tweak meta yamls again

.skeleton/subworkflows/meta.yml

@@ -23,7 +23,7 @@ output:
       pattern: "versions.yml"
 docs:
   meta:
-    title: Bactopia Tools - SUBWORKFLOW_NAME
+    title: SUBWORKFLOW_NAME
     description: >
       A Bactopia Tool which uses...
   introduction: |

subworkflows/local/abricate/meta.yml

@@ -36,7 +36,7 @@ output:
       pattern: "*.{txt}"
 docs:
   meta:
-    title: Bactopia Tools - abricate
+    title: abricate
     description: >-
       A Bactopia Tool which uses Abricate to screen assemblies for antimicrobial 
       resistance and virulence genes

subworkflows/local/agrvate/meta.yml

@@ -37,7 +37,7 @@ output:
       pattern: "versions.yml"
 docs:
   meta:
-    title: Bactopia Tools - argvate
+    title: argvate
     description: >-
       A Bactopia Tool which uses AgrVATE to rapidly identify the _agr_ locus
       type in _Staphylococcus aureus_ assemblies.

subworkflows/local/amrfinderplus/meta.yml

@@ -53,7 +53,7 @@ output:
       pattern: "*-mutations.tsv"
 docs:
   meta:
-    title: Bactopia Tools - amrfinderplus
+    title: amrfinderplus
     description: >-
       A Bactopia Tool which uses AMRFinder+ to screen assemblies and proteins
       for antimicrobial resistance and virulence genes.

subworkflows/local/ariba/meta.yml

@@ -47,7 +47,7 @@ output:
       pattern: "versions.yml"
 docs:
   meta:
-    title: Bactopia Tools - ariba
+    title: ariba
     description: >-
       A Bactopia Tool which uses ARIBA to rapidly identify genes in
       a database by creating local assemblies.

subworkflows/local/bakta/meta.yml

@@ -77,7 +77,7 @@ output:
 
 docs:
   meta:
-    title: Bactopia Tools - bakta
+    title: bakta
     description: >-
       A Bactopia Tool which uses Bakta to rapidly provide extensive annotations (tRNA, tmRNA,
       rRNA, ncRNA, CRISPR, CDS, pseudogenes, and sORFs) in a standardized fashion.

subworkflows/local/busco/meta.yml

@@ -42,7 +42,7 @@ output:
       pattern: "versions.yml"
 docs:
   meta:
-    title: Bactopia Tools - busco
+    title: busco
     description: >-
       A Bactopia Tool which uses BUSCO, or Benchmarking Universal Single-Copy Orthologs,
       to assess the completeness of your assembly.

subworkflows/local/checkm/meta.yml

@@ -40,7 +40,7 @@ output:
       pattern: "*.{txt}"
 docs:
   meta:
-    title: Bactopia Tools - checkm
+    title: checkm
     description: >-
       A Bactopia Tool which uses CheckM to assess the quality of microbial
       genomes recovered from isolates.

subworkflows/local/ectyper/meta.yml

@@ -41,7 +41,7 @@ output:
       pattern: 'versions.yml'
 docs:
   meta:
-    title: Bactopia Tools - ectyper
+    title: ectyper
     description: >-
       A Bactopia Tool which uses ECTyper to conduct _in silico_ prediction
       of serotype for _Escherichia coli_ genomes.

subworkflows/local/eggnog/meta.yml

@@ -70,7 +70,7 @@ output:
       pattern: "versions.yml"
 docs:
   meta:
-    title: Bactopia Tools - eggnog
+    title: eggnog
     description: >-
       A Bactopia Tool which uses eggNOG-mapper to assign functional
       annotation to protein sequences.

subworkflows/local/emmtyper/meta.yml

@@ -38,7 +38,7 @@ output:
       pattern: 'versions.yml'
 docs:
   meta:
-    title: Bactopia Tools - emmtyper
+    title: emmtyper
     description: >-
       A Bactopia Tool which uses emmtyper for emm-typing of _Streptococcus pyogenes_
       using a de novo or complete assembly.

