py-multiqc: Fix patch, test on NetBSD10

To: pkgsrc-wip-changes%NetBSD.org@localhost
Subject: py-multiqc: Fix patch, test on NetBSD10
From: Jason W. Bacon (via pkgsrc-wip) <commit-notify%pkgsrc.org@localhost>
Date: Fri, 22 Nov 2024 13:42:45 +0000
Module Name:	pkgsrc-wip
Committed By:	Jason W. Bacon <bacon%NetBSD.org@localhost>
Pushed By:	outpaddling
Date:		Fri Nov 22 07:42:28 2024 -0600
Changeset:	84a48aa3a8d9cbf0acb4b4d182fdf310562fb92e

Modified Files:
	py-multiqc/Makefile
	py-multiqc/PLIST
	py-multiqc/distinfo
	py-multiqc/patches/patch-multiqc_multiqc.py

Log Message:
py-multiqc: Fix patch, test on NetBSD10

To see a diff of this commit:
https://wip.pkgsrc.org/cgi-bin/gitweb.cgi?p=pkgsrc-wip.git;a=commitdiff;h=84a48aa3a8d9cbf0acb4b4d182fdf310562fb92e

Please note that diffs are not public domain; they are subject to the
copyright notices on the relevant files.

diffstat:
 py-multiqc/Makefile                         |   1 -
 py-multiqc/PLIST                            | 509 ++++++++++++++++++++++------
 py-multiqc/distinfo                         |   2 +-
 py-multiqc/patches/patch-multiqc_multiqc.py |  14 +-
 4 files changed, 422 insertions(+), 104 deletions(-)

diffs:
diff --git a/py-multiqc/Makefile b/py-multiqc/Makefile
index 8a7c02598b..5263a36cc7 100644
--- a/py-multiqc/Makefile
+++ b/py-multiqc/Makefile
@@ -20,7 +20,6 @@ LICENSE=	gnu-gpl-v3
 DEPENDS+=	${PYPKGPREFIX}-humanize-[0-9]*:../../textproc/py-humanize
 DEPENDS+=	${PYPKGPREFIX}-importlib-metadata-[0-9]*:../../devel/py-importlib-metadata
 DEPENDS+=	${PYPKGPREFIX}-orca-[0-9]*:../../wip/py-orca
-DEPENDS+=	${PYPKGPREFIX}-psutil-[0-9]*:../../wip/py-psutil
 DEPENDS+=	${PYPKGPREFIX}-psutil-[0-9]*:../../sysutils/py-psutil
 DEPENDS+=	${PYPKGPREFIX}-packaging-[0-9]*:../../devel/py-packaging
 DEPENDS+=	${PYPKGPREFIX}-pydantic>=2.7.0:../../devel/py-pydantic
diff --git a/py-multiqc/PLIST b/py-multiqc/PLIST
index 45363c8be2..478e788bf7 100644
--- a/py-multiqc/PLIST
+++ b/py-multiqc/PLIST
@@ -1,27 +1,75 @@
 @comment $NetBSD$
 bin/multiqc
-${PYSITELIB}/${EGG_INFODIR}/PKG-INFO
-${PYSITELIB}/${EGG_INFODIR}/SOURCES.txt
-${PYSITELIB}/${EGG_INFODIR}/dependency_links.txt
-${PYSITELIB}/${EGG_INFODIR}/entry_points.txt
-${PYSITELIB}/${EGG_INFODIR}/not-zip-safe
-${PYSITELIB}/${EGG_INFODIR}/requires.txt
-${PYSITELIB}/${EGG_INFODIR}/top_level.txt
+${PYSITELIB}/${WHEEL_INFODIR}/LICENSE
+${PYSITELIB}/${WHEEL_INFODIR}/METADATA
+${PYSITELIB}/${WHEEL_INFODIR}/RECORD
+${PYSITELIB}/${WHEEL_INFODIR}/WHEEL
+${PYSITELIB}/${WHEEL_INFODIR}/entry_points.txt
+${PYSITELIB}/${WHEEL_INFODIR}/top_level.txt
 ${PYSITELIB}/multiqc/__init__.py
 ${PYSITELIB}/multiqc/__init__.pyc
 ${PYSITELIB}/multiqc/__init__.pyo
 ${PYSITELIB}/multiqc/__main__.py
 ${PYSITELIB}/multiqc/__main__.pyc
 ${PYSITELIB}/multiqc/__main__.pyo
+${PYSITELIB}/multiqc/base_module.py
+${PYSITELIB}/multiqc/base_module.pyc
+${PYSITELIB}/multiqc/base_module.pyo
+${PYSITELIB}/multiqc/config.py
+${PYSITELIB}/multiqc/config.pyc
+${PYSITELIB}/multiqc/config.pyo
+${PYSITELIB}/multiqc/config_defaults.yaml
+${PYSITELIB}/multiqc/core/__init__.py
+${PYSITELIB}/multiqc/core/__init__.pyc
+${PYSITELIB}/multiqc/core/__init__.pyo
+${PYSITELIB}/multiqc/core/exceptions.py
+${PYSITELIB}/multiqc/core/exceptions.pyc
+${PYSITELIB}/multiqc/core/exceptions.pyo
+${PYSITELIB}/multiqc/core/exec_modules.py
+${PYSITELIB}/multiqc/core/exec_modules.pyc
+${PYSITELIB}/multiqc/core/exec_modules.pyo
+${PYSITELIB}/multiqc/core/file_search.py
+${PYSITELIB}/multiqc/core/file_search.pyc
+${PYSITELIB}/multiqc/core/file_search.pyo
+${PYSITELIB}/multiqc/core/log_and_rich.py
+${PYSITELIB}/multiqc/core/log_and_rich.pyc
+${PYSITELIB}/multiqc/core/log_and_rich.pyo
+${PYSITELIB}/multiqc/core/order_modules_and_sections.py
+${PYSITELIB}/multiqc/core/order_modules_and_sections.pyc
+${PYSITELIB}/multiqc/core/order_modules_and_sections.pyo
+${PYSITELIB}/multiqc/core/plugin_hooks.py
+${PYSITELIB}/multiqc/core/plugin_hooks.pyc
+${PYSITELIB}/multiqc/core/plugin_hooks.pyo
+${PYSITELIB}/multiqc/core/software_versions.py
+${PYSITELIB}/multiqc/core/software_versions.pyc
+${PYSITELIB}/multiqc/core/software_versions.pyo
+${PYSITELIB}/multiqc/core/strict_helpers.py
+${PYSITELIB}/multiqc/core/strict_helpers.pyc
+${PYSITELIB}/multiqc/core/strict_helpers.pyo
+${PYSITELIB}/multiqc/core/tmp_dir.py
+${PYSITELIB}/multiqc/core/tmp_dir.pyc
+${PYSITELIB}/multiqc/core/tmp_dir.pyo
+${PYSITELIB}/multiqc/core/update_config.py
+${PYSITELIB}/multiqc/core/update_config.pyc
+${PYSITELIB}/multiqc/core/update_config.pyo
+${PYSITELIB}/multiqc/core/version_check.py
+${PYSITELIB}/multiqc/core/version_check.pyc
+${PYSITELIB}/multiqc/core/version_check.pyo
+${PYSITELIB}/multiqc/core/write_results.py
+${PYSITELIB}/multiqc/core/write_results.pyc
+${PYSITELIB}/multiqc/core/write_results.pyo
+${PYSITELIB}/multiqc/interactive.py
+${PYSITELIB}/multiqc/interactive.pyc
+${PYSITELIB}/multiqc/interactive.pyo
 ${PYSITELIB}/multiqc/modules/__init__.py
 ${PYSITELIB}/multiqc/modules/__init__.pyc
 ${PYSITELIB}/multiqc/modules/__init__.pyo
-${PYSITELIB}/multiqc/modules/adapterRemoval/__init__.py
-${PYSITELIB}/multiqc/modules/adapterRemoval/__init__.pyc
-${PYSITELIB}/multiqc/modules/adapterRemoval/__init__.pyo
-${PYSITELIB}/multiqc/modules/adapterRemoval/adapterRemoval.py
-${PYSITELIB}/multiqc/modules/adapterRemoval/adapterRemoval.pyc
-${PYSITELIB}/multiqc/modules/adapterRemoval/adapterRemoval.pyo
+${PYSITELIB}/multiqc/modules/adapterremoval/__init__.py
+${PYSITELIB}/multiqc/modules/adapterremoval/__init__.pyc
+${PYSITELIB}/multiqc/modules/adapterremoval/__init__.pyo
+${PYSITELIB}/multiqc/modules/adapterremoval/adapterremoval.py
+${PYSITELIB}/multiqc/modules/adapterremoval/adapterremoval.pyc
+${PYSITELIB}/multiqc/modules/adapterremoval/adapterremoval.pyo
 ${PYSITELIB}/multiqc/modules/afterqc/__init__.py
 ${PYSITELIB}/multiqc/modules/afterqc/__init__.pyc
 ${PYSITELIB}/multiqc/modules/afterqc/__init__.pyo
@@ -34,6 +82,18 @@ ${PYSITELIB}/multiqc/modules/anglerfish/__init__.pyo
