diff --git a/docs/images/mess-hmp-help.svg b/docs/images/mess-hmp-help.svg
index 5ad13c1..ba5aca9 100644
--- a/docs/images/mess-hmp-help.svg
+++ b/docs/images/mess-hmp-help.svg
@@ -19,395 +19,395 @@
font-weight: 700;
}
- .terminal-3235506595-matrix {
+ .terminal-3090344181-matrix {
font-family: Fira Code, monospace;
font-size: 20px;
line-height: 24.4px;
font-variant-east-asian: full-width;
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- .terminal-3235506595-title {
+ .terminal-3090344181-title {
font-size: 18px;
font-weight: bold;
font-family: arial;
}
- .terminal-3235506595-r1 { fill: #c5c8c6 }
-.terminal-3235506595-r2 { fill: #d0b344 }
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-.terminal-3235506595-r8 { fill: #8a4346 }
-.terminal-3235506595-r9 { fill: #98a84b;font-weight: bold }
+ .terminal-3090344181-r1 { fill: #c5c8c6 }
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+.terminal-3090344181-r9 { fill: #98a84b;font-weight: bold }
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@@ -419,131 +419,131 @@
-
+
-
- $ mess hmp-template -h
-
-Usage:mess hmp-template [OPTIONS] [SNAKE_ARGS]...
-
- Download and simulate healthy human microbiome templates
-
-╭─ Hmp-template options ────────────────────────────────────────────────────────────╮
-│*--site Choose microbiome site (gut|buccal_mucosa|vagina|throat)│
-│[required] │
-│--sample choose sample template (TEXT)│
-╰───────────────────────────────────────────────────────────────────────────────────╯
-╭─ Common options ──────────────────────────────────────────────────────────────────╮
-│--output-o Output directory (PATH)[default: mess_out]│
-│--threads Number of threads to use (INTEGER)[default: 1]│
-│--taxonkit Define path to taxonkit data-dir (PATH)[default: (dynamic)]│
-│--help-h Show this message and exit. │
-╰───────────────────────────────────────────────────────────────────────────────────╯
-╭─ Download options ────────────────────────────────────────────────────────────────╮
-│--api-key NCBI api-key (TEXT)│
-│--limit Limit number of genomes per query (TEXT)│
-│--compressed Download compressed files [default: True]│
-│--include Comma seperated files to download : │
-│ genome,rna,protein,cds,gff3,gtf,gbff,seq-report,none │
-│(TEXT) │
-│[default: genome,seq-report] │
-│--source Download from refseq or genbank or both │
-│(refseq|genbank|all) │
-│[default: all] │
-│--taxon/--accession Are queries taxa names or accession [default: taxon]│
-│--reference Limit to reference and representative genomes │
-│[default: True] │
-│--assembly-level Comma seperated list of assembly level: │
-│ complete,chromosome,scaffold,contig │
-│(TEXT) │
-│--annotated Select annotated genomes only [default: False]│
-│--atypical Exclude atypical genomes [default: True]│
-│--mag Exclude, include or limit to metagenome assembled genomes │
-│(exclude|all|only) │
-│[default: all] │
-│--rank taxonomic rank to filter by assemblies │
-│(superkingdom|phylum|class|order|family|genus|species)│
-│--nrank Number of genomes per taxonomic rank (INTEGER)│
-╰───────────────────────────────────────────────────────────────────────────────────╯
-╭─ Common simulators options ───────────────────────────────────────────────────────╮
-│--tech Sequencing technology (illumina|pacbio|nanopore)│
-│[default: illumina] │
-│--bases Per sample base counts (ignored when coverage is set) (TEXT)│
-│[default: 1G] │
-│--tool Which simulator to use (art|pbsim3)[default: art]│
-│--error Simulator error profile (TEXT)[default: HS25]│
-│--mean-len Mean read length for long and short read sequencing (INTEGER)│
-│--bam/--no-bam Generate gold standard bam files [default: no-bam]│
-│--seed Seed for pseudo random number generator (INTEGER)[default: 1]│
-╰───────────────────────────────────────────────────────────────────────────────────╯
-╭─ art_illumina options ────────────────────────────────────────────────────────────╮
-│--custom-err Path to art custom error profile basename (TEXT)│
-│--paired Illumina reads pairing [default: True]│
-│--frag-len Fragment length for paired short read sequencing (INTEGER)│
-│[default: 200] │
-│--frag-sd Fragment length standard deviation for paired short read │
-│ sequencing │
-│(INTEGER) │
-│[default: 10] │
-╰───────────────────────────────────────────────────────────────────────────────────╯
-╭─ pbsim3 options ──────────────────────────────────────────────────────────────────╮
-│--model Path to pbsim3 sequencing error models │
-│(QSHMM-ONT-HQ|QSHMM-ONT|QSHMM-RSII) │
-│--model-path Path to pbsim3 sequencing error models │
-│(PATH) │
-│[default: │
-│/opt/hostedtoolcache/Python/3.12.5/x64/lib/python3.12/site-packa…│
-│--ratio PBSIM3 substitution, insertion and deletion ratio (TEXT)│
-│[default: 6:55:39] │
-│--accuracy Mean accuracy for long read sequencing (FLOAT)[default: 0.99]│
-│--passes Nmber of passes for pacbio multipass sequencing (2 or more for │
-│ hifi) │
-│(INTEGER) │
-│[default: 1] │
