --bactopia /path/to/your/bactopia/results  
 ```
 
 ## Output Overview
diff --git a/docs/bactopia-tools/fastani.md b/docs/bactopia-tools/fastani.md
@@ -15,8 +15,7 @@ or a species name (`--species`) for which to download all RefSeq genomes.
 ## Example Usage
 ```
 bactopia --wf fastani \
-  --bactopia /path/to/your/bactopia/results \ 
-  --include includes.txt  
+  --bactopia /path/to/your/bactopia/results  
 ```
 
 ## Output Overview
diff --git a/docs/bactopia-tools/gamma.md b/docs/bactopia-tools/gamma.md
@@ -10,8 +10,7 @@ translated gene matches from assemblies.
 ## Example Usage
 ```
 bactopia --wf gamma \
-  --bactopia /path/to/your/bactopia/results \ 
-  --include includes.txt  
+  --bactopia /path/to/your/bactopia/results  
 ```
 
 ## Output Overview
diff --git a/docs/bactopia-tools/genotyphi.md b/docs/bactopia-tools/genotyphi.md
@@ -10,8 +10,7 @@ from the outputs of [Mykrobe](https://github.com/Mykrobe-tools/mykrobe).
 ## Example Usage
 ```
 bactopia --wf genotyphi \
-  --bactopia /path/to/your/bactopia/results \ 
-  --include includes.txt  
+  --bactopia /path/to/your/bactopia/results  
 ```
 
 ## Output Overview
diff --git a/docs/bactopia-tools/gtdb.md b/docs/bactopia-tools/gtdb.md
@@ -13,8 +13,7 @@ the taxonomy of your samples.
 ## Example Usage
 ```
 bactopia --wf gtdb \
-  --bactopia /path/to/your/bactopia/results \ 
-  --include includes.txt  
+  --bactopia /path/to/your/bactopia/results  
 ```
 
 ## Output Overview
diff --git a/docs/bactopia-tools/hicap.md b/docs/bactopia-tools/hicap.md
@@ -10,8 +10,7 @@ the _in silico_ typing of the _Haemophilus influenzae_ cap locus.
 ## Example Usage
 ```
 bactopia --wf hicap \
-  --bactopia /path/to/your/bactopia/results \ 
-  --include includes.txt  
+  --bactopia /path/to/your/bactopia/results  
 ```
 
 ## Output Overview
diff --git a/docs/bactopia-tools/hpsuissero.md b/docs/bactopia-tools/hpsuissero.md
@@ -10,8 +10,7 @@ the serotype of _Haemophilus parasuis_ assemblies.
 ## Example Usage
 ```
 bactopia --wf hpsuissero \
-  --bactopia /path/to/your/bactopia/results \ 
-  --include includes.txt  
+  --bactopia /path/to/your/bactopia/results  
 ```
 
 ## Output Overview
diff --git a/docs/bactopia-tools/ismapper.md b/docs/bactopia-tools/ismapper.md
@@ -10,8 +10,7 @@ insertion sites in your samples.
 ## Example Usage
 ```
 bactopia --wf ismapper \
-  --bactopia /path/to/your/bactopia/results \ 
-  --include includes.txt  
+  --bactopia /path/to/your/bactopia/results  
 ```
 
 ## Output Overview
diff --git a/docs/bactopia-tools/kleborate.md b/docs/bactopia-tools/kleborate.md
@@ -16,8 +16,7 @@ _Klebsiella pneumoniae_ and the _Klebsiella pneumoniae_ species complex (KpSC).
 ## Example Usage
 ```
 bactopia --wf kleborate \
-  --bactopia /path/to/your/bactopia/results \ 
-  --include includes.txt  
+  --bactopia /path/to/your/bactopia/results  
 ```
 
 ## Output Overview
diff --git a/docs/bactopia-tools/kraken2.md b/docs/bactopia-tools/kraken2.md
@@ -10,8 +10,7 @@ classifications to your sequence reads.
 ## Example Usage
 ```
 bactopia --wf kraken2 \
-  --bactopia /path/to/your/bactopia/results \ 
-  --include includes.txt  
+  --bactopia /path/to/your/bactopia/results  
 ```
 
 ## Output Overview
diff --git a/docs/bactopia-tools/legsta.md b/docs/bactopia-tools/legsta.md
@@ -10,8 +10,7 @@ _in silico_ _Legionella pneumophila_ Sequence Based Typing (SBT).