 ${PYSITELIB}/multiqc/modules/anglerfish/anglerfish.py
 ${PYSITELIB}/multiqc/modules/anglerfish/anglerfish.pyc
 ${PYSITELIB}/multiqc/modules/anglerfish/anglerfish.pyo
+${PYSITELIB}/multiqc/modules/bakta/__init__.py
+${PYSITELIB}/multiqc/modules/bakta/__init__.pyc
+${PYSITELIB}/multiqc/modules/bakta/__init__.pyo
+${PYSITELIB}/multiqc/modules/bakta/bakta.py
+${PYSITELIB}/multiqc/modules/bakta/bakta.pyc
+${PYSITELIB}/multiqc/modules/bakta/bakta.pyo
+${PYSITELIB}/multiqc/modules/bamdst/__init__.py
+${PYSITELIB}/multiqc/modules/bamdst/__init__.pyc
+${PYSITELIB}/multiqc/modules/bamdst/__init__.pyo
+${PYSITELIB}/multiqc/modules/bamdst/bamdst.py
+${PYSITELIB}/multiqc/modules/bamdst/bamdst.pyc
+${PYSITELIB}/multiqc/modules/bamdst/bamdst.pyo
 ${PYSITELIB}/multiqc/modules/bamtools/__init__.py
 ${PYSITELIB}/multiqc/modules/bamtools/__init__.pyc
 ${PYSITELIB}/multiqc/modules/bamtools/__init__.pyo
@@ -43,9 +103,6 @@ ${PYSITELIB}/multiqc/modules/bamtools/bamtools.pyo
 ${PYSITELIB}/multiqc/modules/bamtools/stats.py
 ${PYSITELIB}/multiqc/modules/bamtools/stats.pyc
 ${PYSITELIB}/multiqc/modules/bamtools/stats.pyo
-${PYSITELIB}/multiqc/modules/base_module.py
-${PYSITELIB}/multiqc/modules/base_module.pyc
-${PYSITELIB}/multiqc/modules/base_module.pyo
 ${PYSITELIB}/multiqc/modules/bbduk/__init__.py
 ${PYSITELIB}/multiqc/modules/bbduk/__init__.pyc
 ${PYSITELIB}/multiqc/modules/bbduk/__init__.pyo
@@ -172,18 +229,24 @@ ${PYSITELIB}/multiqc/modules/ccs/__init__.pyo
 ${PYSITELIB}/multiqc/modules/ccs/ccs.py
 ${PYSITELIB}/multiqc/modules/ccs/ccs.pyc
 ${PYSITELIB}/multiqc/modules/ccs/ccs.pyo
+${PYSITELIB}/multiqc/modules/ccs/tests/__init__.py
+${PYSITELIB}/multiqc/modules/ccs/tests/__init__.pyc
+${PYSITELIB}/multiqc/modules/ccs/tests/__init__.pyo
+${PYSITELIB}/multiqc/modules/ccs/tests/test_ccs.py
+${PYSITELIB}/multiqc/modules/ccs/tests/test_ccs.pyc
+${PYSITELIB}/multiqc/modules/ccs/tests/test_ccs.pyo
 ${PYSITELIB}/multiqc/modules/cellranger/__init__.py
 ${PYSITELIB}/multiqc/modules/cellranger/__init__.pyc
 ${PYSITELIB}/multiqc/modules/cellranger/__init__.pyo
-${PYSITELIB}/multiqc/modules/cellranger/_utils.py
-${PYSITELIB}/multiqc/modules/cellranger/_utils.pyc
-${PYSITELIB}/multiqc/modules/cellranger/_utils.pyo
 ${PYSITELIB}/multiqc/modules/cellranger/cellranger.py
 ${PYSITELIB}/multiqc/modules/cellranger/cellranger.pyc
 ${PYSITELIB}/multiqc/modules/cellranger/cellranger.pyo
 ${PYSITELIB}/multiqc/modules/cellranger/count.py
 ${PYSITELIB}/multiqc/modules/cellranger/count.pyc
 ${PYSITELIB}/multiqc/modules/cellranger/count.pyo
+${PYSITELIB}/multiqc/modules/cellranger/utils.py
+${PYSITELIB}/multiqc/modules/cellranger/utils.pyc
+${PYSITELIB}/multiqc/modules/cellranger/utils.pyo
 ${PYSITELIB}/multiqc/modules/cellranger/vdj.py
 ${PYSITELIB}/multiqc/modules/cellranger/vdj.pyc
 ${PYSITELIB}/multiqc/modules/cellranger/vdj.pyo
@@ -304,6 +367,9 @@ ${PYSITELIB}/multiqc/modules/dragen/fragment_length.pyo
 ${PYSITELIB}/multiqc/modules/dragen/mapping_metrics.py
 ${PYSITELIB}/multiqc/modules/dragen/mapping_metrics.pyc
 ${PYSITELIB}/multiqc/modules/dragen/mapping_metrics.pyo
+${PYSITELIB}/multiqc/modules/dragen/overall_mean_cov.py
+${PYSITELIB}/multiqc/modules/dragen/overall_mean_cov.pyc
+${PYSITELIB}/multiqc/modules/dragen/overall_mean_cov.pyo
 ${PYSITELIB}/multiqc/modules/dragen/ploidy_estimation_metrics.py
 ${PYSITELIB}/multiqc/modules/dragen/ploidy_estimation_metrics.pyc
 ${PYSITELIB}/multiqc/modules/dragen/ploidy_estimation_metrics.pyo
@@ -319,6 +385,12 @@ ${PYSITELIB}/multiqc/modules/dragen/sc_atac_metrics.pyo
 ${PYSITELIB}/multiqc/modules/dragen/sc_rna_metrics.py
 ${PYSITELIB}/multiqc/modules/dragen/sc_rna_metrics.pyc
 ${PYSITELIB}/multiqc/modules/dragen/sc_rna_metrics.pyo
+${PYSITELIB}/multiqc/modules/dragen/tests/__init__.py
+${PYSITELIB}/multiqc/modules/dragen/tests/__init__.pyc
+${PYSITELIB}/multiqc/modules/dragen/tests/__init__.pyo
+${PYSITELIB}/multiqc/modules/dragen/tests/test_dragen.py
+${PYSITELIB}/multiqc/modules/dragen/tests/test_dragen.pyc
+${PYSITELIB}/multiqc/modules/dragen/tests/test_dragen.pyo
 ${PYSITELIB}/multiqc/modules/dragen/time_metrics.py
 ${PYSITELIB}/multiqc/modules/dragen/time_metrics.pyc
 ${PYSITELIB}/multiqc/modules/dragen/time_metrics.pyo
@@ -383,24 +455,24 @@ ${PYSITELIB}/multiqc/modules/fastqc/fastqc_theoretical_gc/fastqc_theoretical_gc_
 ${PYSITELIB}/multiqc/modules/fastqc/fastqc_theoretical_gc/fastqc_theoretical_gc_hg38_txome.txt
 ${PYSITELIB}/multiqc/modules/fastqc/fastqc_theoretical_gc/fastqc_theoretical_gc_mm10_genome.txt
 ${PYSITELIB}/multiqc/modules/fastqc/fastqc_theoretical_gc/fastqc_theoretical_gc_mm10_txome.txt
-${PYSITELIB}/multiqc/modules/featureCounts/__init__.py
-${PYSITELIB}/multiqc/modules/featureCounts/__init__.pyc
-${PYSITELIB}/multiqc/modules/featureCounts/__init__.pyo
-${PYSITELIB}/multiqc/modules/featureCounts/feature_counts.py
-${PYSITELIB}/multiqc/modules/featureCounts/feature_counts.pyc
-${PYSITELIB}/multiqc/modules/featureCounts/feature_counts.pyo
-${PYSITELIB}/multiqc/modules/fgbio/ErrorRateByReadPosition.py
-${PYSITELIB}/multiqc/modules/fgbio/ErrorRateByReadPosition.pyc
-${PYSITELIB}/multiqc/modules/fgbio/ErrorRateByReadPosition.pyo
+${PYSITELIB}/multiqc/modules/featurecounts/__init__.py
+${PYSITELIB}/multiqc/modules/featurecounts/__init__.pyc
+${PYSITELIB}/multiqc/modules/featurecounts/__init__.pyo
+${PYSITELIB}/multiqc/modules/featurecounts/featurecounts.py
+${PYSITELIB}/multiqc/modules/featurecounts/featurecounts.pyc
+${PYSITELIB}/multiqc/modules/featurecounts/featurecounts.pyo
 ${PYSITELIB}/multiqc/modules/fgbio/__init__.py
 ${PYSITELIB}/multiqc/modules/fgbio/__init__.pyc
 ${PYSITELIB}/multiqc/modules/fgbio/__init__.pyo
+${PYSITELIB}/multiqc/modules/fgbio/error_rate_by_read_position.py
+${PYSITELIB}/multiqc/modules/fgbio/error_rate_by_read_position.pyc
+${PYSITELIB}/multiqc/modules/fgbio/error_rate_by_read_position.pyo
 ${PYSITELIB}/multiqc/modules/fgbio/fgbio.py
 ${PYSITELIB}/multiqc/modules/fgbio/fgbio.pyc
