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Fix anchor keys, pipeline options, and reporting issues #11

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Merged
cokelaer merged 3 commits into from
Aug 22, 2026
Merged

Fix anchor keys, pipeline options, and reporting issues #11

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e7045d5
Fix the anchor keys of the summary sections
cokelaer Aug 21, 2026
1fec3e7
Fix the broken options and the report of the quality_control pipeline
cokelaer Aug 22, 2026
7e1353b
Do not nest the trimming outputs in the summary rule input
cokelaer Aug 22, 2026
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7 changes: 7 additions & 0 deletions README.rst
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Expand Up @@ -93,6 +93,13 @@ ChangeLog
========= ====================================================================
Version Description
========= ====================================================================
1.2.0 * fix --skip-phix-removal and --disable-trimming, which both ended
in a NameError
* compute the FastQ statistics of R2 as well (R1 only before)
* the adapter section of the report shows the trimmed data (it was
showing the phix data) and links the FastQC reports that exist
* do not hide a failure of the final summary.html anymore
* remove the dead fastp rules and the kraken entries of the rulegraph
1.0.0 * switch to click, pyproject. remove kraken (see multitax pipeline
instead). Uses new convention.
0.10.0 * add missing MANIFEST
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2 changes: 1 addition & 1 deletion pyproject.toml
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Expand Up @@ -4,7 +4,7 @@ build-backend = "poetry.core.masonry.api"

[tool.poetry]
name = "sequana-quality-control"
version = "1.1.0"
version = "1.2.0"
description = "Quality control pipeline for NGS data (phix removal, adapter trimming, FastQC)"
authors = ["Sequana Team"]
license = "BSD-3"
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2 changes: 1 addition & 1 deletion sequana_pipelines/quality_control/config.yaml
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Expand Up @@ -6,7 +6,7 @@
# If input_directory provided, use it otherwise if input_pattern provided,
# use it, otherwise use input_samples.
# ============================================================================
input_directory: /home/cokelaer/Data/Hm2
input_directory:
input_readtag: _R[12]_
input_pattern: '*fastq.gz'
reference_file: phiX174.fa
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2 changes: 2 additions & 0 deletions sequana_pipelines/quality_control/main.py
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Expand Up @@ -64,6 +64,8 @@ def main(**options):
# --------------------------------------------------------- trimming
cfg.trimming.software_choice = options.trimming_software_choice
cfg.trimming.do = not options.disable_trimming
# the cutadapt section is the one used by the trimming rules
cfg.cutadapt.do = cfg.trimming.do
qual = options.trimming_quality

if options.trimming_software_choice in ["cutadapt", "atropos"]:
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