diff --git a/README.rst b/README.rst
index cf5131f..5bf1805 100644
--- a/README.rst
+++ b/README.rst
@@ -177,8 +177,8 @@ Changelog
========= ====================================================================
Version Description
========= ====================================================================
-0.19.4 * Fix regression due to new sequana version
- *
+0.20.0 * Fix regression due to new sequana version
+ * Update summary html to use new sequana plots
0.19.3 * fix regression with click to set the default rRNA to 'rRNA' again.
0.19.2 * fix bowtie1 regression in the log file, paired end case in
multiqc and rnadiff script (regression)
diff --git a/pyproject.toml b/pyproject.toml
index 1750b81..066fa6b 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -4,7 +4,7 @@ build-backend = "poetry.core.masonry.api"
[tool.poetry]
name = "sequana-rnaseq"
-version = "0.19.4"
+version = "0.20.0"
description = "A RNAseq pipeline from raw reads to feature counts"
authors = ["Sequana Team"]
license = "BSD-3"
@@ -34,7 +34,7 @@ packages = [
[tool.poetry.dependencies]
python = ">=3.8,<4.0"
-sequana = ">=0.17.2"
+sequana = ">=0.17.3"
sequana_pipetools = ">=1.0.2"
click-completion = "^0.5.2"
pulp = "<2.8.0"
diff --git a/sequana_pipelines/rnaseq/rnaseq.rules b/sequana_pipelines/rnaseq/rnaseq.rules
index 4adb0aa..2d62c0f 100644
--- a/sequana_pipelines/rnaseq/rnaseq.rules
+++ b/sequana_pipelines/rnaseq/rnaseq.rules
@@ -426,8 +426,7 @@ else:
#
if int(config['bowtie1_mapping_rna']['nreads']) != -1:
extra = int(config['bowtie1_mapping_rna']['nreads']) * 4
- config['bowtie1_mapping_rna']['nreads'] -= extra
-
+ config['bowtie1_mapping_rna']['nreads'] = extra
rule sample_rRNA:
input:
@@ -1159,14 +1158,9 @@ onsuccess:
intro += """
Mapping rate
"""
if config['general']['aligner'] == "bowtie2":
from sequana.multiqc.plots import Bowtie2
- if not manager.paired:
- filename = "multiqc/multiqc_data/mqc_bowtie2_se_plot_1.txt"
- if not os.path.exists(filename):
- filename = "multiqc/multiqc_report_data/mqc_bowtie2_se_plot_1.txt"
- else:
- filename = "multiqc/multiqc_data/mqc_bowtie2_pe_plot_1.txt"
- if not os.path.exists(filename):
- filename = "multiqc/multiqc_report_data/mqc_bowtie2_pe_plot_1.txt"
+ filename = "multiqc/multiqc_data/multiqc_bowtie2.txt"
+ if not os.path.exists(filename):
+ filename = "multiqc/multiqc_report_data/multiqc_bowtie2.txt"
br = Bowtie2(filename)
fig = br.plot(html_code=True)
from plotly import offline
@@ -1185,9 +1179,9 @@ onsuccess:
try:
from sequana.multiqc.plots import FeatureCounts
intro += """Annotation rate
"""
- filename = "multiqc/multiqc_report_data/mqc_featureCounts_assignment_plot_1.txt"
+ filename = "multiqc/multiqc_report_data/multiqc_featureCounts.txt"
if not os.path.exists(filename):
- filename = "multiqc/multiqc_data/mqc_featureCounts_assignment_plot_1.txt"
+ filename = "multiqc/multiqc_data/multiqc_featureCounts.txt"
br = FeatureCounts(filename)
fig = br.plot(html_code=True)
diff --git a/sequana_pipelines/rnaseq/schema.yaml b/sequana_pipelines/rnaseq/schema.yaml
index 5921a78..e8ac00d 100644
--- a/sequana_pipelines/rnaseq/schema.yaml
+++ b/sequana_pipelines/rnaseq/schema.yaml
@@ -267,7 +267,7 @@ mapping:
"nreads":
type: int
required: True
- range: { min: -1}
+ range: { min: -1, max: 1e15}
'igvtools':
type: map
diff --git a/test/test_main.py b/test/test_main.py
index a61e336..0e2d84a 100644
--- a/test/test_main.py
+++ b/test/test_main.py
@@ -165,7 +165,7 @@ def test_full():
with tempfile.TemporaryDirectory() as directory:
wk = directory
- cmd = f"sequana_rnaseq --input-directory {sharedir} --genome-directory {saccer3} --aligner-choice bowtie2 --working-directory {wk} --force"
+ cmd = f"sequana_rnaseq --input-directory {sharedir} --genome-directory {saccer3} --aligner-choice bowtie2 --working-directory {wk} --force --rRNA-feature rRNA_gene"
subprocess.call(cmd.split())
cmd = "snakemake -s rnaseq.rules --wrapper-prefix https://raw.githubusercontent.com/sequana/sequana-wrappers/ -p --cores 2 "
@@ -182,7 +182,7 @@ def test_full_star():
with tempfile.TemporaryDirectory() as directory:
wk = directory
- cmd = f"sequana_rnaseq --input-directory {sharedir} --genome-directory {saccer3} --aligner-choice star --working-directory {wk} --force"
+ cmd = f"sequana_rnaseq --input-directory {sharedir} --genome-directory {saccer3} --aligner-choice star --working-directory {wk} --force --rRNA-feature rRNA_gene"
subprocess.call(cmd.split())
cmd = "snakemake -s rnaseq.rules --wrapper-prefix https://raw.githubusercontent.com/sequana/sequana-wrappers/ -p --cores 2 "