 ${PYSITELIB}/multiqc/modules/fgbio/fgbio.pyo
-${PYSITELIB}/multiqc/modules/fgbio/groupreadsbyumi.py
-${PYSITELIB}/multiqc/modules/fgbio/groupreadsbyumi.pyc
-${PYSITELIB}/multiqc/modules/fgbio/groupreadsbyumi.pyo
+${PYSITELIB}/multiqc/modules/fgbio/group_reads_by_umi.py
+${PYSITELIB}/multiqc/modules/fgbio/group_reads_by_umi.pyc
+${PYSITELIB}/multiqc/modules/fgbio/group_reads_by_umi.pyo
 ${PYSITELIB}/multiqc/modules/filtlong/__init__.py
 ${PYSITELIB}/multiqc/modules/filtlong/__init__.pyc
 ${PYSITELIB}/multiqc/modules/filtlong/__init__.pyo
@@ -419,9 +491,24 @@ ${PYSITELIB}/multiqc/modules/flexbar/__init__.pyo
 ${PYSITELIB}/multiqc/modules/flexbar/flexbar.py
 ${PYSITELIB}/multiqc/modules/flexbar/flexbar.pyc
 ${PYSITELIB}/multiqc/modules/flexbar/flexbar.pyo
+${PYSITELIB}/multiqc/modules/freyja/__init__.py
+${PYSITELIB}/multiqc/modules/freyja/__init__.pyc
+${PYSITELIB}/multiqc/modules/freyja/__init__.pyo
+${PYSITELIB}/multiqc/modules/freyja/freyja.py
+${PYSITELIB}/multiqc/modules/freyja/freyja.pyc
+${PYSITELIB}/multiqc/modules/freyja/freyja.pyo
+${PYSITELIB}/multiqc/modules/ganon/__init__.py
+${PYSITELIB}/multiqc/modules/ganon/__init__.pyc
+${PYSITELIB}/multiqc/modules/ganon/__init__.pyo
+${PYSITELIB}/multiqc/modules/ganon/ganon.py
+${PYSITELIB}/multiqc/modules/ganon/ganon.pyc
+${PYSITELIB}/multiqc/modules/ganon/ganon.pyo
 ${PYSITELIB}/multiqc/modules/gatk/__init__.py
 ${PYSITELIB}/multiqc/modules/gatk/__init__.pyc
 ${PYSITELIB}/multiqc/modules/gatk/__init__.pyo
+${PYSITELIB}/multiqc/modules/gatk/analyze_saturation_mutagenesis.py
+${PYSITELIB}/multiqc/modules/gatk/analyze_saturation_mutagenesis.pyc
+${PYSITELIB}/multiqc/modules/gatk/analyze_saturation_mutagenesis.pyo
 ${PYSITELIB}/multiqc/modules/gatk/base_recalibrator.py
 ${PYSITELIB}/multiqc/modules/gatk/base_recalibrator.pyc
 ${PYSITELIB}/multiqc/modules/gatk/base_recalibrator.pyo
@@ -437,6 +524,18 @@ ${PYSITELIB}/multiqc/modules/gffcompare/__init__.pyo
 ${PYSITELIB}/multiqc/modules/gffcompare/gffcompare.py
 ${PYSITELIB}/multiqc/modules/gffcompare/gffcompare.pyc
 ${PYSITELIB}/multiqc/modules/gffcompare/gffcompare.pyo
+${PYSITELIB}/multiqc/modules/glimpse/__init__.py
+${PYSITELIB}/multiqc/modules/glimpse/__init__.pyc
+${PYSITELIB}/multiqc/modules/glimpse/__init__.pyo
+${PYSITELIB}/multiqc/modules/glimpse/err_grp.py
+${PYSITELIB}/multiqc/modules/glimpse/err_grp.pyc
+${PYSITELIB}/multiqc/modules/glimpse/err_grp.pyo
+${PYSITELIB}/multiqc/modules/glimpse/err_spl.py
+${PYSITELIB}/multiqc/modules/glimpse/err_spl.pyc
+${PYSITELIB}/multiqc/modules/glimpse/err_spl.pyo
+${PYSITELIB}/multiqc/modules/glimpse/glimpse.py
+${PYSITELIB}/multiqc/modules/glimpse/glimpse.pyc
+${PYSITELIB}/multiqc/modules/glimpse/glimpse.pyo
 ${PYSITELIB}/multiqc/modules/goleft_indexcov/__init__.py
 ${PYSITELIB}/multiqc/modules/goleft_indexcov/__init__.pyc
 ${PYSITELIB}/multiqc/modules/goleft_indexcov/__init__.pyo
@@ -449,6 +548,12 @@ ${PYSITELIB}/multiqc/modules/gopeaks/__init__.pyo
 ${PYSITELIB}/multiqc/modules/gopeaks/gopeaks.py
 ${PYSITELIB}/multiqc/modules/gopeaks/gopeaks.pyc
 ${PYSITELIB}/multiqc/modules/gopeaks/gopeaks.pyo
+${PYSITELIB}/multiqc/modules/haplocheck/__init__.py
+${PYSITELIB}/multiqc/modules/haplocheck/__init__.pyc
+${PYSITELIB}/multiqc/modules/haplocheck/__init__.pyo
+${PYSITELIB}/multiqc/modules/haplocheck/haplocheck.py
+${PYSITELIB}/multiqc/modules/haplocheck/haplocheck.pyc
+${PYSITELIB}/multiqc/modules/haplocheck/haplocheck.pyo
 ${PYSITELIB}/multiqc/modules/happy/__init__.py
 ${PYSITELIB}/multiqc/modules/happy/__init__.pyc
 ${PYSITELIB}/multiqc/modules/happy/__init__.pyo
@@ -503,6 +608,12 @@ ${PYSITELIB}/multiqc/modules/hops/__init__.pyo
 ${PYSITELIB}/multiqc/modules/hops/hops.py
 ${PYSITELIB}/multiqc/modules/hops/hops.pyc
 ${PYSITELIB}/multiqc/modules/hops/hops.pyo
+${PYSITELIB}/multiqc/modules/hostile/__init__.py
+${PYSITELIB}/multiqc/modules/hostile/__init__.pyc
+${PYSITELIB}/multiqc/modules/hostile/__init__.pyo
+${PYSITELIB}/multiqc/modules/hostile/hostile.py
+${PYSITELIB}/multiqc/modules/hostile/hostile.pyc
+${PYSITELIB}/multiqc/modules/hostile/hostile.pyo
 ${PYSITELIB}/multiqc/modules/htseq/__init__.py
 ${PYSITELIB}/multiqc/modules/htseq/__init__.pyc
 ${PYSITELIB}/multiqc/modules/htseq/__init__.pyo
@@ -512,15 +623,33 @@ ${PYSITELIB}/multiqc/modules/htseq/htseq.pyo
 ${PYSITELIB}/multiqc/modules/humid/__init__.py
 ${PYSITELIB}/multiqc/modules/humid/__init__.pyc
 ${PYSITELIB}/multiqc/modules/humid/__init__.pyo
+${PYSITELIB}/multiqc/modules/humid/clusters.py
+${PYSITELIB}/multiqc/modules/humid/clusters.pyc
+${PYSITELIB}/multiqc/modules/humid/clusters.pyo
+${PYSITELIB}/multiqc/modules/humid/counts.py
+${PYSITELIB}/multiqc/modules/humid/counts.pyc
+${PYSITELIB}/multiqc/modules/humid/counts.pyo
 ${PYSITELIB}/multiqc/modules/humid/humid.py
 ${PYSITELIB}/multiqc/modules/humid/humid.pyc
 ${PYSITELIB}/multiqc/modules/humid/humid.pyo
+${PYSITELIB}/multiqc/modules/humid/neighbours.py
+${PYSITELIB}/multiqc/modules/humid/neighbours.pyc
+${PYSITELIB}/multiqc/modules/humid/neighbours.pyo
+${PYSITELIB}/multiqc/modules/humid/stats.py
+${PYSITELIB}/multiqc/modules/humid/stats.pyc
+${PYSITELIB}/multiqc/modules/humid/stats.pyo
 ${PYSITELIB}/multiqc/modules/interop/__init__.py
 ${PYSITELIB}/multiqc/modules/interop/__init__.pyc
 ${PYSITELIB}/multiqc/modules/interop/__init__.pyo
 ${PYSITELIB}/multiqc/modules/interop/interop.py
 ${PYSITELIB}/multiqc/modules/interop/interop.pyc
 ${PYSITELIB}/multiqc/modules/interop/interop.pyo
+${PYSITELIB}/multiqc/modules/isoseq/__init__.py
+${PYSITELIB}/multiqc/modules/isoseq/__init__.pyc
+${PYSITELIB}/multiqc/modules/isoseq/__init__.pyo
+${PYSITELIB}/multiqc/modules/isoseq/isoseq.py
+${PYSITELIB}/multiqc/modules/isoseq/isoseq.pyc
+${PYSITELIB}/multiqc/modules/isoseq/isoseq.pyo
 ${PYSITELIB}/multiqc/modules/ivar/__init__.py
 ${PYSITELIB}/multiqc/modules/ivar/__init__.pyc
 ${PYSITELIB}/multiqc/modules/ivar/__init__.pyo
@@ -569,6 +698,12 @@ ${PYSITELIB}/multiqc/modules/leehom/__init__.pyo
