map_reports_sarek: Map out Sarek _report_ files

In nf-osi/nfportalutils: NF Portal Utilities

Map out Sarek report files

Description

This is in the family of helper funs to annotate secondary report files from certain nextflow workflows. For Sarek, many report files are conveniently outputted in a top-level "Reports" folder, which organize reports by sample and then tool (BFCTools, FastQC, etc.). An example reference starting at the sample-level: https://www.synapse.org/#!Synapse:syn31665258 While most things in "Reports" can indeed generally be called a "workflow report" (a subclass of the "report" resource), some files in the bamQC reports directory are misc web assets (.css, .js, .gif, etc.) used for the HTML report. HTML reports should have these asset files are directly embedded/bundled in the .html file, but when they don't these misc files become an extra annotation burden. Since it's debatable to call something like a .css file a report, these files are classified instead as "report asset".

Usage

map_reports_sarek(syn_out, project)

Arguments

syn_out	The Reports output folder which is set as scope for fileview.
project	Project in which to put fileview.

Details

Unlike the other ⁠map_*⁠ functions, this requires a fileview instead of using walk and will create one.

nf-osi/nfportalutils documentation built on Feb. 26, 2024, 1:05 p.m.