subworkflows/local/fastani/meta.yml

@@ -41,7 +41,7 @@ output:
       pattern: 'versions.yml'
 docs:
   meta:
-    title: Bactopia Tools - fastani
+    title: fastani
     description: >-
       A Bactopia Tool which uses FastANI to calculate the average nucleotide identity
       (ANI) between your samples.

subworkflows/local/gamma/meta.yml

@@ -49,7 +49,7 @@ output:
       pattern: "*.fasta"
 docs:
   meta:
-    title: Bactopia Tools - gamma
+    title: gamma
     description: >-
       A Bactopia Tool which uses GAMMA to identify, classify, and annotate translated
       gene matches from assemblies.

subworkflows/local/genotyphi/meta.yml

@@ -46,7 +46,7 @@ output:
       pattern: "*.json"
 docs:
   meta:
-    title: Bactopia Tools - genotyphi
+    title: genotyphi
     description: >-
       A Bactopia Tool which uses GenoTyphi to genotype Salmonella Typhi from the outputs
       of Mykrobe.

subworkflows/local/gtdb/meta.yml

@@ -67,7 +67,7 @@ output:
       pattern: "*.{failed_genomes.tsv}"
 docs:
   meta:
-    title: Bactopia Tools - gtdb
+    title: gtdb
     description: >-
       A Bactopia Tool which uses GTDB-Tk's classify workflow to assign taxonomic classifications
       to your set of samples.

subworkflows/local/hicap/meta.yml

@@ -53,7 +53,7 @@ output:
       pattern: 'versions.yml'
 docs:
   meta:
-    title: Bactopia Tools - hicap
+    title: hicap
     description: >-
       A Bactopia Tool which uses hicap along wih an assembly for the _in silico_ typing of
       the _Haemophilus influenzae_ cap locus.

subworkflows/local/hpsuissero/meta.yml

@@ -32,7 +32,7 @@ output:
 
 docs:
   meta:
-    title: Bactopia Tools - hpsuissero
+    title: hpsuissero
     description: >-
       A Bactopia Tool which uses HpsuisSero to predict the serotype of _Haemophilus parasuis_
       assemblies.

subworkflows/local/ismapper/meta.yml

@@ -40,7 +40,7 @@ output:
       pattern: "*/*"
 docs:
   meta:
-    title: Bactopia Tools - ismapper
+    title: ismapper
     description: >-
       A Bactopia Tool which uses ISMapper to search for insertion sites in
       your samples.

subworkflows/local/kleborate/meta.yml

@@ -38,7 +38,7 @@ output:
       pattern: "versions.yml"
 docs:
   meta:
-    title: Bactopia Tools - kleborate
+    title: kleborate
     description: >-
       A Bactopia Tool which uses Kleborate to screen genome assemblies of _Klebsiella pneumoniae_
       and the _Klebsiella pneumoniae_ species complex (KpSC).

subworkflows/local/kraken2/meta.yml

@@ -50,7 +50,7 @@ output:
       pattern: "versions.yml"
 docs:
   meta:
-    title: Bactopia Tools - kraken2
+    title: kraken2
     description: >-
       A Bactopia Tool which uses Kraken2 to assign taxonomic classifications
       to your sequence reads.

subworkflows/local/legsta/meta.yml

@@ -36,7 +36,7 @@ output:
       pattern: "*.{tsv}"
 docs:
   meta:
-    title: Bactopia Tools - legsta
+    title: legsta
     description: >-
       A Bactopia Tool which uses legsta for _in silico_ _Legionella pneumophila_
       Sequence Based Typing (SBT).

subworkflows/local/lissero/meta.yml

@@ -37,7 +37,7 @@ output:
       pattern: 'versions.yml'
 docs:
   meta:
-    title: Bactopia Tools - lissero
+    title: lissero
     description: >-
       A Bactopia Tool which uses LisSero for _in silico_ serotype prediction
       for _Listeria monocytogenes_ assemblies.