 ${PYSITELIB}/multiqc/modules/leehom/leehom.py
 ${PYSITELIB}/multiqc/modules/leehom/leehom.pyc
 ${PYSITELIB}/multiqc/modules/leehom/leehom.pyo
+${PYSITELIB}/multiqc/modules/librarian/__init__.py
+${PYSITELIB}/multiqc/modules/librarian/__init__.pyc
+${PYSITELIB}/multiqc/modules/librarian/__init__.pyo
+${PYSITELIB}/multiqc/modules/librarian/librarian.py
+${PYSITELIB}/multiqc/modules/librarian/librarian.pyc
+${PYSITELIB}/multiqc/modules/librarian/librarian.pyo
 ${PYSITELIB}/multiqc/modules/lima/__init__.py
 ${PYSITELIB}/multiqc/modules/lima/__init__.pyc
 ${PYSITELIB}/multiqc/modules/lima/__init__.pyo
@@ -593,12 +728,30 @@ ${PYSITELIB}/multiqc/modules/malt/__init__.pyo
 ${PYSITELIB}/multiqc/modules/malt/malt.py
 ${PYSITELIB}/multiqc/modules/malt/malt.pyc
 ${PYSITELIB}/multiqc/modules/malt/malt.pyo
-${PYSITELIB}/multiqc/modules/methylQA/__init__.py
-${PYSITELIB}/multiqc/modules/methylQA/__init__.pyc
-${PYSITELIB}/multiqc/modules/methylQA/__init__.pyo
-${PYSITELIB}/multiqc/modules/methylQA/methylQA.py
-${PYSITELIB}/multiqc/modules/methylQA/methylQA.pyc
-${PYSITELIB}/multiqc/modules/methylQA/methylQA.pyo
+${PYSITELIB}/multiqc/modules/mapdamage/__init__.py
+${PYSITELIB}/multiqc/modules/mapdamage/__init__.pyc
+${PYSITELIB}/multiqc/modules/mapdamage/__init__.pyo
+${PYSITELIB}/multiqc/modules/mapdamage/mapdamage.py
+${PYSITELIB}/multiqc/modules/mapdamage/mapdamage.pyc
+${PYSITELIB}/multiqc/modules/mapdamage/mapdamage.pyo
+${PYSITELIB}/multiqc/modules/megahit/__init__.py
+${PYSITELIB}/multiqc/modules/megahit/__init__.pyc
+${PYSITELIB}/multiqc/modules/megahit/__init__.pyo
+${PYSITELIB}/multiqc/modules/megahit/megahit.py
+${PYSITELIB}/multiqc/modules/megahit/megahit.pyc
+${PYSITELIB}/multiqc/modules/megahit/megahit.pyo
+${PYSITELIB}/multiqc/modules/metaphlan/__init__.py
+${PYSITELIB}/multiqc/modules/metaphlan/__init__.pyc
+${PYSITELIB}/multiqc/modules/metaphlan/__init__.pyo
+${PYSITELIB}/multiqc/modules/metaphlan/metaphlan.py
+${PYSITELIB}/multiqc/modules/metaphlan/metaphlan.pyc
+${PYSITELIB}/multiqc/modules/metaphlan/metaphlan.pyo
+${PYSITELIB}/multiqc/modules/methylqa/__init__.py
+${PYSITELIB}/multiqc/modules/methylqa/__init__.pyc
+${PYSITELIB}/multiqc/modules/methylqa/__init__.pyo
+${PYSITELIB}/multiqc/modules/methylqa/methylqa.py
+${PYSITELIB}/multiqc/modules/methylqa/methylqa.pyc
+${PYSITELIB}/multiqc/modules/methylqa/methylqa.pyo
 ${PYSITELIB}/multiqc/modules/minionqc/__init__.py
 ${PYSITELIB}/multiqc/modules/minionqc/__init__.pyc
 ${PYSITELIB}/multiqc/modules/minionqc/__init__.pyo
@@ -641,6 +794,12 @@ ${PYSITELIB}/multiqc/modules/multivcfanalyzer/__init__.pyo
 ${PYSITELIB}/multiqc/modules/multivcfanalyzer/multivcfanalyzer.py
 ${PYSITELIB}/multiqc/modules/multivcfanalyzer/multivcfanalyzer.pyc
 ${PYSITELIB}/multiqc/modules/multivcfanalyzer/multivcfanalyzer.pyo
+${PYSITELIB}/multiqc/modules/nanoq/__init__.py
+${PYSITELIB}/multiqc/modules/nanoq/__init__.pyc
+${PYSITELIB}/multiqc/modules/nanoq/__init__.pyo
+${PYSITELIB}/multiqc/modules/nanoq/nanoq.py
+${PYSITELIB}/multiqc/modules/nanoq/nanoq.pyc
+${PYSITELIB}/multiqc/modules/nanoq/nanoq.pyo
 ${PYSITELIB}/multiqc/modules/nanostat/__init__.py
 ${PYSITELIB}/multiqc/modules/nanostat/__init__.pyc
 ${PYSITELIB}/multiqc/modules/nanostat/__init__.pyo
@@ -653,12 +812,36 @@ ${PYSITELIB}/multiqc/modules/nextclade/__init__.pyo
 ${PYSITELIB}/multiqc/modules/nextclade/nextclade.py
 ${PYSITELIB}/multiqc/modules/nextclade/nextclade.pyc
 ${PYSITELIB}/multiqc/modules/nextclade/nextclade.pyo
+${PYSITELIB}/multiqc/modules/ngsbits/__init__.py
+${PYSITELIB}/multiqc/modules/ngsbits/__init__.pyc
+${PYSITELIB}/multiqc/modules/ngsbits/__init__.pyo
+${PYSITELIB}/multiqc/modules/ngsbits/mappingqc.py
+${PYSITELIB}/multiqc/modules/ngsbits/mappingqc.pyc
+${PYSITELIB}/multiqc/modules/ngsbits/mappingqc.pyo
+${PYSITELIB}/multiqc/modules/ngsbits/ngsbits.py
+${PYSITELIB}/multiqc/modules/ngsbits/ngsbits.pyc
+${PYSITELIB}/multiqc/modules/ngsbits/ngsbits.pyo
+${PYSITELIB}/multiqc/modules/ngsbits/readqc.py
+${PYSITELIB}/multiqc/modules/ngsbits/readqc.pyc
+${PYSITELIB}/multiqc/modules/ngsbits/readqc.pyo
+${PYSITELIB}/multiqc/modules/ngsbits/samplegender.py
+${PYSITELIB}/multiqc/modules/ngsbits/samplegender.pyc
+${PYSITELIB}/multiqc/modules/ngsbits/samplegender.pyo
+${PYSITELIB}/multiqc/modules/ngsbits/utils.py
+${PYSITELIB}/multiqc/modules/ngsbits/utils.pyc
+${PYSITELIB}/multiqc/modules/ngsbits/utils.pyo
 ${PYSITELIB}/multiqc/modules/ngsderive/__init__.py
 ${PYSITELIB}/multiqc/modules/ngsderive/__init__.pyc
 ${PYSITELIB}/multiqc/modules/ngsderive/__init__.pyo
 ${PYSITELIB}/multiqc/modules/ngsderive/ngsderive.py
 ${PYSITELIB}/multiqc/modules/ngsderive/ngsderive.pyc
 ${PYSITELIB}/multiqc/modules/ngsderive/ngsderive.pyo
+${PYSITELIB}/multiqc/modules/nonpareil/__init__.py
+${PYSITELIB}/multiqc/modules/nonpareil/__init__.pyc
+${PYSITELIB}/multiqc/modules/nonpareil/__init__.pyo
+${PYSITELIB}/multiqc/modules/nonpareil/nonpareil.py
+${PYSITELIB}/multiqc/modules/nonpareil/nonpareil.pyc
+${PYSITELIB}/multiqc/modules/nonpareil/nonpareil.pyo
 ${PYSITELIB}/multiqc/modules/odgi/__init__.py
 ${PYSITELIB}/multiqc/modules/odgi/__init__.pyc
 ${PYSITELIB}/multiqc/modules/odgi/__init__.pyo
@@ -671,6 +854,16 @@ ${PYSITELIB}/multiqc/modules/optitype/__init__.pyo
 ${PYSITELIB}/multiqc/modules/optitype/optitype.py
 ${PYSITELIB}/multiqc/modules/optitype/optitype.pyc
 ${PYSITELIB}/multiqc/modules/optitype/optitype.pyo
+${PYSITELIB}/multiqc/modules/pairtools/__init__.py
+${PYSITELIB}/multiqc/modules/pairtools/__init__.pyc
+${PYSITELIB}/multiqc/modules/pairtools/__init__.pyo
+${PYSITELIB}/multiqc/modules/pairtools/pairtools.py
+${PYSITELIB}/multiqc/modules/pairtools/pairtools.pyc
+${PYSITELIB}/multiqc/modules/pairtools/pairtools.pyo
+${PYSITELIB}/multiqc/modules/pairtools/params.yml
+${PYSITELIB}/multiqc/modules/pairtools/utils.py
+${PYSITELIB}/multiqc/modules/pairtools/utils.pyc
+${PYSITELIB}/multiqc/modules/pairtools/utils.pyo
 ${PYSITELIB}/multiqc/modules/pangolin/__init__.py
