updated trident docs

Author: stschiff

.DS_Store

@@ -14,6 +14,7 @@ trident_guide_archive/trident_guide_1.4.1.0_to_1.5.0.1.md	trident_guide_archive/
 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
+trident_guide_archive/trident_guide_1.6.7.1_to_1.6.7.3.md	trident_guide_archive/trident_guide_1.6.7.1_to_1.6.7.3.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

pdf_conversion/pdf_conversion_list.tsv

@@ -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 v1.6.7.1 to v1.6.7.3](https://github.com/poseidon-framework/poseidon-framework.github.io/blob/master/trident.pdf) (shown below)
+- [🗎 Guide for trident v1.7.0.0](https://github.com/poseidon-framework/poseidon-framework.github.io/blob/master/trident.pdf) (shown below)
+- [🗎 Guide for trident v1.6.7.1 to v1.6.7.3](https://github.com/poseidon-framework/poseidon-framework.github.io/blob/master/trident_guid_1.6.7.1_to_1.6.7.3.pdf)
 - [🗎 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)
@@ -47,7 +48,7 @@ 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 v1.6.7.1 to v1.6.7.3
+# Guide for trident v1.7.0.0
 
 ## Installation
 
@@ -58,7 +59,7 @@ See the Poseidon website (<https://www.poseidon-adna.org/#/trident>) or the GitH
 Trident is a command line software tool structured in multiple subcommands. If you installed it properly you can call it on the command line by typing `trident`. This will show an overview of the general options and all subcommands, which are explained in detail below.
 
 ```default
-Usage: trident [--version] [--logMode MODE | --debug] [--errLength INT]
+Usage: trident [--version] [--logMode MODE | --debug] [--errLength INT] 
                [--inPlinkPopName MODE] (COMMAND | COMMAND)
 
   trident is a management and analysis tool for Poseidon packages. Report issues
@@ -815,22 +816,27 @@ With `-z|--zip` the genotype data output can be wrapped in gzipped archives with
  <summary><i class="fas fa-search"></i> <i class="fas fa-terminal"></i> <b>Command line details</b></summary>
 
 ```default
-Usage: trident jannocoalesce ((-s|--sourceFile FILE) | (-d|--baseDir DIR))
-                             (-t|--targetFile FILE) [-o|--outFile FILE]
-                             [--includeColumns ARG | --excludeColumns ARG]
-                             [-f|--force] [--sourceKey ARG] [--targetKey ARG]
+Usage: trident jannocoalesce ([--pvSource VERSION] (-s|--sourceFile FILE) | 
+                               (-d|--baseDir DIR)) [--pvTarget VERSION]
+                             (-t|--targetFile FILE) (-o|--outFile FILE) 
+                             [--includeColumns ARG | --excludeColumns ARG] 
+                             [-f|--force] [--sourceKey ARG] [--targetKey ARG] 
                              [--stripIdRegex ARG]
 
   Coalesce information from one or multiple janno files to another one
 
 Available options:
   -h,--help                Show this help text
+  --pvSource VERSION       Poseidon version (e.g. 2.7.1). (default: 3.0.0)
   -s,--sourceFile FILE     The source .janno file.
   -d,--baseDir DIR         A base directory to search for Poseidon packages.
+  --pvTarget VERSION       Poseidon version (e.g. 2.7.1). (default: 3.0.0)
   -t,--targetFile FILE     The target .janno file to fill.
-  -o,--outFile FILE        An optional file to write the results to. If not
-                           specified, change the target file in place.
-                           (default: Nothing)
+  -o,--outFile FILE        File path to write the result to. Can be identical to
+                           --targetFile to overwrite the target file in place.
+                           Note that trident only writes .janno files in the
+                           latest Poseidon version it supports, so in this case
+                           v3.0.0.
   --includeColumns ARG     A comma-separated list of .janno column names to
                            coalesce. If not specified, all columns that can be
                            found in the source and target will get filled.
@@ -1094,14 +1100,17 @@ Again you can use the `--raw` option to output the survey table in a tab-delimit
  <summary><i class="fas fa-search"></i> <i class="fas fa-terminal"></i> <b>Command line details</b></summary>
 
 ```default
-Usage: trident validate ((-d|--baseDir DIR) [--ignoreGeno] [--fullGeno]
-                          [--ignoreDuplicates] [-c|--ignoreChecksums]
+Usage: trident validate ((-d|--baseDir DIR) [--ignoreGeno] [--fullGeno] 
+                          [--ignoreDuplicates] [-c|--ignoreChecksums] 
                           [--ignorePoseidonVersion] |
                           --pyml FILE | (-p|--genoOne FILE) | --genoFile FILE
                           --snpFile FILE --indFile FILE |
-                          --bedFile FILE --bimFile FILE --famFile FILE |
-                          --vcfFile FILE | --janno FILE | --ssf FILE |
-                          --bib FILE) [--noExitCode] [--onlyLatest]
+                          --bedFile FILE --bimFile FILE --famFile FILE | 
+                          --vcfFile FILE | [--pvJanno VERSION] --janno FILE | 
+                          [--pvSSF VERSION] --ssf FILE |
+                          --bib FILE) [-j|--mandatoryJannoColumn COLNAME] 
+                        [-s|--mandatorySSFColumn COLNAME] [--noExitCode] 
+                        [--onlyLatest]
 
   Check Poseidon packages or package components for structural correctness
 
@@ -1142,9 +1151,19 @@ Available options:
   --famFile FILE           Plink individual file. Accepted file endings are .fam
   --vcfFile FILE           VCF (Variant Call Format) file, optionall gzipped.
                            Accepted file endings are .vcf, .vcf.gz
+  --pvJanno VERSION        Poseidon version (e.g. 2.7.1). (default: 3.0.0)
   --janno FILE             Path to a .janno file.
+  --pvSSF VERSION          Poseidon version (e.g. 2.7.1). (default: 3.0.0)
   --ssf FILE               Path to a .ssf file.
   --bib FILE               Path to a .bib file.
+  -j,--mandatoryJannoColumn COLNAME
+                           Usually optional .janno file column that should be
+                           treated as mandatory, such as e.g. Individual_ID. Can
+                           be given multiple times.
+  -s,--mandatorySSFColumn COLNAME
+                           Usually optional .ssf file column that should be
+                           treated as mandatory, such as e.g. poseidon_IDs. Can
+                           be given multiple times.
   --noExitCode             Do not produce an explicit exit code.
   --onlyLatest             Consider only the latest versions of packages, or the
                            groups and individuals within the latest versions of