What’s new in msgen 0.7.*

This version of msgen allows multiple file submission and adds new functionality for the list command. Previously, it was possible to submit only a pair of FASTQ files or a single BAM file, and users had no options to control the output of the list command.

Submitting multiple FASTQ or multiple BAM files

You can now submit multiple FASTQ files or multiple BAM files at once, if they come from the same sample. Note that you still cannot mix FASTQ and BAM files in the same submission, even if they originate from the same sample; you would have to bring them all to a single format. Instructions on how to submit multiple files are here: How do I submit multiple FASTQ and BAM files for processing?

Filtering options

You can now filter completed workflows by their outcome and all workflows by their description and process name. Below is a table showing all filtering options.

Argument of the list command Explanation
-o/--outcome fail | pass Show only completed workflows that failed (fail) or succeeded (pass)
-d/--with-description substring Show any workflows that contain substring in their description
-p/--with-process substring Show any workflows that contain substring in their process name

Range limiting options

You can now limit the list of workflows returned by the service using a Python-like slice notation. Imagine that all your workflows constitute a list starting with the oldest workflow and ending with the most recently submitted one. In that case, your oldest workflow will have index 0, and your most recent, index -1. Here are some examples.

Value of -r/–in-range Explanation
-r/--in-range :10 List ten oldest workflows
-r/--in-range -10: List ten most recent workflows
-r/--in-range 1:10 List nine workflows starting from the second oldest
-r/--in-range -10:-1 List nine workflows starting from the tenth most recent and excluding the very last one submitted
-r/--in-range 0 List only the first workflow
-r/--in-range -1 List only the last workflow
-r/--in-range 5:-5 Error; such values are not allowed
-r/--in-range -5:5
-r/--in-range 5:15:2

Note that this notation is not as powerful as the full Python slice notation. For example, we do not accept increments, and you can only work with one end of the range at a time, i.e. either with the most recent workflows or with the oldest ones.

Another important thing is that range is applied after filtering. For example, if your command line includes these arguments, -o fail -r -10:, first, all failing workflows will be selected, and then the ten most recent of those will be returned.

Export to CSV

You can now save a list of workflows into the CSV format. You can either print it to the screen or save it to a file.

Argument of the list command Explanation
-e/--export-to csv Currently, the only allowed value is csv. If this option is omitted, the list will be printed as before.
-of/--output-file file Saves output (CSV or plaintext) to a given file.