subworkflows/local/mashdist/meta.yml

@@ -35,7 +35,7 @@ output:
       pattern: "mashdist.tsv"
 docs:
   meta:
-    title: Bactopia Tools - mashdist
+    title: mashdist
     description: >-
       A Bactopia Tool which uses Mash to determine the Mash distance from
       a given reference genome(s).

subworkflows/local/mashtree/meta.yml

@@ -43,7 +43,7 @@ output:
       pattern: 'versions.yml'
 docs:
   meta:
-    title: Bactopia Tools - mashtree
+    title: mashtree
     description: >-
       A Bactopia Tool which uses Mashtree to create a tree of your samples
       using Mash distances.

subworkflows/local/mcroni/meta.yml

@@ -36,7 +36,7 @@ output:
       pattern: "*.fa"
 docs:
   meta:
-    title: Bactopia Tools - mcroni
+    title: mcroni
     description: >-
       A Bactopia Tool which uses mcroni to identify _mcr-1_ genes in 
       assemblies.

subworkflows/local/meningotype/meta.yml

@@ -38,7 +38,7 @@ output:
 
 docs:
   meta:
-    title: Bactopia Tools - meningotype
+    title: meningotype
     description: >-
       A Bactopia Tool which uses meningotype for _in silico_ typing of
       _Neisseria meningitidis_ genomes.

subworkflows/local/merlin/meta.yml

@@ -45,7 +45,7 @@ output:
 
 docs:
   meta:
-    title: Bactopia Tools - merlin
+    title: merlin
     description: >-
       A Bactopia Tool which for the automatic selection and executions of 
       species-specific tools.

subworkflows/local/mlst/meta.yml

@@ -36,7 +36,7 @@ output:
       pattern: 'versions.yml'
 docs:
   meta:
-    title: Bactopia Tools - mlst
+    title: mlst
     description: >-
       A Bactopia Tool which uses mlst scan assemblies and determine the sequence type based
       on PubMLST schemas.

subworkflows/local/mobsuite/meta.yml

@@ -44,7 +44,7 @@ output:
       pattern: "mobtyper_results.txt"
 docs:
   meta:
-    title: Bactopia Tools - mobsuite
+    title: mobsuite
     description: >-
       A Bactopia Tool which uses MOB-suite to reconstruct and annotate plasmids in
       draft assemblies.

subworkflows/local/mykrobe/meta.yml

@@ -44,7 +44,7 @@ output:
       pattern: "*.json"
 docs:
   meta:
-    title: Bactopia Tools - mykrobe
+    title: mykrobe
     description: >-
       A Bactopia Tool which uses Mykrobe to predict antimicrobial resistance for _Mycobacterium tuberculosis_,
       _Staphylococcus aureus_, _Shigella sonnei_, and _Salmonella typhi_.

subworkflows/local/ngmaster/meta.yml

@@ -38,7 +38,7 @@ output:
       pattern: 'versions.yml'
 docs:
   meta:
-    title: Bactopia Tools - ngmaster
+    title: ngmaster
     description: >-
       A Bactopia Tool which uses ngmaster for _in silico_ multi-antigen sequence
       typing for _Neisseria gonorrhoeae_ (NG-MAST).

subworkflows/local/pangenome/meta.yml

@@ -33,7 +33,7 @@ output:
       pattern: 'versions.yml'
 docs:
   meta:
-    title: Bactopia Tools - pangenome
+    title: pangenome
     description: >-
       A Bactopia Tool which creates a pangenome, then a core-genome phylogeny
       with multiple different tools.

subworkflows/local/rgi/meta.yml

@@ -44,7 +44,7 @@ output:
       pattern: "*.{csv,eps,png}"
 docs:
   meta:
-    title: Bactopia Tools - rgi
+    title: rgi
     description: >-
       A Bactopia Tool which uses Resistance Gene Identifier (RGI) to identify antibiotic
       resistance genes in assemblies.