 ${PYSITELIB}/multiqc/modules/pangolin/__init__.pyc
 ${PYSITELIB}/multiqc/modules/pangolin/__init__.pyo
@@ -701,12 +894,6 @@ ${PYSITELIB}/multiqc/modules/picard/AlignmentSummaryMetrics.pyo
 ${PYSITELIB}/multiqc/modules/picard/BaseDistributionByCycleMetrics.py
 ${PYSITELIB}/multiqc/modules/picard/BaseDistributionByCycleMetrics.pyc
 ${PYSITELIB}/multiqc/modules/picard/BaseDistributionByCycleMetrics.pyo
-${PYSITELIB}/multiqc/modules/picard/CollectIlluminaBasecallingMetrics.py
-${PYSITELIB}/multiqc/modules/picard/CollectIlluminaBasecallingMetrics.pyc
-${PYSITELIB}/multiqc/modules/picard/CollectIlluminaBasecallingMetrics.pyo
-${PYSITELIB}/multiqc/modules/picard/CollectIlluminaLaneMetrics.py
-${PYSITELIB}/multiqc/modules/picard/CollectIlluminaLaneMetrics.pyc
-${PYSITELIB}/multiqc/modules/picard/CollectIlluminaLaneMetrics.pyo
 ${PYSITELIB}/multiqc/modules/picard/CrosscheckFingerprints.py
 ${PYSITELIB}/multiqc/modules/picard/CrosscheckFingerprints.pyc
 ${PYSITELIB}/multiqc/modules/picard/CrosscheckFingerprints.pyo
@@ -719,6 +906,12 @@ ${PYSITELIB}/multiqc/modules/picard/GcBiasMetrics.pyo
 ${PYSITELIB}/multiqc/modules/picard/HsMetrics.py
 ${PYSITELIB}/multiqc/modules/picard/HsMetrics.pyc
 ${PYSITELIB}/multiqc/modules/picard/HsMetrics.pyo
+${PYSITELIB}/multiqc/modules/picard/IlluminaBasecallingMetrics.py
+${PYSITELIB}/multiqc/modules/picard/IlluminaBasecallingMetrics.pyc
+${PYSITELIB}/multiqc/modules/picard/IlluminaBasecallingMetrics.pyo
+${PYSITELIB}/multiqc/modules/picard/IlluminaLaneMetrics.py
+${PYSITELIB}/multiqc/modules/picard/IlluminaLaneMetrics.pyc
+${PYSITELIB}/multiqc/modules/picard/IlluminaLaneMetrics.pyo
 ${PYSITELIB}/multiqc/modules/picard/InsertSizeMetrics.py
 ${PYSITELIB}/multiqc/modules/picard/InsertSizeMetrics.pyc
 ${PYSITELIB}/multiqc/modules/picard/InsertSizeMetrics.pyo
@@ -764,6 +957,12 @@ ${PYSITELIB}/multiqc/modules/picard/__init__.pyo
 ${PYSITELIB}/multiqc/modules/picard/picard.py
 ${PYSITELIB}/multiqc/modules/picard/picard.pyc
 ${PYSITELIB}/multiqc/modules/picard/picard.pyo
+${PYSITELIB}/multiqc/modules/picard/tests/__init__.py
+${PYSITELIB}/multiqc/modules/picard/tests/__init__.pyc
+${PYSITELIB}/multiqc/modules/picard/tests/__init__.pyo
+${PYSITELIB}/multiqc/modules/picard/tests/test_picard.py
+${PYSITELIB}/multiqc/modules/picard/tests/test_picard.pyc
+${PYSITELIB}/multiqc/modules/picard/tests/test_picard.pyo
 ${PYSITELIB}/multiqc/modules/picard/util.py
 ${PYSITELIB}/multiqc/modules/picard/util.pyc
 ${PYSITELIB}/multiqc/modules/picard/util.pyo
@@ -785,6 +984,9 @@ ${PYSITELIB}/multiqc/modules/prinseqplusplus/__init__.pyo
 ${PYSITELIB}/multiqc/modules/prinseqplusplus/prinseqplusplus.py
 ${PYSITELIB}/multiqc/modules/prinseqplusplus/prinseqplusplus.pyc
 ${PYSITELIB}/multiqc/modules/prinseqplusplus/prinseqplusplus.pyo
+${PYSITELIB}/multiqc/modules/profile_runtime.py
+${PYSITELIB}/multiqc/modules/profile_runtime.pyc
+${PYSITELIB}/multiqc/modules/profile_runtime.pyo
 ${PYSITELIB}/multiqc/modules/prokka/__init__.py
 ${PYSITELIB}/multiqc/modules/prokka/__init__.pyc
 ${PYSITELIB}/multiqc/modules/prokka/__init__.pyo
@@ -860,7 +1062,6 @@ ${PYSITELIB}/multiqc/modules/rsem/rsem.pyo
 ${PYSITELIB}/multiqc/modules/rseqc/__init__.py
 ${PYSITELIB}/multiqc/modules/rseqc/__init__.pyc
 ${PYSITELIB}/multiqc/modules/rseqc/__init__.pyo
-${PYSITELIB}/multiqc/modules/rseqc/assets/js/multiqc_rseqc.js
 ${PYSITELIB}/multiqc/modules/rseqc/bam_stat.py
 ${PYSITELIB}/multiqc/modules/rseqc/bam_stat.pyc
 ${PYSITELIB}/multiqc/modules/rseqc/bam_stat.pyo
@@ -918,12 +1119,18 @@ ${PYSITELIB}/multiqc/modules/samblaster/samblaster.pyo
 ${PYSITELIB}/multiqc/modules/samtools/__init__.py
 ${PYSITELIB}/multiqc/modules/samtools/__init__.pyc
 ${PYSITELIB}/multiqc/modules/samtools/__init__.pyo
+${PYSITELIB}/multiqc/modules/samtools/coverage.py
+${PYSITELIB}/multiqc/modules/samtools/coverage.pyc
+${PYSITELIB}/multiqc/modules/samtools/coverage.pyo
 ${PYSITELIB}/multiqc/modules/samtools/flagstat.py
 ${PYSITELIB}/multiqc/modules/samtools/flagstat.pyc
 ${PYSITELIB}/multiqc/modules/samtools/flagstat.pyo
 ${PYSITELIB}/multiqc/modules/samtools/idxstats.py
 ${PYSITELIB}/multiqc/modules/samtools/idxstats.pyc
 ${PYSITELIB}/multiqc/modules/samtools/idxstats.pyo
+${PYSITELIB}/multiqc/modules/samtools/markdup.py
+${PYSITELIB}/multiqc/modules/samtools/markdup.pyc
+${PYSITELIB}/multiqc/modules/samtools/markdup.pyo
 ${PYSITELIB}/multiqc/modules/samtools/rmdup.py
 ${PYSITELIB}/multiqc/modules/samtools/rmdup.pyc
 ${PYSITELIB}/multiqc/modules/samtools/rmdup.pyo
@@ -933,27 +1140,36 @@ ${PYSITELIB}/multiqc/modules/samtools/samtools.pyo
 ${PYSITELIB}/multiqc/modules/samtools/stats.py
 ${PYSITELIB}/multiqc/modules/samtools/stats.pyc
 ${PYSITELIB}/multiqc/modules/samtools/stats.pyo
+${PYSITELIB}/multiqc/modules/samtools/tests/__init__.py
+${PYSITELIB}/multiqc/modules/samtools/tests/__init__.pyc
+${PYSITELIB}/multiqc/modules/samtools/tests/__init__.pyo
+${PYSITELIB}/multiqc/modules/samtools/tests/test_flagstat.py
+${PYSITELIB}/multiqc/modules/samtools/tests/test_flagstat.pyc
+${PYSITELIB}/multiqc/modules/samtools/tests/test_flagstat.pyo
 ${PYSITELIB}/multiqc/modules/sargasso/__init__.py
 ${PYSITELIB}/multiqc/modules/sargasso/__init__.pyc
 ${PYSITELIB}/multiqc/modules/sargasso/__init__.pyo
 ${PYSITELIB}/multiqc/modules/sargasso/sargasso.py
 ${PYSITELIB}/multiqc/modules/sargasso/sargasso.pyc
 ${PYSITELIB}/multiqc/modules/sargasso/sargasso.pyo
-${PYSITELIB}/multiqc/modules/sentieon/AlignmentSummaryMetrics.py
-${PYSITELIB}/multiqc/modules/sentieon/AlignmentSummaryMetrics.pyc
-${PYSITELIB}/multiqc/modules/sentieon/AlignmentSummaryMetrics.pyo
-${PYSITELIB}/multiqc/modules/sentieon/GcBiasMetrics.py
-${PYSITELIB}/multiqc/modules/sentieon/GcBiasMetrics.pyc
-${PYSITELIB}/multiqc/modules/sentieon/GcBiasMetrics.pyo
-${PYSITELIB}/multiqc/modules/sentieon/InsertSizeMetrics.py
-${PYSITELIB}/multiqc/modules/sentieon/InsertSizeMetrics.pyc
-${PYSITELIB}/multiqc/modules/sentieon/InsertSizeMetrics.pyo
-${PYSITELIB}/multiqc/modules/sentieon/__init__.py
