From 2ff35605a65d53b3621a08cb8e2ab3d91d2f9099 Mon Sep 17 00:00:00 2001 From: Ivan Blagoev Topolsky Date: Sat, 28 Dec 2024 22:07:30 +0100 Subject: [PATCH] Update documentation - latest jsonschema-for-humans converts `--` into emdashes --- config/config.html | 111 ++++++++++++++++++++++++++-- workflow/schemas/config_schema.json | 2 +- 2 files changed, 104 insertions(+), 9 deletions(-) diff --git a/config/config.html b/config/config.html index 8eaa09b1..a1cc28d6 100644 --- a/config/config.html +++ b/config/config.html @@ -1214,6 +1214,61 @@

+
+
+
+

+ +

+
+ +
+
+ +
root + + + + input + + + + primers_trim_cutoff
Type: null or number Default: 0.5
+

Functionally similar to property trim_percent_cutoff, but happens at a later stage, after primer trimming.

+ +

Using this parameter, the user can specify the minimum read-length threshold that should be applied during the primers trimming (aka amplicon clipping), either as a percentage (0 < trim_percent_cutoff <= 1) or as an absolute base pair lenght.

+ +

Leave empty (json: null) to leave the triming software’s default

+ +

Note: This option works better than iVar’s own average-based autodetection which can fail in case of abundant primer dimers in the alignment, because V-pipe knows the exact read-lenght from either the property read_length or the samples file.

+ + + + + + +
+
Examples:
+
None
+
+
0.7
+
+
200
+
+
+
+
+
+
@@ -11055,6 +11110,46 @@

+

+
+
+ +
+
+
+

+ +

+
+ +
+
+ +
root + + + + lofreq + + + + threads
Type: integer Default: 4
+ + + + + + +
@@ -13650,15 +13745,15 @@

It will receive the following parameters (in addition to what is specified in property options:

    -
  • --output <OUTPUT>: the output TSV file that must be created by the script.
    • +
  • --output <OUTPUT>: the output TSV file that must be created by the script.
  • <SAMPLE_TSV>: the input samples TSV file

For an example, see the default script file_parser.py, it uses regular expressions (regex) to parse the first two columns (sample and batch names) and extract a date, and a location code that is further look-ed up in a table. It takes two additional parameters:

    -
  • --locations <LOOKUP>: look-up TSV table mapping the code to full location names
    • -
  • --regex_yaml <YAML>: YAML file with regular expressions defining how the date and code are extracted.
    • +
  • --locations <LOOKUP>: look-up TSV table mapping the code to full location names
    • +
  • --regex_yaml <YAML>: YAML file with regular expressions defining how the date and code are extracted.
@@ -14009,7 +14104,7 @@

/> timeline_file

Type: string Default: ""
-

If set, this user-provided TSV file (e.g.: generated with an external tool, prior of running V-pipe) will be used for obtaining locations and dates -- as needed by LolliPop -- instead of generating results/timeline.tsv with the rule timeline.
+

If set, this user-provided TSV file (e.g.: generated with an external tool, prior of running V-pipe) will be used for obtaining locations and dates – as needed by LolliPop – instead of generating results/timeline.tsv with the rule timeline.
This follows the following format (similar to the output of rule timeline):

sample  batch   reads   proto   location_code   date    location
@@ -14452,7 +14547,7 @@ 

             />
         
     filtersType: string Default: ""

-
List of filters for removing problematic mutations from tally. Some mutations might be problematic and need to be taken out -- e.g. due to drop-outs in the multiplex PCR amplification, they do not show up in the data and this could be misinterpreted by LolliPop as proof of absence of a variant.

+
List of filters for removing problematic mutations from tally. Some mutations might be problematic and need to be taken out – e.g. due to drop-outs in the multiplex PCR amplification, they do not show up in the data and this could be misinterpreted by LolliPop as proof of absence of a variant.

 
         
 
@@ -15235,7 +15330,7 @@ 

             />
         
     catchupType: boolean Default: false

-
Use this option when generating dehumanized raw reads (dehuman.cram) on old samples that have already been processed in the past --- a catch up.

+
Use this option when generating dehumanized raw reads (dehuman.cram) on old samples that have already been processed in the past — a catch up.

 
 
Normally, removing host-mapping reads requires analyzing reads which were rejected by V-pipe’s main processing (as specified in section general, property aligner). But this output is considered temporary and will get deleted by Snakemake once the processing of a sample has finished. To generate dehuman.cram V-pipe would need to run the aligner again, which will both regenerate the data necessary for this output but also generate a new alignment which will trigger the whole workflow again.

 Use this property catchup to only generate the input necessary for dehuman.cram, leaving untouched the alignment and everything else that has already been processed.

@@ -15867,7 +15962,7 @@ 

 
  • <OUTPUT>: the output file that must be created by the script.
    • 
 
  • <SAMPLE_ID>: a string (with no path separator slashes) that can be used as a name, uniquely identifying the sample and the date.
    • 
 
  • <SAMPLE_DIR>: the base directory of the sample.
    • 
-
  • <UPLOAD_FILES>...: a list of files to consider for upload
    • 
+
  • <UPLOAD_FILES>…: a list of files to consider for upload
    • 
 
 
 
    For an example, see the default script prepare_upload_symlinks.sh, it generates symlinks that help tracking which samples are new and/or updated between runs of V-pipe and thus should be considered for upload.
    
@@ -15929,6 +16024,6 @@ 
    
 
 
     
 
\ No newline at end of file
diff --git a/workflow/schemas/config_schema.json b/workflow/schemas/config_schema.json
index feb908eb..59b89c65 100644
--- a/workflow/schemas/config_schema.json
+++ b/workflow/schemas/config_schema.json
@@ -1593,7 +1593,7 @@
                 "script": {
                     "type": "string",
                     "default": "{VPIPE_BASEDIR}/scripts/file_parser.py",
-                    "description": "Script that sets up a timeline of the samples.\n\nIts purpose is to take the V-pipe's samples TSV file and add two columns:\n - _location_: location of the sampes\n - _date_: sampling date of the samples\n\nIt will receive the following parameters (in addition to what is specified in property _options_:\n - *--output <OUTPUT>*: the output TSV file that must be created by the script.\n - *<SAMPLE_TSV>*: the input samples TSV file\n\nFor an example, see the default script `file_parser.py`, it uses regular expressions (regex) to parse the first two columns (sample and batch names) and extract a date, and a location code that is further look-ed up in a table. It takes two additional parameters:\n - *--locations <LOOKUP>*: look-up TSV table mapping the code to full location names\n - *--regex_yaml <YAML>*: YAML file with regular expressions defining how the date and code are extracted.",
+                    "description": "Script that sets up a timeline of the samples.\n\nIts purpose is to take the V-pipe's samples TSV file and add two columns:\n - _location_: location of the sampes\n - _date_: sampling date of the samples\n\nIt will receive the following parameters (in addition to what is specified in property _options_:\n - *`--output` <OUTPUT>*: the output TSV file that must be created by the script.\n - *<SAMPLE_TSV>*: the input samples TSV file\n\nFor an example, see the default script `file_parser.py`, it uses regular expressions (regex) to parse the first two columns (sample and batch names) and extract a date, and a location code that is further look-ed up in a table. It takes two additional parameters:\n - *`--locations` <LOOKUP>*: look-up TSV table mapping the code to full location names\n - *`--regex_yaml` <YAML>*: YAML file with regular expressions defining how the date and code are extracted.",
                     "example": ["custom_scripts/uploader.py"]
                 },
                 "options": {