-│--min-len Minimum read length for long read sequencing (INTEGER)│
-│[default: 100] │
-│--max-len Maximum read length for long read sequencing (INTEGER)│
-│[default: 1000000] │
-│--sd-len Standard read length deviation for long read sequencing (INTEGER)│
-│[default: 7000] │
-╰───────────────────────────────────────────────────────────────────────────────────╯
-╭─ Replicates options ──────────────────────────────────────────────────────────────╮
-│--replicates Number of replicates per sample (INTEGER)[default: 1]│
-│--rep-sd Standard deviation between replicate coverages (0: no deviation) │
-│(INTEGER) │
-│[default: 0] │
-╰───────────────────────────────────────────────────────────────────────────────────╯
-╭─ Abundance distribution options ──────────────────────────────────────────────────╮
-│--dist Sample taxonomic abundances from a distribution (none|lognormal|even)│
-│[default: none] │
-│--mu Mu of lognormal dist (INTEGER)│
-│--sigma Sigma of lognormal dist (INTEGER)│
-╰───────────────────────────────────────────────────────────────────────────────────╯
-╭─ Taxonomic profile options ───────────────────────────────────────────────────────╮
-│--ranks Ranks to show in the taxonomic profile │
-│(TEXT) │
-│[default: superkingdom,phylum,class,order,family,genus,species,strain]│
-╰───────────────────────────────────────────────────────────────────────────────────╯
-╭─ Skip options ────────────────────────────────────────────────────────────────────╮
-│--skip-shuffle Skip fastq shuffling │
-╰───────────────────────────────────────────────────────────────────────────────────╯
-╭─ Snakemake options ───────────────────────────────────────────────────────────────╮
-│--configfile Custom config file [default: (outputDir)/config.yaml] (TEXT)│
-│--profile Snakemake profile to use (TEXT)│
-│--sdm Software deplolyment method (conda|apptainer)[default: conda]│
-│--prefix Custom softawre deployment directory (PATH)│
-│--snake-default Customise Snakemake runtime args │
-│(TEXT) │
-│[default: --printshellcmds, --nolock, --show-failed-logs]│
-╰───────────────────────────────────────────────────────────────────────────────────╯
-
- Command to download and simulate healthy human microbiome templates
- EXAMPLES:
- mess hmp-template --site gut -o gut
- or
- mess hmp-template --site buccal_mucosa --sample SRS013506 -o SRS013506
-
-
+
+ $ mess hmp-template -h
+
+Usage:mess hmp-template [OPTIONS] [SNAKE_ARGS]...
+
+ Download and simulate healthy human microbiome templates
+
+╭─ Hmp-template options ────────────────────────────────────────────────────────────╮
+│*--site Choose microbiome site (gut|buccal_mucosa|vagina|throat)│
+│[required] │
+│--sample choose sample template (TEXT)│
+╰───────────────────────────────────────────────────────────────────────────────────╯
+╭─ Common options ──────────────────────────────────────────────────────────────────╮
+│--output-o Output directory (PATH)[default: mess_out]│
+│--threads Number of threads to use (INTEGER)[default: 1]│
+│--taxonkit Define path to taxonkit data-dir (PATH)[default: (dynamic)]│
+│--help-h Show this message and exit. │
+╰───────────────────────────────────────────────────────────────────────────────────╯
+╭─ Download options ────────────────────────────────────────────────────────────────╮
+│--api-key NCBI api-key (TEXT)│
+│--limit Limit number of genomes per query (TEXT)│
+│--compressed Download compressed files [default: True]│
+│--include Comma seperated files to download : │
+│ genome,rna,protein,cds,gff3,gtf,gbff,seq-report,none │
+│(TEXT) │
+│[default: genome,seq-report] │
+│--source Download from refseq or genbank or both │
+│(refseq|genbank|all) │
+│[default: all] │
+│--taxon/--accession Are queries taxa names or accession [default: taxon]│
+│--reference Limit to reference and representative genomes │
+│[default: True] │
+│--assembly-level Comma seperated list of assembly level: │
+│ complete,chromosome,scaffold,contig │
+│(TEXT) │
+│--annotated Select annotated genomes only [default: False]│
+│--atypical Exclude atypical genomes [default: True]│
+│--mag Exclude, include or limit to metagenome assembled genomes │
+│(exclude|all|only) │
+│[default: all] │
+│--rank taxonomic rank to filter by assemblies │
+│(superkingdom|phylum|class|order|family|genus|species)│
+│--nrank Number of genomes per taxonomic rank (INTEGER)│
+╰───────────────────────────────────────────────────────────────────────────────────╯
+╭─ Common simulators options ───────────────────────────────────────────────────────╮
+│--tech Sequencing technology (illumina|pacbio|nanopore)│
+│[default: illumina] │
+│--bases Per sample base counts (ignored when coverage is set) (TEXT)│
+│[default: 1G] │
+│--tool Which simulator to use (art|pbsim3)[default: art]│
+│--error Simulator error profile (TEXT)[default: HS25]│
+│--mean-len Mean read length for long and short read sequencing (INTEGER)│
+│--bam/--no-bam Generate gold standard bam files [default: no-bam]│