subworkflows/local/seqsero2/meta.yml

@@ -38,7 +38,7 @@ output:
       pattern: "seqsero2.tsv"
 docs:
   meta:
-    title: Bactopia Tools - seqsero2
+    title: seqsero2
     description: >-
       A Bactopia Tool which uses SeqSero2 for Salmonella serotype prediction
       from reads and assemblies.

subworkflows/local/seroba/meta.yml

@@ -41,7 +41,7 @@ output:
       pattern: "*.txt"
 docs:
   meta:
-    title: Bactopia Tools - seroba
+    title: seroba
     description: >-
       A Bactopia Tool which uses Seroba to predict the serotype of _Streptococcus pneumoniae_
       samples with Illumina paired-end reads.

subworkflows/local/shigatyper/meta.yml

@@ -39,7 +39,7 @@ output:
       pattern: "versions.yml"
 docs:
   meta:
-    title: Bactopia Tools - shigatyper
+    title: shigatyper
     description: >-
       A Bactopia Tool which uses ShigaTyyper to rapidly determine Shigella serotype using
       Illumina or Oxford Nanopore reads.

subworkflows/local/sistr/meta.yml

@@ -48,7 +48,7 @@ output:
       pattern: "*.{csv}"
 docs:
   meta:
-    title: Bactopia Tools - sistr
+    title: sistr
     description: >-
       A Bactopia Tool which uses Salmonella In Silico Typing Resource, or SISTR, for
       serovar prediction of Salmonella assemblies.

subworkflows/local/snippy/meta.yml

@@ -35,7 +35,7 @@ output:
       pattern: "versions.yml"
 docs:
   meta:
-    title: Bactopia Tools - snippy
+    title: snippy
     description: >-
       A Bactopia Tool which uses Snippy to call SNPs and InDels against a reference and
       create a core-SNP phylogeny using IQ-Tree and Gubbins.

subworkflows/local/spatyper/meta.yml

@@ -45,7 +45,7 @@ output:
       pattern: "spatyper.tsv"
 docs:
   meta:
-    title: Bactopia Tools - spatyper
+    title: spatyper
     description: >-
       A Bactopia Tool which uses spaTyper to assign _spa_ types to
       _Staphylococcus aureus_ assemblies.

subworkflows/local/ssuissero/meta.yml

@@ -31,7 +31,7 @@ output:
       pattern: 'versions.yml'
 docs:
   meta:
-    title: Bactopia Tools - ssuissero
+    title: ssuissero
     description: >-
       A Bactopia Tool which uses SsuisSero to predict the serotype of
       _Streptococcus suis_ assemblies.

subworkflows/local/staphopiasccmec/meta.yml

@@ -38,7 +38,7 @@ output:
       pattern: "staphopiasccmec.tsv"
 docs:
   meta:
-    title: Bactopia Tools - staphopiasccmec
+    title: staphopiasccmec
     description: >-
       A Bactopia Tool which uses staphopia-sccmec to assign SCCmec types
       to _Staphylococcus aureus_ assemblies.

subworkflows/local/staphtyper/meta.yml

@@ -54,7 +54,7 @@ output:
       pattern: "versions.yml"
 docs:
   meta:
-    title: Bactopia Tools - staphtyper
+    title: staphtyper
     description: >-
       A Bactopia Tool which includes multiple tools that are specific for typing certain features
       of _Staphylococcus aureus_.

subworkflows/local/tbprofiler/meta.yml

@@ -45,7 +45,7 @@ output:
       pattern: "*.vcf"
 docs:
   meta:
-    title: Bactopia Tools - tbprofiler
+    title: tbprofiler
     description: >-
       A Bactopia Tool which uses TBProfiler for profiling reads to determine resistance
       and _Mycobacterium tuberculosis_ strain type.