MultiQC: summarize analysis results for multiple tools and samples in a single report

Highlights

Better configs

As of this release, you can now set all of your config variables via environment variables! (see docs).

Better still, YAML config files can now use string interpolation to parse environment variables within strings (see docs), eg:

report_header_info:
  - Contact E-mail: !ENV "${NAME:info}@${DOMAIN:example.com}"

Picard refactoring

In this release, there was a significant refactoring of the Picard module. It has been generalized for better code sharing with other Picard-based software, like Sentieon and Parabricks. As a result of this, the standalone Sentieon module was removed: Sentieon QC files will be interpreted directly as Picard QC files.

If you were using the Sentieon module in your pipelines, make sure to update any places that reference the module name:

• MultiQC command line (e.g. replace --module sentieon with --module picard).
• MultiQC configs (e.g. replace sentieon with picard in options like run_modules, exclude_modules, module_order).
• Downstream code that relies on names of the files in multiqc_data or multiqc_plots saves (e.g., multiqc_data/multiqc_sentieon_AlignmentSummaryMetrics.txt becomes multiqc_data/multiqc_picard_AlignmentSummaryMetrics.txt).
• Code that parses data files like multiqc_data/multiqc_data.json.
• Custom plugins and templates that rely on HTML anchors (e.g. #sentieon_aligned_reads becomes #picard_AlignmentSummaryMetrics).
• Also, note that Picard fetches sample names from the commands it finds inside the QC headers (e.g. # net.sf.picard.analysis.CollectMultipleMetrics INPUT=Szabo_160930_SN583_0215_AC9H20ACXX.bam ... -> Szabo_160930_SN583_0215_AC9H20ACXX), whereas the removed Sentieon module prioritized the QC file names. To revert to the old Sentieon approach, use the use_filename_as_sample_name config flag.

MultiQC updates

• Config can be set with environment variables, including env var interpolation (#2178)
• Try find config in ~/.config or $XDG_CONFIG_HOME (#2183)
• Better sample name cleaning with pairs of input filenames (#2181)
• Software versions: allow any string as a version tag (#2166)
• Table columns with non-numeric values and now trigger a linting error if scale is set (#2176)
• Stricter config variable typing (#2178)
• Remove position:absolute CSS from table values (#2169)
• Fix column sorting in exported TSV files from a matplotlib linegraph plot (#2143)
• Fix custom anchors for kraken (#2170)
• Fix logging spillover bug (#2174)

New Modules

• Seqera Platform CLI (#2151)
  • Seqera Platform CLI reports statistics generated by the Seqera Platform CLI.
• Xenome (#1860)
  • A tool for classifying reads from xenograft sources.
• xengsort (#2168)
  • xengsort is a fast xenograft read sorter based on space-efficient k-mer hashing

Module updates

• fastp: add version parsing (#2159)
• fastp: correctly parse sample name from --in1/--in2 in bash command. Prefer file name if not fastp.json; fallback to file name when error (#2139)
• Kaiju: fix division by zero error (#2179)
• Nanostat: account for both tab and spaces in v1.41+ search pattern (#2155)
• Pangolin: update for v4: add QC Note , update tool versions columns (#2157)
• Picard: Generalize to directly support Sentieon and Parabricks outputs (#2110)
• Sentieon: Removed the module in favour of directly supporting parsing by the Picard module (#2110)
  • Note that any code that relies on the module name needs to be updated, e.g. -m sentieon will no longer work
  • The exported plot and data files will be now be prefixed as picard instead of sentieon, etc.
  • Note that the Sentieon module used to fetch the sample names from the file names by default, and now it follows the Picard module's logic, and prioritizes the commands recorded in the logs. To override, use the use_filename_as_sample_name config flag