Merge pull request #47 from cokelaer/main

Update summary, pin sequana to use new plots

Author: cokelaer

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)

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"

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 += """<h2>Mapping rate</h2>"""
     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 += """<h2>Annotation rate</h2>"""
-        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)

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

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 "