update of trident documentation for v1.6.7.1

Author: nevrome

pdf_conversion/pdf_conversion_list.tsv

@@ -13,6 +13,7 @@ trident_guide_archive/trident_guide_1.4.0.2_to_1.4.0.3.md	trident_guide_archive/
 trident_guide_archive/trident_guide_1.4.1.0_to_1.5.0.1.md	trident_guide_archive/trident_guide_1.4.1.0_to_1.5.0.1.pdf
 trident_guide_archive/trident_guide_1.5.4.0.md	trident_guide_archive/trident_guide_1.5.4.0.pdf
 trident_guide_archive/trident_guide_1.5.7.0_to_1.5.7.3.md	trident_guide_archive/trident_guide_1.5.7.0_to_1.5.7.3.pdf
+trident_guide_archive/trident_guide_1.6.2.1.md	trident_guide_archive/trident_guide_1.6.2.1.pdf
 xerxes_guide_archive/xerxes_guide_0.2.0.0.md	xerxes_guide_archive/xerxes_guide_0.2.0.0.pdf
 xerxes_guide_archive/xerxes_guide_1.0.0.2.md	xerxes_guide_archive/xerxes_guide_1.0.0.2.pdf
 janno_details.md	janno_details.pdf

trident.md

@@ -30,7 +30,8 @@ On GitHub you will also find [older release versions](https://github.com/poseido
 
 With `trident --help` and `trident <subcommand> --help` you can get information about each subcommand and parameter directly on the command line. The guide below explains the subcommands in more detail. It is available in .pdf format for the current and previous versions here:
 
-- [🗎 Guide for trident v1.6.2.1](https://github.com/poseidon-framework/poseidon-framework.github.io/blob/master/trident.pdf) (shown below)
+- [🗎 Guide for trident v1.6.7.1](https://github.com/poseidon-framework/poseidon-framework.github.io/blob/master/trident.pdf) (shown below)
+- [🗎 Guide for trident v1.6.2.1](https://github.com/poseidon-framework/poseidon-framework.github.io/blob/master/trident_guide_archive/trident_guide_1.6.2.1.pdf)
 - [🗎 Guide for trident v1.5.7.0 to v1.5.7.3](https://github.com/poseidon-framework/poseidon-framework.github.io/blob/master/trident_guide_archive/trident_guide_1.5.7.0_to_1.5.7.3.pdf)
 - [🗎 Guide for trident v1.5.4.0](https://github.com/poseidon-framework/poseidon-framework.github.io/blob/master/trident_guide_archive/trident_guide_1.5.4.0.pdf)
 - [🗎 Guide for trident v1.4.1.0 to v1.5.0.1](https://github.com/poseidon-framework/poseidon-framework.github.io/blob/master/trident_guide_archive/trident_guide_1.4.1.0_to_1.5.0.1.pdf)
@@ -46,7 +47,7 @@ With `trident --help` and `trident <subcommand> --help` you can get information
 - [🗎 Guide for trident v0.29.0](https://github.com/poseidon-framework/poseidon-framework.github.io/blob/master/trident_guide_archive/trident_guide_0.29.0.pdf)
 - [🗎 Guide for trident v0.28.0](https://github.com/poseidon-framework/poseidon-framework.github.io/blob/master/trident_guide_archive/trident_guide_0.28.0.pdf)
 
-# Guide for trident v1.6.2.1
+# Guide for trident v1.6.7.1
 
 ## Installation
 
@@ -445,8 +446,8 @@ Available options:
                            do not have a SNP that is present in another package.
                            With this option set, the forged dataset will
                            typically have fewer SNPs, but less missingness.
-  --outFormat FORMAT       The format of the output genotype data: EIGENSTRAT or
-                           PLINK. (default: "PLINK")
+  --outFormat FORMAT       The format of the output genotype data: EIGENSTRAT,
+                           PLINK or VCF. (default: PLINK)
   --onlyGeno               Should only the resulting genotype data be returned?
                            This means the output will not be a Poseidon package.
   --minimal                Should the output Poseidon package be reduced to a
@@ -761,8 +762,8 @@ Available options:
                            packages in a -d|--baseDir already have this
                            information in their respective POSEIDON.yml files.
                            (default: Other)
-  --outFormat FORMAT       the format of the output genotype data: EIGENSTRAT or
-                           PLINK.
+  --outFormat FORMAT       the format of the output genotype data: EIGENSTRAT,
+                           PLINK or VCF.
   -o,--outPackagePath DIR  Path for the converted genotype files to be written
                            to. If a path is provided, only the converted
                            genotype files are written out, with no change of the
@@ -945,7 +946,7 @@ As `rectify` reads and rewrites POSEIDON.yml files, it may change their inner or
 ```default
 Usage: trident list ((-d|--baseDir DIR) | --remote [--remoteURL URL]
                       [--archive STRING])
-                    (--packages | --groups | --individuals
+                    (--packages [--fullOutput] | --groups | --individuals
                       [--fullJanno | [-j|--jannoColumn COLNAME]] |
                       --bibliography [--fullBib | [-b|--bibField BIB-FIELD]])
                     [--raw] [--onlyLatest]
@@ -968,6 +969,8 @@ Available options:
                            a list of archives currently available from the
                            official Poseidon Web API. (default: Nothing)
   --packages               List all packages.
+  --fullOutput             extend the output to include information contained
+                           the POSEIDON.yml file
   --groups                 List all groups, ignoring any group names after the
                            first as specified in the .janno-file.
   --individuals            List all individuals/samples.
@@ -998,7 +1001,7 @@ To list packages from your local repositories, as seen above you can run
 trident list -d ... -d ... --packages
 ```
 
-This will yield a nicely formatted table of all packages, their version and the number of individuals in them.
+This will yield a nicely formatted table of all packages, their version and the number of individuals in them. With `--fullOutput` the table includes additional fields from the packages' POSEIDON.yml files.
 
 You can use `--remote` to show packages on the remote server. For example