+│--seed Seed for pseudo random number generator (INTEGER)[default: 1]│
+╰───────────────────────────────────────────────────────────────────────────────────╯
+╭─ art_illumina options ────────────────────────────────────────────────────────────╮
+│--custom-err Path to art custom error profile basename (TEXT)│
+│--paired Illumina reads pairing [default: True]│
+│--frag-len Fragment length for paired short read sequencing (INTEGER)│
+│[default: 200] │
+│--frag-sd Fragment length standard deviation for paired short read │
+│ sequencing │
+│(INTEGER) │
+│[default: 10] │
+╰───────────────────────────────────────────────────────────────────────────────────╯
+╭─ pbsim3 options ──────────────────────────────────────────────────────────────────╮
+│--model Path to pbsim3 sequencing error models │
+│(QSHMM-ONT-HQ|QSHMM-ONT|QSHMM-RSII) │
+│--model-path Path to pbsim3 sequencing error models │
+│(PATH) │
+│[default: │
+│/opt/hostedtoolcache/Python/3.12.7/x64/lib/python3.12/site-packa…│
+│--ratio PBSIM3 substitution, insertion and deletion ratio (TEXT)│
+│[default: 6:55:39] │
+│--accuracy Mean accuracy for long read sequencing (FLOAT)[default: 0.99]│
+│--passes Nmber of passes for pacbio multipass sequencing (2 or more for │
+│ hifi) │
+│(INTEGER) │
+│[default: 1] │
+│--min-len Minimum read length for long read sequencing (INTEGER)│
+│[default: 100] │
+│--max-len Maximum read length for long read sequencing (INTEGER)│
+│[default: 1000000] │
+│--sd-len Standard read length deviation for long read sequencing (INTEGER)│
+│[default: 7000] │
+╰───────────────────────────────────────────────────────────────────────────────────╯
+╭─ Replicates options ──────────────────────────────────────────────────────────────╮
+│--replicates Number of replicates per sample (INTEGER)[default: 1]│
+│--rep-sd Standard deviation between replicate coverages (0: no deviation) │
+│(INTEGER) │
+│[default: 0] │
+╰───────────────────────────────────────────────────────────────────────────────────╯
+╭─ Abundance distribution options ──────────────────────────────────────────────────╮
+│--dist Sample taxonomic abundances from a distribution (none|lognormal|even)│
+│[default: none] │
+│--mu Mu of lognormal dist (FLOAT)│
+│--sigma Sigma of lognormal dist (FLOAT)│
+╰───────────────────────────────────────────────────────────────────────────────────╯
+╭─ Taxonomic profile options ───────────────────────────────────────────────────────╮
+│--ranks Ranks to show in the taxonomic profile │
+│(TEXT) │
+│[default: superkingdom,phylum,class,order,family,genus,species,strain]│
+╰───────────────────────────────────────────────────────────────────────────────────╯
+╭─ Skip options ────────────────────────────────────────────────────────────────────╮
+│--skip-shuffle Skip fastq shuffling │
+╰───────────────────────────────────────────────────────────────────────────────────╯
+╭─ Snakemake options ───────────────────────────────────────────────────────────────╮
+│--configfile Custom config file [default: (outputDir)/config.yaml] (TEXT)│
+│--profile Snakemake profile to use (TEXT)│
+│--sdm Software deplolyment method (conda|apptainer)[default: conda]│
+│--prefix Custom softawre deployment directory (PATH)│
+│--snake-default Customise Snakemake runtime args │
+│(TEXT) │
+│[default: --printshellcmds, --nolock, --show-failed-logs]│
+╰───────────────────────────────────────────────────────────────────────────────────╯
+
+ Command to download and simulate healthy human microbiome templates
+ EXAMPLES:
+ mess hmp-template --site gut -o gut
+ or
+ mess hmp-template --site buccal_mucosa --sample SRS013506 -o SRS013506
+
+
diff --git a/docs/images/mess-run-help.svg b/docs/images/mess-run-help.svg
index 3421d8d..3f3a5db 100644
--- a/docs/images/mess-run-help.svg
+++ b/docs/images/mess-run-help.svg
@@ -19,389 +19,389 @@
font-weight: 700;
}
- .terminal-1629683079-matrix {
+ .terminal-1348992217-matrix {
font-family: Fira Code, monospace;
font-size: 20px;
line-height: 24.4px;
font-variant-east-asian: full-width;
}
- .terminal-1629683079-title {
+ .terminal-1348992217-title {
font-size: 18px;
font-weight: bold;
font-family: arial;
}
- .terminal-1629683079-r1 { fill: #c5c8c6 }
-.terminal-1629683079-r2 { fill: #d0b344 }
-.terminal-1629683079-r3 { fill: #c5c8c6;font-weight: bold }
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-.terminal-1629683079-r8 { fill: #8d7b39 }
-.terminal-1629683079-r9 { fill: #8a4346 }
+ .terminal-1348992217-r1 { fill: #c5c8c6 }
+.terminal-1348992217-r2 { fill: #d0b344 }
+.terminal-1348992217-r3 { fill: #c5c8c6;font-weight: bold }
+.terminal-1348992217-r4 { fill: #68a0b3;font-weight: bold }
+.terminal-1348992217-r5 { fill: #868887 }
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+.terminal-1348992217-r8 { fill: #8d7b39 }
+.terminal-1348992217-r9 { fill: #8a4346 }
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@@ -413,129 +413,129 @@
-
+
-
- $ mess run -h
-
-Usage:mess run [OPTIONS] [SNAKE_ARGS]...