-${PYSITELIB}/multiqc/modules/sentieon/__init__.pyc
-${PYSITELIB}/multiqc/modules/sentieon/__init__.pyo
-${PYSITELIB}/multiqc/modules/sentieon/sentieon.py
-${PYSITELIB}/multiqc/modules/sentieon/sentieon.pyc
-${PYSITELIB}/multiqc/modules/sentieon/sentieon.pyo
+${PYSITELIB}/multiqc/modules/seqera_cli/__init__.py
+${PYSITELIB}/multiqc/modules/seqera_cli/__init__.pyc
+${PYSITELIB}/multiqc/modules/seqera_cli/__init__.pyo
+${PYSITELIB}/multiqc/modules/seqera_cli/seqera_cli.py
+${PYSITELIB}/multiqc/modules/seqera_cli/seqera_cli.pyc
+${PYSITELIB}/multiqc/modules/seqera_cli/seqera_cli.pyo
+${PYSITELIB}/multiqc/modules/sequali/__init__.py
+${PYSITELIB}/multiqc/modules/sequali/__init__.pyc
+${PYSITELIB}/multiqc/modules/sequali/__init__.pyo
+${PYSITELIB}/multiqc/modules/sequali/sequali.py
+${PYSITELIB}/multiqc/modules/sequali/sequali.pyc
+${PYSITELIB}/multiqc/modules/sequali/sequali.pyo
+${PYSITELIB}/multiqc/modules/seqwho/__init__.py
+${PYSITELIB}/multiqc/modules/seqwho/__init__.pyc
+${PYSITELIB}/multiqc/modules/seqwho/__init__.pyo
+${PYSITELIB}/multiqc/modules/seqwho/seqwho.py
+${PYSITELIB}/multiqc/modules/seqwho/seqwho.pyc
+${PYSITELIB}/multiqc/modules/seqwho/seqwho.pyo
 ${PYSITELIB}/multiqc/modules/seqyclean/__init__.py
 ${PYSITELIB}/multiqc/modules/seqyclean/__init__.pyc
 ${PYSITELIB}/multiqc/modules/seqyclean/__init__.pyo
@@ -1002,6 +1218,9 @@ ${PYSITELIB}/multiqc/modules/snpsplit/__init__.pyo
 ${PYSITELIB}/multiqc/modules/snpsplit/snpsplit.py
 ${PYSITELIB}/multiqc/modules/snpsplit/snpsplit.pyc
 ${PYSITELIB}/multiqc/modules/snpsplit/snpsplit.pyo
+${PYSITELIB}/multiqc/modules/software_versions.py
+${PYSITELIB}/multiqc/modules/software_versions.pyc
+${PYSITELIB}/multiqc/modules/software_versions.pyo
 ${PYSITELIB}/multiqc/modules/somalier/__init__.py
 ${PYSITELIB}/multiqc/modules/somalier/__init__.pyc
 ${PYSITELIB}/multiqc/modules/somalier/__init__.pyo
@@ -1014,6 +1233,30 @@ ${PYSITELIB}/multiqc/modules/sortmerna/__init__.pyo
 ${PYSITELIB}/multiqc/modules/sortmerna/sortmerna.py
 ${PYSITELIB}/multiqc/modules/sortmerna/sortmerna.pyc
 ${PYSITELIB}/multiqc/modules/sortmerna/sortmerna.pyo
+${PYSITELIB}/multiqc/modules/sourmash/__init__.py
+${PYSITELIB}/multiqc/modules/sourmash/__init__.pyc
+${PYSITELIB}/multiqc/modules/sourmash/__init__.pyo
+${PYSITELIB}/multiqc/modules/sourmash/compare.py
+${PYSITELIB}/multiqc/modules/sourmash/compare.pyc
+${PYSITELIB}/multiqc/modules/sourmash/compare.pyo
+${PYSITELIB}/multiqc/modules/sourmash/gather.py
+${PYSITELIB}/multiqc/modules/sourmash/gather.pyc
+${PYSITELIB}/multiqc/modules/sourmash/gather.pyo
+${PYSITELIB}/multiqc/modules/sourmash/sourmash.py
+${PYSITELIB}/multiqc/modules/sourmash/sourmash.pyc
+${PYSITELIB}/multiqc/modules/sourmash/sourmash.pyo
+${PYSITELIB}/multiqc/modules/spaceranger/__init__.py
+${PYSITELIB}/multiqc/modules/spaceranger/__init__.pyc
+${PYSITELIB}/multiqc/modules/spaceranger/__init__.pyo
+${PYSITELIB}/multiqc/modules/spaceranger/count.py
+${PYSITELIB}/multiqc/modules/spaceranger/count.pyc
+${PYSITELIB}/multiqc/modules/spaceranger/count.pyo
+${PYSITELIB}/multiqc/modules/spaceranger/spaceranger.py
+${PYSITELIB}/multiqc/modules/spaceranger/spaceranger.pyc
+${PYSITELIB}/multiqc/modules/spaceranger/spaceranger.pyo
+${PYSITELIB}/multiqc/modules/spaceranger/utils.py
+${PYSITELIB}/multiqc/modules/spaceranger/utils.pyc
+${PYSITELIB}/multiqc/modules/spaceranger/utils.pyo
 ${PYSITELIB}/multiqc/modules/stacks/__init__.py
 ${PYSITELIB}/multiqc/modules/stacks/__init__.pyc
 ${PYSITELIB}/multiqc/modules/stacks/__init__.pyo
@@ -1050,9 +1293,33 @@ ${PYSITELIB}/multiqc/modules/trimmomatic/__init__.pyo
 ${PYSITELIB}/multiqc/modules/trimmomatic/trimmomatic.py
 ${PYSITELIB}/multiqc/modules/trimmomatic/trimmomatic.pyc
 ${PYSITELIB}/multiqc/modules/trimmomatic/trimmomatic.pyo
+${PYSITELIB}/multiqc/modules/truvari/__init__.py
+${PYSITELIB}/multiqc/modules/truvari/__init__.pyc
+${PYSITELIB}/multiqc/modules/truvari/__init__.pyo
+${PYSITELIB}/multiqc/modules/truvari/truvari.py
+${PYSITELIB}/multiqc/modules/truvari/truvari.pyc
+${PYSITELIB}/multiqc/modules/truvari/truvari.pyo
+${PYSITELIB}/multiqc/modules/umicollapse/__init__.py
+${PYSITELIB}/multiqc/modules/umicollapse/__init__.pyc
+${PYSITELIB}/multiqc/modules/umicollapse/__init__.pyo
+${PYSITELIB}/multiqc/modules/umicollapse/tests/__init__.py
+${PYSITELIB}/multiqc/modules/umicollapse/tests/__init__.pyc
+${PYSITELIB}/multiqc/modules/umicollapse/tests/__init__.pyo
+${PYSITELIB}/multiqc/modules/umicollapse/tests/test_umicollapse.py
+${PYSITELIB}/multiqc/modules/umicollapse/tests/test_umicollapse.pyc
+${PYSITELIB}/multiqc/modules/umicollapse/tests/test_umicollapse.pyo
+${PYSITELIB}/multiqc/modules/umicollapse/umicollapse.py
+${PYSITELIB}/multiqc/modules/umicollapse/umicollapse.pyc
+${PYSITELIB}/multiqc/modules/umicollapse/umicollapse.pyo
 ${PYSITELIB}/multiqc/modules/umitools/__init__.py
 ${PYSITELIB}/multiqc/modules/umitools/__init__.pyc
 ${PYSITELIB}/multiqc/modules/umitools/__init__.pyo
+${PYSITELIB}/multiqc/modules/umitools/tests/__init__.py
+${PYSITELIB}/multiqc/modules/umitools/tests/__init__.pyc
+${PYSITELIB}/multiqc/modules/umitools/tests/__init__.pyo
+${PYSITELIB}/multiqc/modules/umitools/tests/test_umitools.py
+${PYSITELIB}/multiqc/modules/umitools/tests/test_umitools.pyc
+${PYSITELIB}/multiqc/modules/umitools/tests/test_umitools.pyo
 ${PYSITELIB}/multiqc/modules/umitools/umitools.py
 ${PYSITELIB}/multiqc/modules/umitools/umitools.pyc
 ${PYSITELIB}/multiqc/modules/umitools/umitools.pyo
@@ -1092,12 +1359,30 @@ ${PYSITELIB}/multiqc/modules/verifybamid/__init__.pyo
 ${PYSITELIB}/multiqc/modules/verifybamid/verifybamid.py
 ${PYSITELIB}/multiqc/modules/verifybamid/verifybamid.pyc
 ${PYSITELIB}/multiqc/modules/verifybamid/verifybamid.pyo
+${PYSITELIB}/multiqc/modules/vg/__init__.py
+${PYSITELIB}/multiqc/modules/vg/__init__.pyc
+${PYSITELIB}/multiqc/modules/vg/__init__.pyo
+${PYSITELIB}/multiqc/modules/vg/vg.py
+${PYSITELIB}/multiqc/modules/vg/vg.pyc
