Dotfiles¶

Several dotfiles (files prefixed by a single ., as in .status) are created at the beginning of every nextflow process that has the following placeholder (see Create process template):

process myProcess {
{% include "post.txt" ignore missing %}
(...)
}


The actual script that creates the dotfiles is found in flowcraft/bin, is called set_dotfiles.sh and executes the following command:

touch .status .warning .fail .report.json .versions


Status¶

The .status file simply stores a string with the run status of the process. The supported status are:

• pass: The process finished successfully
• fail: The process ran without unexpected issues but failed due to some quality control check
• error: The process exited with an unexpected error.

Warning¶

The .warning file stores any warnings that may occur during the execution of the process. There is no particular format for the warning messages other than that each individual warning should be in a separate line.

Fail¶

The .fail file stores any fail messages that may occur during the execution of the process. When this occurs, the .status channel must have the fail string as well. As in the warning dotfile, there is no particular format for the fail message.

Report JSON¶

Important

The general specification of the report JSON changed in version 1.2.2. See the issue tracker for details.

The .report.json file stores any information from a given process that is deemed worthy of being reported and displayed at the end of the pipeline. Any information can be stored in this file, as long as it is in JSON format, but there are a couple of recommendations that are necessary to follow for them to be processed by a reporting web app (Currently hosted at flowcraft-webapp). However, if data processing will be performed with custom scripts, feel free to specify your own format.

Information for tables¶

Information meant to be displayed in tables should be in the following format:

json_dic = {
"tableRow": [{
"sample": "A",
"data": [{
"value": 123,
"table": "qc"
}, {
"value": 32,
"table": "qc"
}]
}, {
"sample": "B",
"data": [{
"value": 35,
"table": "qc"
}]
}]
}


This provides table information for multiple samples in the same process. In this case, data for two samples is provided. For each sample, values for one or more headers can be provided. For instance, this report provides information about the Raw BP and Coverage for sample A and this information should go to the qc table. If any other information is relevant to build the table, feel free to add more elements to the JSON.

Information for plots¶

Information meant to be displayed in plots should be in the following format:

json_dic = {
"plotData": [{
"sample": "strainA",
"data": {
"sparkline": 23123,
"otherplot": [1,2,3]
}
}],
}


As in the table JSON, plotData should be an array with an entry for each sample. The data for each sample should be another JSON where the keys are the plot signatures, so that we know to which plot the data belongs. The corresponding values are whatever data object you need.

Other information¶

Other than tables and plots, which have a somewhat predefined format, there is not particular format for other information. They will simply store the data of interest to report and it will be the job of a downstream report app to process that data into an actual visual report.

Versions¶

The .version dotfile should contain a list of JSON objects with the version information of the programs used in any given process. There are only two required key:value pairs:

• program: String with the name of the software/script/template
• version: String with the version of said software.

As an example:

version = {
"program": "abricate"
"version": "0.3.7"
}


Key:value pairs with other metadata can be included at will for downstream processing.