 ## Example Usage
 ```
 bactopia --wf legsta \
-  --bactopia /path/to/your/bactopia/results \ 
-  --include includes.txt  
+  --bactopia /path/to/your/bactopia/results  
 ```
 
 ## Output Overview
diff --git a/docs/bactopia-tools/lissero.md b/docs/bactopia-tools/lissero.md
@@ -10,8 +10,7 @@ _in silico_ serotype prediction for _Listeria monocytogenes_ assemblies.
 ## Example Usage
 ```
 bactopia --wf lissero \
-  --bactopia /path/to/your/bactopia/results \ 
-  --include includes.txt  
+  --bactopia /path/to/your/bactopia/results  
 ```
 
 ## Output Overview
diff --git a/docs/bactopia-tools/mashdist.md b/docs/bactopia-tools/mashdist.md
@@ -10,8 +10,7 @@ distance from a given reference genome(s).
 ## Example Usage
 ```
 bactopia --wf mashdist \
-  --bactopia /path/to/your/bactopia/results \ 
-  --include includes.txt  
+  --bactopia /path/to/your/bactopia/results  
 ```
 
 ## Output Overview
diff --git a/docs/bactopia-tools/mashtree.md b/docs/bactopia-tools/mashtree.md
@@ -14,8 +14,7 @@ genomes available from RefSeq and they will be included in your tree.
 ## Example Usage
 ```
 bactopia --wf mashtree \
-  --bactopia /path/to/your/bactopia/results \ 
-  --include includes.txt  
+  --bactopia /path/to/your/bactopia/results  
 ```
 
 ## Output Overview
diff --git a/docs/bactopia-tools/mcroni.md b/docs/bactopia-tools/mcroni.md
@@ -10,8 +10,7 @@ assemblies. If _mcr-1_ is found, the variations will be reported and available i
 ## Example Usage
 ```
 bactopia --wf mcroni \
-  --bactopia /path/to/your/bactopia/results \ 
-  --include includes.txt  
+  --bactopia /path/to/your/bactopia/results  
 ```
 
 ## Output Overview
diff --git a/docs/bactopia-tools/meningotype.md b/docs/bactopia-tools/meningotype.md
@@ -12,8 +12,7 @@ Bexsero antigen sequence typing (BAST) (_fHbp_, _NHBA_, _NadA_, _PorA_).
 ## Example Usage
 ```
 bactopia --wf meningotype \
-  --bactopia /path/to/your/bactopia/results \ 
-  --include includes.txt  
+  --bactopia /path/to/your/bactopia/results  
 ```
 
 ## Output Overview
diff --git a/docs/bactopia-tools/merlin.md b/docs/bactopia-tools/merlin.md
@@ -30,8 +30,7 @@ Then all the spells will be unleashed!
 ## Example Usage
 ```
 bactopia --wf merlin \
-  --bactopia /path/to/your/bactopia/results \ 
-  --include includes.txt  
+  --bactopia /path/to/your/bactopia/results  
 ```
 
 ## Output Overview
diff --git a/docs/bactopia-tools/midas.md b/docs/bactopia-tools/midas.md
@@ -12,8 +12,7 @@ more than 30,000 reference genomes to estimate abundances.
 ## Example Usage
 ```
 bactopia --wf midas \
-  --bactopia /path/to/your/bactopia/results \ 
-  --include includes.txt  
+  --bactopia /path/to/your/bactopia/results  
 ```
 
 ## Output Overview
diff --git a/docs/bactopia-tools/mlst.md b/docs/bactopia-tools/mlst.md
@@ -11,8 +11,7 @@ a specific scheme to scan, you can provide it with `--scheme`.
 ## Example Usage
 ```
 bactopia --wf mlst \
-  --bactopia /path/to/your/bactopia/results \ 
-  --include includes.txt  
+  --bactopia /path/to/your/bactopia/results  
 ```
 
 ## Output Overview
diff --git a/docs/bactopia-tools/mobsuite.md b/docs/bactopia-tools/mobsuite.md
@@ -8,8 +8,7 @@ The `mobsuite` module uses [MOB-suite](https://github.com/phac-nml/mob-suite) to
 ## Example Usage
 ```
 bactopia --wf mobsuite \
-  --bactopia /path/to/your/bactopia/results \ 
-  --include includes.txt  
+  --bactopia /path/to/your/bactopia/results  
 ```
 
 ## Output Overview
diff --git a/docs/bactopia-tools/mykrobe.md b/docs/bactopia-tools/mykrobe.md
@@ -10,8 +10,7 @@ antimicrobial resistance for _Mycobacterium tuberculosis_, _Staphylococcus aureu
 ## Example Usage
 ```
 bactopia --wf mykrobe \
-  --bactopia /path/to/your/bactopia/results \ 
-  --include includes.txt  
+  --bactopia /path/to/your/bactopia/results  
 ```
 
 ## Output Overview
diff --git a/docs/bactopia-tools/ngmaster.md b/docs/bactopia-tools/ngmaster.md
@@ -10,8 +10,7 @@ _in silico_ multi-antigen sequence typing for _Neisseria gonorrhoeae_ (NG-MAST).