-
- Run MeSS workflow: download and simulate commands
-
-╭─ Common options ──────────────────────────────────────────────────────────────────╮
-│*--input-i Path to input table(s) (PATH)[required]│
-│--output-o Output directory (PATH)[default: mess_out]│
-│--threads Number of threads to use (INTEGER)[default: 1]│
-│--taxonkit Define path to taxonkit data-dir (PATH)[default: (dynamic)]│
-│--help-h Show this message and exit. │
-╰───────────────────────────────────────────────────────────────────────────────────╯
-╭─ Download options ────────────────────────────────────────────────────────────────╮
-│--api-key NCBI api-key (TEXT)│
-│--limit Limit number of genomes per query (TEXT)│
-│--compressed Download compressed files [default: True]│
-│--include Comma seperated files to download : │
-│ genome,rna,protein,cds,gff3,gtf,gbff,seq-report,none │
-│(TEXT) │
-│[default: genome,seq-report] │
-│--source Download from refseq or genbank or both │
-│(refseq|genbank|all) │
-│[default: all] │
-│--taxon/--accession Are queries taxa names or accession [default: taxon]│
-│--reference Limit to reference and representative genomes │
-│[default: True] │
-│--assembly-level Comma seperated list of assembly level: │
-│ complete,chromosome,scaffold,contig │
-│(TEXT) │
-│--annotated Select annotated genomes only [default: False]│
-│--atypical Exclude atypical genomes [default: True]│
-│--mag Exclude, include or limit to metagenome assembled genomes │
-│(exclude|all|only) │
-│[default: all] │
-│--rank taxonomic rank to filter by assemblies │
-│(superkingdom|phylum|class|order|family|genus|species)│
-│--nrank Number of genomes per taxonomic rank (INTEGER)│
-╰───────────────────────────────────────────────────────────────────────────────────╯
-╭─ Common simulators options ───────────────────────────────────────────────────────╮
-│--tech Sequencing technology (illumina|pacbio|nanopore)│
-│[default: illumina] │
-│--bases Per sample base counts (ignored when coverage is set) (TEXT)│
-│[default: 1G] │
-│--tool Which simulator to use (art|pbsim3)[default: art]│
-│--error Simulator error profile (TEXT)[default: HS25]│
-│--mean-len Mean read length for long and short read sequencing (INTEGER)│
-│--bam/--no-bam Generate gold standard bam files [default: no-bam]│
-│--seed Seed for pseudo random number generator (INTEGER)[default: 1]│
-╰───────────────────────────────────────────────────────────────────────────────────╯
-╭─ art_illumina options ────────────────────────────────────────────────────────────╮
-│--custom-err Path to art custom error profile basename (TEXT)│
-│--paired Illumina reads pairing [default: True]│
-│--frag-len Fragment length for paired short read sequencing (INTEGER)│
-│[default: 200] │
-│--frag-sd Fragment length standard deviation for paired short read │
-│ sequencing │
-│(INTEGER) │
-│[default: 10] │
-╰───────────────────────────────────────────────────────────────────────────────────╯
-╭─ pbsim3 options ──────────────────────────────────────────────────────────────────╮
-│--model Path to pbsim3 sequencing error models │
-│(QSHMM-ONT-HQ|QSHMM-ONT|QSHMM-RSII) │
-│--model-path Path to pbsim3 sequencing error models │
-│(PATH) │
-│[default: │
-│/opt/hostedtoolcache/Python/3.12.5/x64/lib/python3.12/site-packa…│
-│--ratio PBSIM3 substitution, insertion and deletion ratio (TEXT)│
-│[default: 6:55:39] │
-│--accuracy Mean accuracy for long read sequencing (FLOAT)[default: 0.99]│
-│--passes Nmber of passes for pacbio multipass sequencing (2 or more for │
-│ hifi) │
-│(INTEGER) │
-│[default: 1] │
-│--min-len Minimum read length for long read sequencing (INTEGER)│
-│[default: 100] │
-│--max-len Maximum read length for long read sequencing (INTEGER)│
-│[default: 1000000] │
-│--sd-len Standard read length deviation for long read sequencing (INTEGER)│
-│[default: 7000] │
-╰───────────────────────────────────────────────────────────────────────────────────╯
-╭─ Replicates options ──────────────────────────────────────────────────────────────╮
-│--replicates Number of replicates per sample (INTEGER)[default: 1]│
-│--rep-sd Standard deviation between replicate coverages (0: no deviation) │
-│(INTEGER) │
-│[default: 0] │
-╰───────────────────────────────────────────────────────────────────────────────────╯
-╭─ Abundance distribution options ──────────────────────────────────────────────────╮
-│--dist Sample taxonomic abundances from a distribution (none|lognormal|even)│
-│[default: none] │
-│--mu Mu of lognormal dist (INTEGER)│
-│--sigma Sigma of lognormal dist (INTEGER)│
-╰───────────────────────────────────────────────────────────────────────────────────╯