+${PYSITELIB}/multiqc/modules/vg/vg.pyo
 ${PYSITELIB}/multiqc/modules/whatshap/__init__.py
 ${PYSITELIB}/multiqc/modules/whatshap/__init__.pyc
 ${PYSITELIB}/multiqc/modules/whatshap/__init__.pyo
 ${PYSITELIB}/multiqc/modules/whatshap/whatshap.py
 ${PYSITELIB}/multiqc/modules/whatshap/whatshap.pyc
 ${PYSITELIB}/multiqc/modules/whatshap/whatshap.pyo
+${PYSITELIB}/multiqc/modules/xengsort/__init__.py
+${PYSITELIB}/multiqc/modules/xengsort/__init__.pyc
+${PYSITELIB}/multiqc/modules/xengsort/__init__.pyo
+${PYSITELIB}/multiqc/modules/xengsort/xengsort.py
+${PYSITELIB}/multiqc/modules/xengsort/xengsort.pyc
+${PYSITELIB}/multiqc/modules/xengsort/xengsort.pyo
+${PYSITELIB}/multiqc/modules/xenome/__init__.py
+${PYSITELIB}/multiqc/modules/xenome/__init__.pyc
+${PYSITELIB}/multiqc/modules/xenome/__init__.pyo
+${PYSITELIB}/multiqc/modules/xenome/xenome.py
+${PYSITELIB}/multiqc/modules/xenome/xenome.pyc
+${PYSITELIB}/multiqc/modules/xenome/xenome.pyo
 ${PYSITELIB}/multiqc/multiqc.py
 ${PYSITELIB}/multiqc/multiqc.pyc
 ${PYSITELIB}/multiqc/multiqc.pyo
@@ -1107,18 +1392,42 @@ ${PYSITELIB}/multiqc/plots/__init__.pyo
 ${PYSITELIB}/multiqc/plots/bargraph.py
 ${PYSITELIB}/multiqc/plots/bargraph.pyc
 ${PYSITELIB}/multiqc/plots/bargraph.pyo
-${PYSITELIB}/multiqc/plots/beeswarm.py
-${PYSITELIB}/multiqc/plots/beeswarm.pyc
-${PYSITELIB}/multiqc/plots/beeswarm.pyo
-${PYSITELIB}/multiqc/plots/boxplot.py
-${PYSITELIB}/multiqc/plots/boxplot.pyc
-${PYSITELIB}/multiqc/plots/boxplot.pyo
+${PYSITELIB}/multiqc/plots/box.py
+${PYSITELIB}/multiqc/plots/box.pyc
+${PYSITELIB}/multiqc/plots/box.pyo
 ${PYSITELIB}/multiqc/plots/heatmap.py
 ${PYSITELIB}/multiqc/plots/heatmap.pyc
 ${PYSITELIB}/multiqc/plots/heatmap.pyo
 ${PYSITELIB}/multiqc/plots/linegraph.py
 ${PYSITELIB}/multiqc/plots/linegraph.pyc
 ${PYSITELIB}/multiqc/plots/linegraph.pyo
+${PYSITELIB}/multiqc/plots/plotly/__init__.py
+${PYSITELIB}/multiqc/plots/plotly/__init__.pyc
+${PYSITELIB}/multiqc/plots/plotly/__init__.pyo
+${PYSITELIB}/multiqc/plots/plotly/bar.py
+${PYSITELIB}/multiqc/plots/plotly/bar.pyc
+${PYSITELIB}/multiqc/plots/plotly/bar.pyo
+${PYSITELIB}/multiqc/plots/plotly/box.py
+${PYSITELIB}/multiqc/plots/plotly/box.pyc
+${PYSITELIB}/multiqc/plots/plotly/box.pyo
+${PYSITELIB}/multiqc/plots/plotly/heatmap.py
+${PYSITELIB}/multiqc/plots/plotly/heatmap.pyc
+${PYSITELIB}/multiqc/plots/plotly/heatmap.pyo
+${PYSITELIB}/multiqc/plots/plotly/line.py
+${PYSITELIB}/multiqc/plots/plotly/line.pyc
+${PYSITELIB}/multiqc/plots/plotly/line.pyo
+${PYSITELIB}/multiqc/plots/plotly/plot.py
+${PYSITELIB}/multiqc/plots/plotly/plot.pyc
+${PYSITELIB}/multiqc/plots/plotly/plot.pyo
+${PYSITELIB}/multiqc/plots/plotly/scatter.py
+${PYSITELIB}/multiqc/plots/plotly/scatter.pyc
+${PYSITELIB}/multiqc/plots/plotly/scatter.pyo
+${PYSITELIB}/multiqc/plots/plotly/table.py
+${PYSITELIB}/multiqc/plots/plotly/table.pyc
+${PYSITELIB}/multiqc/plots/plotly/table.pyo
+${PYSITELIB}/multiqc/plots/plotly/violin.py
+${PYSITELIB}/multiqc/plots/plotly/violin.pyc
+${PYSITELIB}/multiqc/plots/plotly/violin.pyo
 ${PYSITELIB}/multiqc/plots/scatter.py
 ${PYSITELIB}/multiqc/plots/scatter.pyc
 ${PYSITELIB}/multiqc/plots/scatter.pyo
@@ -1128,6 +1437,14 @@ ${PYSITELIB}/multiqc/plots/table.pyo
 ${PYSITELIB}/multiqc/plots/table_object.py
 ${PYSITELIB}/multiqc/plots/table_object.pyc
 ${PYSITELIB}/multiqc/plots/table_object.pyo
+${PYSITELIB}/multiqc/plots/violin.py
+${PYSITELIB}/multiqc/plots/violin.pyc
+${PYSITELIB}/multiqc/plots/violin.pyo
+${PYSITELIB}/multiqc/py.typed
+${PYSITELIB}/multiqc/report.py
+${PYSITELIB}/multiqc/report.pyc
+${PYSITELIB}/multiqc/report.pyo
+${PYSITELIB}/multiqc/search_patterns.yaml
 ${PYSITELIB}/multiqc/templates/__init__.py
 ${PYSITELIB}/multiqc/templates/__init__.pyc
 ${PYSITELIB}/multiqc/templates/__init__.pyo
@@ -1143,28 +1460,35 @@ ${PYSITELIB}/multiqc/templates/default/assets/fonts/glyphicons-halflings-regular
 ${PYSITELIB}/multiqc/templates/default/assets/fonts/glyphicons-halflings-regular.woff
 ${PYSITELIB}/multiqc/templates/default/assets/fonts/glyphicons-halflings-regular.woff2
 ${PYSITELIB}/multiqc/templates/default/assets/img/MultiQC_logo.png
-${PYSITELIB}/multiqc/templates/default/assets/img/Seqera-Labs.png
+${PYSITELIB}/multiqc/templates/default/assets/img/MultiQC_logo_dark.svg
 ${PYSITELIB}/multiqc/templates/default/assets/img/favicon-16x16.png
 ${PYSITELIB}/multiqc/templates/default/assets/img/favicon-32x32.png
 ${PYSITELIB}/multiqc/templates/default/assets/img/favicon-96x96.png
+${PYSITELIB}/multiqc/templates/default/assets/img/seqera_logo.png
+${PYSITELIB}/multiqc/templates/default/assets/img/seqera_logo_mono.png
+${PYSITELIB}/multiqc/templates/default/assets/js/decompress.js
+${PYSITELIB}/multiqc/templates/default/assets/js/flat.js
 ${PYSITELIB}/multiqc/templates/default/assets/js/multiqc.js
-${PYSITELIB}/multiqc/templates/default/assets/js/multiqc_mpl.js
-${PYSITELIB}/multiqc/templates/default/assets/js/multiqc_plotting.js
-${PYSITELIB}/multiqc/templates/default/assets/js/multiqc_tables.js
-${PYSITELIB}/multiqc/templates/default/assets/js/multiqc_toolbox.js
 ${PYSITELIB}/multiqc/templates/default/assets/js/packages/FileSaver.min.js
 ${PYSITELIB}/multiqc/templates/default/assets/js/packages/bootstrap.min.js
-${PYSITELIB}/multiqc/templates/default/assets/js/packages/clipboard.min.js
-${PYSITELIB}/multiqc/templates/default/assets/js/packages/highcharts.export-csv.js
-${PYSITELIB}/multiqc/templates/default/assets/js/packages/highcharts.exporting.js
-${PYSITELIB}/multiqc/templates/default/assets/js/packages/highcharts.heatmap.js
-${PYSITELIB}/multiqc/templates/default/assets/js/packages/highcharts.js
-${PYSITELIB}/multiqc/templates/default/assets/js/packages/highcharts.offline-exporting.js
 ${PYSITELIB}/multiqc/templates/default/assets/js/packages/jquery-3.1.1.min.js
 ${PYSITELIB}/multiqc/templates/default/assets/js/packages/jquery-ui.min.js
 ${PYSITELIB}/multiqc/templates/default/assets/js/packages/jquery.tablesorter.min.js