 ## Example Usage
 ```
 bactopia --wf ngmaster \
-  --bactopia /path/to/your/bactopia/results \ 
-  --include includes.txt  
+  --bactopia /path/to/your/bactopia/results  
 ```
 
 ## Output Overview
diff --git a/docs/bactopia-tools/pangenome.md b/docs/bactopia-tools/pangenome.md
@@ -23,8 +23,7 @@ using [Scoary](https://github.com/AdmiralenOla/Scoary).
 ## Example Usage
 ```
 bactopia --wf pangenome \
-  --bactopia /path/to/your/bactopia/results \ 
-  --include includes.txt  
+  --bactopia /path/to/your/bactopia/results  
 ```
 
 ## Output Overview
diff --git a/docs/bactopia-tools/pasty.md b/docs/bactopia-tools/pasty.md
@@ -10,8 +10,7 @@ serogrouping of _Pseudomonas aeruginosa_ isolates.
 ## Example Usage
 ```
 bactopia --wf pasty \
-  --bactopia /path/to/your/bactopia/results \ 
-  --include includes.txt  
+  --bactopia /path/to/your/bactopia/results  
 ```
 
 ## Output Overview
diff --git a/docs/bactopia-tools/pbptyper.md b/docs/bactopia-tools/pbptyper.md
@@ -10,8 +10,7 @@ the Penicillin Binding Protein (PBP) of _Streptococcus pneumoniae_ assemblies.
 ## Example Usage
 ```
 bactopia --wf pbptyper \
-  --bactopia /path/to/your/bactopia/results \ 
-  --include includes.txt  
+  --bactopia /path/to/your/bactopia/results  
 ```
 
 ## Output Overview
diff --git a/docs/bactopia-tools/phispy.md b/docs/bactopia-tools/phispy.md
diff --git a/docs/bactopia-tools/plasmidfinder.md b/docs/bactopia-tools/plasmidfinder.md
diff --git a/docs/bactopia-tools/pneumocat.md b/docs/bactopia-tools/pneumocat.md
diff --git a/docs/bactopia-tools/quast.md b/docs/bactopia-tools/quast.md
diff --git a/docs/bactopia-tools/rgi.md b/docs/bactopia-tools/rgi.md
diff --git a/docs/bactopia-tools/scrubber.md b/docs/bactopia-tools/scrubber.md
diff --git a/docs/bactopia-tools/seqsero2.md b/docs/bactopia-tools/seqsero2.md
diff --git a/docs/bactopia-tools/seroba.md b/docs/bactopia-tools/seroba.md
diff --git a/docs/bactopia-tools/shigatyper.md b/docs/bactopia-tools/shigatyper.md
diff --git a/docs/bactopia-tools/shigeifinder.md b/docs/bactopia-tools/shigeifinder.md
diff --git a/docs/bactopia-tools/sistr.md b/docs/bactopia-tools/sistr.md
diff --git a/docs/bactopia-tools/snippy.md b/docs/bactopia-tools/snippy.md
diff --git a/docs/bactopia-tools/spatyper.md b/docs/bactopia-tools/spatyper.md
diff --git a/docs/bactopia-tools/ssuissero.md b/docs/bactopia-tools/ssuissero.md
diff --git a/docs/bactopia-tools/staphopiasccmec.md b/docs/bactopia-tools/staphopiasccmec.md
diff --git a/docs/bactopia-tools/staphtyper.md b/docs/bactopia-tools/staphtyper.md
diff --git a/docs/bactopia-tools/stecfinder.md b/docs/bactopia-tools/stecfinder.md
diff --git a/docs/bactopia-tools/tblastn.md b/docs/bactopia-tools/tblastn.md
diff --git a/docs/bactopia-tools/tblastx.md b/docs/bactopia-tools/tblastx.md
diff --git a/docs/bactopia-tools/tbprofiler.md b/docs/bactopia-tools/tbprofiler.md