-╭─ Taxonomic profile options ───────────────────────────────────────────────────────╮
-│--ranks Ranks to show in the taxonomic profile │
-│(TEXT) │
-│[default: superkingdom,phylum,class,order,family,genus,species,strain]│
-╰───────────────────────────────────────────────────────────────────────────────────╯
-╭─ Skip options ────────────────────────────────────────────────────────────────────╮
-│--skip-shuffle Skip fastq shuffling │
-╰───────────────────────────────────────────────────────────────────────────────────╯
-╭─ Snakemake options ───────────────────────────────────────────────────────────────╮
-│--configfile Custom config file [default: (outputDir)/config.yaml] (TEXT)│
-│--profile Snakemake profile to use (TEXT)│
-│--sdm Software deplolyment method (conda|apptainer)[default: conda]│
-│--prefix Custom softawre deployment directory (PATH)│
-│--snake-default Customise Snakemake runtime args │
-│(TEXT) │
-│[default: --printshellcmds, --nolock, --show-failed-logs]│
-╰───────────────────────────────────────────────────────────────────────────────────╯
-
- CLUSTER EXECUTION: mess run ... --profile [profile] For information on Snakemake
- profiles see:
- https://snakemake.readthedocs.io/en/stable/executing/cli.html#profiles RUN
- EXAMPLES: Required: mess run --input [file] Specify threads: mess run
- ... --threads [threads] Use conda: mess run ... --sdm conda Change
- defaults: mess run ... --snake-default="-k--nolock" Add Snakemake args: mess
- run ... --dry-run--keep-going--touch
-
-
+
+ $ mess run -h
+
+Usage:mess run [OPTIONS] [SNAKE_ARGS]...
+
+ Run MeSS workflow: download and simulate commands
+
+╭─ Common options ──────────────────────────────────────────────────────────────────╮
+│*--input-i Path to input table(s) (PATH)[required]│
+│--output-o Output directory (PATH)[default: mess_out]│
+│--threads Number of threads to use (INTEGER)[default: 1]│
+│--taxonkit Define path to taxonkit data-dir (PATH)[default: (dynamic)]│
+│--help-h Show this message and exit. │
+╰───────────────────────────────────────────────────────────────────────────────────╯
+╭─ Download options ────────────────────────────────────────────────────────────────╮
+│--api-key NCBI api-key (TEXT)│
+│--limit Limit number of genomes per query (TEXT)│
+│--compressed Download compressed files [default: True]│
+│--include Comma seperated files to download : │
+│ genome,rna,protein,cds,gff3,gtf,gbff,seq-report,none │
+│(TEXT) │
+│[default: genome,seq-report] │
+│--source Download from refseq or genbank or both │
+│(refseq|genbank|all) │
+│[default: all] │
+│--taxon/--accession Are queries taxa names or accession [default: taxon]│
+│--reference Limit to reference and representative genomes │
+│[default: True] │
+│--assembly-level Comma seperated list of assembly level: │
+│ complete,chromosome,scaffold,contig │
+│(TEXT) │
+│--annotated Select annotated genomes only [default: False]│
+│--atypical Exclude atypical genomes [default: True]│
+│--mag Exclude, include or limit to metagenome assembled genomes │
+│(exclude|all|only) │
+│[default: all] │
+│--rank taxonomic rank to filter by assemblies │
+│(superkingdom|phylum|class|order|family|genus|species)│
+│--nrank Number of genomes per taxonomic rank (INTEGER)│
+╰───────────────────────────────────────────────────────────────────────────────────╯
+╭─ Common simulators options ───────────────────────────────────────────────────────╮
+│--tech Sequencing technology (illumina|pacbio|nanopore)│
+│[default: illumina] │
+│--bases Per sample base counts (ignored when coverage is set) (TEXT)│
+│[default: 1G] │
+│--tool Which simulator to use (art|pbsim3)[default: art]│
+│--error Simulator error profile (TEXT)[default: HS25]│
+│--mean-len Mean read length for long and short read sequencing (INTEGER)│
+│--bam/--no-bam Generate gold standard bam files [default: no-bam]│
+│--seed Seed for pseudo random number generator (INTEGER)[default: 1]│
+╰───────────────────────────────────────────────────────────────────────────────────╯
+╭─ art_illumina options ────────────────────────────────────────────────────────────╮
+│--custom-err Path to art custom error profile basename (TEXT)│
+│--paired Illumina reads pairing [default: True]│
+│--frag-len Fragment length for paired short read sequencing (INTEGER)│
+│[default: 200] │
+│--frag-sd Fragment length standard deviation for paired short read │
+│ sequencing │
+│(INTEGER) │
+│[default: 10] │
+╰───────────────────────────────────────────────────────────────────────────────────╯
+╭─ pbsim3 options ──────────────────────────────────────────────────────────────────╮