 ${PYSITELIB}/multiqc/templates/default/assets/js/packages/jquery.toast.min.js
-${PYSITELIB}/multiqc/templates/default/assets/js/packages/lz-string.min.js
+${PYSITELIB}/multiqc/templates/default/assets/js/packages/jszip.min.js
+${PYSITELIB}/multiqc/templates/default/assets/js/packages/pako_inflate.min.js
+${PYSITELIB}/multiqc/templates/default/assets/js/packages/plotly-2.27.0.js
+${PYSITELIB}/multiqc/templates/default/assets/js/packages/plotly-2.27.0.min.js
+${PYSITELIB}/multiqc/templates/default/assets/js/plots/bar.js
+${PYSITELIB}/multiqc/templates/default/assets/js/plots/box.js
+${PYSITELIB}/multiqc/templates/default/assets/js/plots/heatmap.js
+${PYSITELIB}/multiqc/templates/default/assets/js/plots/line.js
+${PYSITELIB}/multiqc/templates/default/assets/js/plots/scatter.js
+${PYSITELIB}/multiqc/templates/default/assets/js/plots/violin.js
+${PYSITELIB}/multiqc/templates/default/assets/js/plotting.js
+${PYSITELIB}/multiqc/templates/default/assets/js/render.js
+${PYSITELIB}/multiqc/templates/default/assets/js/tables.js
+${PYSITELIB}/multiqc/templates/default/assets/js/toolbox.js
 ${PYSITELIB}/multiqc/templates/default/base.html
 ${PYSITELIB}/multiqc/templates/default/content.html
 ${PYSITELIB}/multiqc/templates/default/foot.html
@@ -1175,10 +1499,6 @@ ${PYSITELIB}/multiqc/templates/default/header.html
 ${PYSITELIB}/multiqc/templates/default/includes.html
 ${PYSITELIB}/multiqc/templates/default/nav.html
 ${PYSITELIB}/multiqc/templates/default/toolbox.html
-${PYSITELIB}/multiqc/templates/default_dev/__init__.py
-${PYSITELIB}/multiqc/templates/default_dev/__init__.pyc
-${PYSITELIB}/multiqc/templates/default_dev/__init__.pyo
-${PYSITELIB}/multiqc/templates/default_dev/includes.html
 ${PYSITELIB}/multiqc/templates/gathered/__init__.py
 ${PYSITELIB}/multiqc/templates/gathered/__init__.pyc
 ${PYSITELIB}/multiqc/templates/gathered/__init__.pyo
@@ -1209,39 +1529,38 @@ ${PYSITELIB}/multiqc/templates/simple/__init__.py
 ${PYSITELIB}/multiqc/templates/simple/__init__.pyc
 ${PYSITELIB}/multiqc/templates/simple/__init__.pyo
 ${PYSITELIB}/multiqc/templates/simple/foot.html
+${PYSITELIB}/multiqc/templates/simple/footer.html
 ${PYSITELIB}/multiqc/templates/simple/header.html
 ${PYSITELIB}/multiqc/templates/simple/includes.html
 ${PYSITELIB}/multiqc/templates/simple/nav.html
 ${PYSITELIB}/multiqc/templates/simple/toolbox.html
+${PYSITELIB}/multiqc/types.py
+${PYSITELIB}/multiqc/types.pyc
+${PYSITELIB}/multiqc/types.pyo
 ${PYSITELIB}/multiqc/utils/__init__.py
 ${PYSITELIB}/multiqc/utils/__init__.pyc
 ${PYSITELIB}/multiqc/utils/__init__.pyo
 ${PYSITELIB}/multiqc/utils/config.py
 ${PYSITELIB}/multiqc/utils/config.pyc
 ${PYSITELIB}/multiqc/utils/config.pyo
-${PYSITELIB}/multiqc/utils/config_defaults.yaml
-${PYSITELIB}/multiqc/utils/lint_helpers.py
-${PYSITELIB}/multiqc/utils/lint_helpers.pyc
-${PYSITELIB}/multiqc/utils/lint_helpers.pyo
-${PYSITELIB}/multiqc/utils/log.py
-${PYSITELIB}/multiqc/utils/log.pyc
-${PYSITELIB}/multiqc/utils/log.pyo
 ${PYSITELIB}/multiqc/utils/megaqc.py
 ${PYSITELIB}/multiqc/utils/megaqc.pyc
 ${PYSITELIB}/multiqc/utils/megaqc.pyo
 ${PYSITELIB}/multiqc/utils/mqc_colour.py
 ${PYSITELIB}/multiqc/utils/mqc_colour.pyc
 ${PYSITELIB}/multiqc/utils/mqc_colour.pyo
-${PYSITELIB}/multiqc/utils/plugin_hooks.py
-${PYSITELIB}/multiqc/utils/plugin_hooks.pyc
-${PYSITELIB}/multiqc/utils/plugin_hooks.pyo
-${PYSITELIB}/multiqc/utils/profile_runtime.py
-${PYSITELIB}/multiqc/utils/profile_runtime.pyc
-${PYSITELIB}/multiqc/utils/profile_runtime.pyo
+${PYSITELIB}/multiqc/utils/pyaml_env.py
+${PYSITELIB}/multiqc/utils/pyaml_env.pyc
+${PYSITELIB}/multiqc/utils/pyaml_env.pyo
 ${PYSITELIB}/multiqc/utils/report.py
 ${PYSITELIB}/multiqc/utils/report.pyc
 ${PYSITELIB}/multiqc/utils/report.pyo
-${PYSITELIB}/multiqc/utils/search_patterns.yaml
+${PYSITELIB}/multiqc/utils/testing.py
+${PYSITELIB}/multiqc/utils/testing.pyc
+${PYSITELIB}/multiqc/utils/testing.pyo
 ${PYSITELIB}/multiqc/utils/util_functions.py
 ${PYSITELIB}/multiqc/utils/util_functions.pyc
 ${PYSITELIB}/multiqc/utils/util_functions.pyo
+${PYSITELIB}/multiqc/validation.py
+${PYSITELIB}/multiqc/validation.pyc
+${PYSITELIB}/multiqc/validation.pyo
diff --git a/py-multiqc/distinfo b/py-multiqc/distinfo
index de5985be47..0351eb7a2b 100644
--- a/py-multiqc/distinfo
+++ b/py-multiqc/distinfo
@@ -3,4 +3,4 @@ $NetBSD$
 BLAKE2s (multiqc-1.25.2.tar.gz) = 16e776d47cbbc78460a481d6403523fffb7b580887238c8e9df18cb12c608330
 SHA512 (multiqc-1.25.2.tar.gz) = 38649171bb51fa39cf9b5969891c7b1b12531d4a5b1b15e5f2d886b242546b967c3847afe485b8e0d411809347c998eff35310ad0cbe806dc7bf967c18eac2d0
 Size (multiqc-1.25.2.tar.gz) = 4326758 bytes
-SHA1 (patch-multiqc_multiqc.py) = 666b3c1a7af2a05582d38540fbfdc32a264120ff
+SHA1 (patch-multiqc_multiqc.py) = 3a81d977f6c773e97b3b87d4f8c658958c31f83f
diff --git a/py-multiqc/patches/patch-multiqc_multiqc.py b/py-multiqc/patches/patch-multiqc_multiqc.py
index f3f0abd21a..9e9fe58664 100644
--- a/py-multiqc/patches/patch-multiqc_multiqc.py
+++ b/py-multiqc/patches/patch-multiqc_multiqc.py
@@ -1,13 +1,13 @@
 $NetBSD$
 
-# Ensure proper terminal output
+# Validate env at run time
 
---- multiqc/multiqc.py.orig	2023-05-11 13:19:10 UTC
+--- multiqc/multiqc.py.orig	2024-11-20 15:21:45.000000000 +0000
 +++ multiqc/multiqc.py
-@@ -24,7 +24,13 @@ from urllib.request import urlopen
+@@ -12,7 +12,13 @@ import time
+ import traceback
+ from typing import Optional, Tuple
  
- import jinja2
- import rich
 -import rich_click as click
 +if 'LC_ALL' in os.environ and 'LANG' in os.environ:
 +    import rich_click as click
@@ -16,6 +16,6 @@ $NetBSD$
 +    print('in your environment in order for the click module to function.')
 +    print('E.g. export LC_ALL=en_US.UTF-8 or setenv LC_ALL en_US.UTF-8')
 +    sys.exit()
- from rich.syntax import Syntax
  
- from .plots import table
+ from multiqc import config, report, validation
+ from multiqc.core import log_and_rich, plugin_hooks
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