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 "