+│--model Path to pbsim3 sequencing error models │
+│(QSHMM-ONT-HQ|QSHMM-ONT|QSHMM-RSII) │
+│--model-path Path to pbsim3 sequencing error models │
+│(PATH) │
+│[default: │
+│/opt/hostedtoolcache/Python/3.12.7/x64/lib/python3.12/site-packa…│
+│--ratio PBSIM3 substitution, insertion and deletion ratio (TEXT)│
+│[default: 6:55:39] │
+│--accuracy Mean accuracy for long read sequencing (FLOAT)[default: 0.99]│
+│--passes Nmber of passes for pacbio multipass sequencing (2 or more for │
+│ hifi) │
+│(INTEGER) │
+│[default: 1] │
+│--min-len Minimum read length for long read sequencing (INTEGER)│
+│[default: 100] │
+│--max-len Maximum read length for long read sequencing (INTEGER)│
+│[default: 1000000] │
+│--sd-len Standard read length deviation for long read sequencing (INTEGER)│
+│[default: 7000] │
+╰───────────────────────────────────────────────────────────────────────────────────╯
+╭─ Replicates options ──────────────────────────────────────────────────────────────╮
+│--replicates Number of replicates per sample (INTEGER)[default: 1]│
+│--rep-sd Standard deviation between replicate coverages (0: no deviation) │
+│(INTEGER) │
+│[default: 0] │
+╰───────────────────────────────────────────────────────────────────────────────────╯
+╭─ Abundance distribution options ──────────────────────────────────────────────────╮
+│--dist Sample taxonomic abundances from a distribution (none|lognormal|even)│
+│[default: none] │
+│--mu Mu of lognormal dist (FLOAT)│
+│--sigma Sigma of lognormal dist (FLOAT)│
+╰───────────────────────────────────────────────────────────────────────────────────╯
+╭─ Taxonomic profile options ───────────────────────────────────────────────────────╮
+│--ranks Ranks to show in the taxonomic profile │
+│(TEXT) │
+│[default: superkingdom,phylum,class,order,family,genus,species,strain]│
+╰───────────────────────────────────────────────────────────────────────────────────╯
+╭─ Skip options ────────────────────────────────────────────────────────────────────╮
+│--skip-shuffle Skip fastq shuffling │
+╰───────────────────────────────────────────────────────────────────────────────────╯
+╭─ Snakemake options ───────────────────────────────────────────────────────────────╮
+│--configfile Custom config file [default: (outputDir)/config.yaml] (TEXT)│
+│--profile Snakemake profile to use (TEXT)│
+│--sdm Software deplolyment method (conda|apptainer)[default: conda]│
+│--prefix Custom softawre deployment directory (PATH)│
+│--snake-default Customise Snakemake runtime args │
+│(TEXT) │
+│[default: --printshellcmds, --nolock, --show-failed-logs]│
+╰───────────────────────────────────────────────────────────────────────────────────╯
+
+ CLUSTER EXECUTION: mess run ... --profile [profile] For information on Snakemake
+ profiles see:
+ https://snakemake.readthedocs.io/en/stable/executing/cli.html#profiles RUN
+ EXAMPLES: Required: mess run --input [file] Specify threads: mess run
+ ... --threads [threads] Use conda: mess run ... --sdm conda Change
+ defaults: mess run ... --snake-default="-k--nolock" Add Snakemake args: mess
+ run ... --dry-run--keep-going--touch
+
+
diff --git a/docs/images/mess-simulate-help.svg b/docs/images/mess-simulate-help.svg
index 46462b0..987d372 100644
--- a/docs/images/mess-simulate-help.svg
+++ b/docs/images/mess-simulate-help.svg
@@ -19,323 +19,323 @@
font-weight: 700;
}
- .terminal-4251418855-matrix {
+ .terminal-1791393849-matrix {
font-family: Fira Code, monospace;
font-size: 20px;
line-height: 24.4px;
font-variant-east-asian: full-width;
}
- .terminal-4251418855-title {
+ .terminal-1791393849-title {
font-size: 18px;
font-weight: bold;
font-family: arial;
}
- .terminal-4251418855-r1 { fill: #c5c8c6 }
-.terminal-4251418855-r2 { fill: #d0b344 }
-.terminal-4251418855-r3 { fill: #c5c8c6;font-weight: bold }
-.terminal-4251418855-r4 { fill: #68a0b3;font-weight: bold }
-.terminal-4251418855-r5 { fill: #868887 }
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-.terminal-4251418855-r8 { fill: #8d7b39 }
-.terminal-4251418855-r9 { fill: #8a4346 }
+ .terminal-1791393849-r1 { fill: #c5c8c6 }
+.terminal-1791393849-r2 { fill: #d0b344 }
+.terminal-1791393849-r3 { fill: #c5c8c6;font-weight: bold }
+.terminal-1791393849-r4 { fill: #68a0b3;font-weight: bold }
+.terminal-1791393849-r5 { fill: #868887 }
+.terminal-1791393849-r6 { fill: #cc555a }
+.terminal-1791393849-r7 { fill: #98a84b;font-weight: bold }
+.terminal-1791393849-r8 { fill: #8d7b39 }
+.terminal-1791393849-r9 { fill: #8a4346 }
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-
+
-
- $ mess simulate -h
-
-Usage:mess simulate [OPTIONS] [SNAKE_ARGS]...
