increment to v0.9.0 synchronized with sequana 0.11.0.

Fixes logger issue and add --pacbio option to fill automatically the config file

Author: cokelaer

README.rst

@@ -1,8 +1,8 @@
 This is is the **mapper** pipeline from the `Sequana <https://sequana.readthedocs.org>`_ projet
 
 :Overview: This is a simple pipeline to map several FastQ files onto a reference using different mappers/aligners
-:Input: A set of FastQ files.
-:Output: A set of BAM files (and/or bigwig)
+:Input: A set of FastQ files (illumina, pacbio, etc).
+:Output: A set of BAM files (and/or bigwig) and HTML report
 :Status: Production
 :Citation: Cokelaer et al, (2017), ‘Sequana’: a Set of Snakemake NGS pipelines, Journal of Open Source Software, 2(16), 352, JOSS DOI doi:10.21105/joss.00352
 
@@ -60,7 +60,10 @@ Details
 ~~~~~~~~~
 
 This pipeline runs **mapper** in parallel on the input fastq files (paired or not). 
-A brief sequana summary report is also produced.
+A brief sequana summary report is also produced. When using **--pacbio** option, 
+*-x map-pb* options ia automatically added to the config.yaml file and the
+readtag is set to None. 
+
 
 
 Rules and configuration details
@@ -76,6 +79,9 @@ Changelog
 ========= ====================================================================
 Version   Description
 ========= ====================================================================
+0.9.0     * fix issue with logger and increments requirements
+          * add new option --pacbio to automatically set the options for 
+            pacbio data (-x map-pb and readtag set to None)
 0.8.13    * add the thread option in minimap2 case
 0.8.12    * factorise multiqc rule
 0.8.11    * Implemente the --from-project option and new framework

requirements.txt

@@ -1,2 +1,2 @@
-sequana>=0.8.4
-sequana_pipetools>=0.2.2
+sequana>=0.11.0
+sequana_pipetools>=0.5.2

sequana_pipelines/mapper/config.yaml

@@ -19,6 +19,7 @@ general:
     reference_file:
     annotation_file:
     create_bigwig: false
+    
 
 
 bwa_mem_mapping:

sequana_pipelines/mapper/main.py

@@ -34,15 +34,19 @@ def __init__(self, prog=NAME, epilog=None):
 
         pipeline_group = self.add_argument_group("pipeline")
         pipeline_group.add_argument("--mapper", default='bwa',
-             choices=['bwa', 'minimap2', 'bowtie2'])
+             choices=['bwa', 'minimap2', 'bowtie2'], 
+            help="Choose one of the valid mapper")
         pipeline_group.add_argument("--reference-file", required=True,
-             )
+             help="You input reference file in fasta format")
         pipeline_group.add_argument("--annotation-file",
             help="Used by the sequana_coverage tool if provided" )
 
         pipeline_group.add_argument("--do-coverage", action="store_true",
             help="Use sequana_coverage (prokaryotes)" )
 
+        pipeline_group.add_argument("--pacbio", action="store_true",
+            help="If set, automatically set the input-readtag to None and set minimap2 options to -x map-pb" )
+
         pipeline_group.add_argument("--create-bigwig", action="store_true",
             help="create the bigwig files from the BAM files" )
 
@@ -104,6 +108,11 @@ def main(args=None):
         if options.create_bigwig:
             cfg.general.create_bigwig = True
 
+        if options.pacbio:
+            cfg.minimap2.options = " -x map-pb "
+            cfg.input_readtag = ""
+
+
 
     # finalise the command and save it; copy the snakemake. update the config
     # file and save it.

sequana_pipelines/mapper/mapper.rules

@@ -40,6 +40,7 @@ exec(open(sequana.modules["bowtie2_index_dynamic"], "r").read())
 
 # A convenient manager
 manager = sm.PipelineManager("mapper", config)
+
 manager.setup(globals(), mode="warning")
 
 
@@ -197,7 +198,7 @@ onsuccess:
     shell("chmod -R g+w .")
 
     from sequana import logger
-    logger.level = "INFO"
+    logger.setLevel("INFO")
 
     # This should create the stats plot and the Makefile
     manager.teardown()
@@ -218,22 +219,23 @@ If coverage was selected, you should also have HTML reports for each sample with
         intro += """<h2>Coverage plots overview</h2>"""
         import glob
         filenames = glob.glob("*/sequana_coverage/*/coverage.png")
-        if len(filenames)<100:
-            for filename in filenames:
-                parts = filename.split("/")
-                image = SummaryModule2.png_to_embedded_png("self_dummy", 
+        for count, filename in enumerate(filenames):
+            parts = filename.split("/")
+            image = SummaryModule2.png_to_embedded_png("self_dummy", 
                         filename,
                         #style="align:center; width:30%; height:30%",
                         style="align:center; width:95%; height:95%",
                         alt=parts[0])
-                parts = filename.split("/")
-                link = "/".join(parts[0:-1] + [parts[-2] + ".cov.html"])
-
-                intro += """
-                <div class="box_1_3" ><a href="{}">{}</a><hr>
-                <a href="{}">{}</a>
-                </div>
-                """.format(link, image, link, parts[0])
+            parts = filename.split("/")
+            link = "/".join(parts[0:-1] + [parts[-2] + ".cov.html"])
+
+            intro += """
+            <div class="box_1_3" ><a href="{}">{}</a><hr>
+            <a href="{}">{}</a>
+            </div>
+            """.format(link, image, link, parts[0])
+            if count > 0:
+                break
 
 
     s = SummaryModule2(data, intro=intro)

setup.py

@@ -6,8 +6,8 @@
 import subprocess
 
 _MAJOR               = 0
-_MINOR               = 8
-_MICRO               = 13
+_MINOR               = 9
+_MICRO               = 0
 version              = '%d.%d.%d' % (_MAJOR, _MINOR, _MICRO)
 release              = '%d.%d' % (_MAJOR, _MINOR)