-
- Simulate reads from local fastas
-
-╭─ Common options ──────────────────────────────────────────────────────────────────╮
-│*--input-i Path to input table(s) (PATH)[required]│
-│--output-o Output directory (PATH)[default: mess_out]│
-│--threads Number of threads to use (INTEGER)[default: 1]│
-│--taxonkit Define path to taxonkit data-dir (PATH)[default: (dynamic)]│
-│--help-h Show this message and exit. │
-╰───────────────────────────────────────────────────────────────────────────────────╯
-╭─ Local genomes options ───────────────────────────────────────────────────────────╮
-│--asm-summary Summary table with genome sizes, fasta paths, contig counts... │
-│(TEXT) │
-│--fasta Path to local fasta directory if no path is set in summary or │
-│ input table │
-│(TEXT) │
-╰───────────────────────────────────────────────────────────────────────────────────╯
-╭─ Common simulators options ───────────────────────────────────────────────────────╮
-│--tech Sequencing technology (illumina|pacbio|nanopore)│
-│[default: illumina] │
-│--bases Per sample base counts (ignored when coverage is set) (TEXT)│
-│[default: 1G] │
-│--tool Which simulator to use (art|pbsim3)[default: art]│
-│--error Simulator error profile (TEXT)[default: HS25]│
-│--mean-len Mean read length for long and short read sequencing (INTEGER)│
-│--bam/--no-bam Generate gold standard bam files [default: no-bam]│
-│--seed Seed for pseudo random number generator (INTEGER)[default: 1]│
-╰───────────────────────────────────────────────────────────────────────────────────╯
-╭─ art_illumina options ────────────────────────────────────────────────────────────╮
-│--custom-err Path to art custom error profile basename (TEXT)│
-│--paired Illumina reads pairing [default: True]│
-│--frag-len Fragment length for paired short read sequencing (INTEGER)│
-│[default: 200] │
-│--frag-sd Fragment length standard deviation for paired short read │
-│ sequencing │
-│(INTEGER) │
-│[default: 10] │
-╰───────────────────────────────────────────────────────────────────────────────────╯
-╭─ pbsim3 options ──────────────────────────────────────────────────────────────────╮
-│--model Path to pbsim3 sequencing error models │
-│(QSHMM-ONT-HQ|QSHMM-ONT|QSHMM-RSII) │
-│--model-path Path to pbsim3 sequencing error models │
-│(PATH) │
-│[default: │
-│/opt/hostedtoolcache/Python/3.12.5/x64/lib/python3.12/site-packa…│
-│--ratio PBSIM3 substitution, insertion and deletion ratio (TEXT)│
-│[default: 6:55:39] │
-│--accuracy Mean accuracy for long read sequencing (FLOAT)[default: 0.99]│
-│--passes Nmber of passes for pacbio multipass sequencing (2 or more for │
-│ hifi) │
-│(INTEGER) │
-│[default: 1] │
-│--min-len Minimum read length for long read sequencing (INTEGER)│
-│[default: 100] │
-│--max-len Maximum read length for long read sequencing (INTEGER)│
-│[default: 1000000] │
-│--sd-len Standard read length deviation for long read sequencing (INTEGER)│
-│[default: 7000] │
-╰───────────────────────────────────────────────────────────────────────────────────╯
-╭─ Replicates options ──────────────────────────────────────────────────────────────╮
-│--replicates Number of replicates per sample (INTEGER)[default: 1]│
-│--rep-sd Standard deviation between replicate coverages (0: no deviation) │
-│(INTEGER) │
-│[default: 0] │
-╰───────────────────────────────────────────────────────────────────────────────────╯
-╭─ Abundance distribution options ──────────────────────────────────────────────────╮
-│--dist Sample taxonomic abundances from a distribution (none|lognormal|even)│
-│[default: none] │
-│--mu Mu of lognormal dist (INTEGER)│
-│--sigma Sigma of lognormal dist (INTEGER)│
-╰───────────────────────────────────────────────────────────────────────────────────╯
-╭─ Taxonomic profile options ───────────────────────────────────────────────────────╮
-│--ranks Ranks to show in the taxonomic profile │
-│(TEXT) │
-│[default: superkingdom,phylum,class,order,family,genus,species,strain]│
-╰───────────────────────────────────────────────────────────────────────────────────╯
-╭─ Skip options ────────────────────────────────────────────────────────────────────╮
-│--skip-shuffle Skip fastq shuffling │
-╰───────────────────────────────────────────────────────────────────────────────────╯
-╭─ Snakemake options ───────────────────────────────────────────────────────────────╮
-│--configfile Custom config file [default: (outputDir)/config.yaml] (TEXT)│
-│--profile Snakemake profile to use (TEXT)│
-│--sdm Software deplolyment method (conda|apptainer)[default: conda]│
-│--prefix Custom softawre deployment directory (PATH)│
-│--snake-default Customise Snakemake runtime args │
-│(TEXT) │
-│[default: --printshellcmds, --nolock, --show-failed-logs]│
-╰───────────────────────────────────────────────────────────────────────────────────╯
-
- Simulate reads from local fasta
- EXAMPLES: mess simulate -i [input] --tech [tech] --fasta [fasta-dir] -o [output]
- or
- mess simulate -i [input] --tech [tech] --asm-summary [asm-summary] -o [output]
-
-
+
+ $ mess simulate -h
+
+Usage:mess simulate [OPTIONS] [SNAKE_ARGS]...
+
+ Simulate reads from local fastas
+
+╭─ Common options ──────────────────────────────────────────────────────────────────╮
+│*--input-i Path to input table(s) (PATH)[required]│
+│--output-o Output directory (PATH)[default: mess_out]│
+│--threads Number of threads to use (INTEGER)[default: 1]│
+│--taxonkit Define path to taxonkit data-dir (PATH)[default: (dynamic)]│
+│--help-h Show this message and exit. │
+╰───────────────────────────────────────────────────────────────────────────────────╯
+╭─ Local genomes options ───────────────────────────────────────────────────────────╮
+│--asm-summary Summary table with genome sizes, fasta paths, contig counts... │
+│(TEXT) │
+│--fasta Path to local fasta directory if no path is set in summary or │
+│ input table │
+│(TEXT) │
+╰───────────────────────────────────────────────────────────────────────────────────╯
+╭─ Common simulators options ───────────────────────────────────────────────────────╮
+│--tech Sequencing technology (illumina|pacbio|nanopore)│
+│[default: illumina] │
+│--bases Per sample base counts (ignored when coverage is set) (TEXT)│
+│[default: 1G] │
+│--tool Which simulator to use (art|pbsim3)[default: art]│
+│--error Simulator error profile (TEXT)[default: HS25]│
+│--mean-len Mean read length for long and short read sequencing (INTEGER)│
+│--bam/--no-bam Generate gold standard bam files [default: no-bam]│
+│--seed Seed for pseudo random number generator (INTEGER)[default: 1]│
+╰───────────────────────────────────────────────────────────────────────────────────╯
+╭─ art_illumina options ────────────────────────────────────────────────────────────╮
+│--custom-err Path to art custom error profile basename (TEXT)│
+│--paired Illumina reads pairing [default: True]│
+│--frag-len Fragment length for paired short read sequencing (INTEGER)│
+│[default: 200] │
+│--frag-sd Fragment length standard deviation for paired short read │
+│ sequencing │
+│(INTEGER) │
+│[default: 10] │
+╰───────────────────────────────────────────────────────────────────────────────────╯
+╭─ pbsim3 options ──────────────────────────────────────────────────────────────────╮
+│--model Path to pbsim3 sequencing error models │
+│(QSHMM-ONT-HQ|QSHMM-ONT|QSHMM-RSII) │
+│--model-path Path to pbsim3 sequencing error models │
+│(PATH) │
+│[default: │
+│/opt/hostedtoolcache/Python/3.12.7/x64/lib/python3.12/site-packa…│
+│--ratio PBSIM3 substitution, insertion and deletion ratio (TEXT)│
+│[default: 6:55:39] │
+│--accuracy Mean accuracy for long read sequencing (FLOAT)[default: 0.99]│
+│--passes Nmber of passes for pacbio multipass sequencing (2 or more for │
+│ hifi) │
+│(INTEGER) │
+│[default: 1] │
+│--min-len Minimum read length for long read sequencing (INTEGER)│
+│[default: 100] │
+│--max-len Maximum read length for long read sequencing (INTEGER)│
+│[default: 1000000] │
+│--sd-len Standard read length deviation for long read sequencing (INTEGER)│
+│[default: 7000] │
+╰───────────────────────────────────────────────────────────────────────────────────╯
+╭─ Replicates options ──────────────────────────────────────────────────────────────╮
+│--replicates Number of replicates per sample (INTEGER)[default: 1]│
+│--rep-sd Standard deviation between replicate coverages (0: no deviation) │
+│(INTEGER) │
+│[default: 0] │
+╰───────────────────────────────────────────────────────────────────────────────────╯
+╭─ Abundance distribution options ──────────────────────────────────────────────────╮
+│--dist Sample taxonomic abundances from a distribution (none|lognormal|even)│
+│[default: none] │
+│--mu Mu of lognormal dist (FLOAT)│
+│--sigma Sigma of lognormal dist (FLOAT)│
+╰───────────────────────────────────────────────────────────────────────────────────╯
+╭─ Taxonomic profile options ───────────────────────────────────────────────────────╮
+│--ranks Ranks to show in the taxonomic profile │
+│(TEXT) │
+│[default: superkingdom,phylum,class,order,family,genus,species,strain]│
+╰───────────────────────────────────────────────────────────────────────────────────╯
+╭─ Skip options ────────────────────────────────────────────────────────────────────╮
+│--skip-shuffle Skip fastq shuffling │
+╰───────────────────────────────────────────────────────────────────────────────────╯
+╭─ Snakemake options ───────────────────────────────────────────────────────────────╮
+│--configfile Custom config file [default: (outputDir)/config.yaml] (TEXT)│
+│--profile Snakemake profile to use (TEXT)│
+│--sdm Software deplolyment method (conda|apptainer)[default: conda]│
+│--prefix Custom softawre deployment directory (PATH)│
+│--snake-default Customise Snakemake runtime args │
+│(TEXT) │
+│[default: --printshellcmds, --nolock, --show-failed-logs]│
+╰───────────────────────────────────────────────────────────────────────────────────╯
+
+ Simulate reads from local fasta
+ EXAMPLES: mess simulate -i [input] --tech [tech] --fasta [fasta-dir] -o [output]
+ or
+ mess simulate -i [input] --tech [tech] --asm-summary [asm-summary] -o [output]
+
+