Merge pull request #30 from cokelaer/main

Fix options not used in star_mapping

Author: cokelaer

.github/workflows/main.yml

@@ -16,7 +16,7 @@ jobs:
     strategy:
       max-parallel: 5
       matrix:
-        python: [3.7, 3.8, 3.9]
+        python: [3.8, 3.9, '3.10']
       fail-fast: false
 
 
@@ -30,25 +30,28 @@ jobs:
       uses: actions/checkout@v2
 
     - name: conda/mamba
-      uses: mamba-org/provision-with-micromamba@main
+      uses: mamba-org/setup-micromamba@v1
       with:
+          micromamba-version: '1.3.1-0'
           environment-file: environment.yml
-          extra-specs: |
+          create-args: |
             python=${{ matrix.python }}
+          cache-environment: true
+          cache-downloads: true
 
     - name: install package itself
-      shell: bash -l {0}
+      shell: bash -el {0}
       run: |
         pip install .
 
 
     - name: Install dependencies
-      shell: bash -l {0}
+      shell: bash -el {0}
       run: |
         pip install coveralls pytest-cov pytest pytest-xdist
 
     - name: testing
-      shell: bash -l {0}
+      shell: bash -el {0}
       run: |
         pytest -v --cov-report term-missing --cov=sequana_pipelines.rnaseq
 

README.rst

@@ -144,12 +144,23 @@ to be used with the pipeline. Each rule used in the pipeline may have a section
 .. warning:: the RNAseQC rule is switch off and is not currently functional in
    version 0.9.X
 
+Issues
+~~~~~~
+
+In the context of eukaryotes, you will need 32G of memory most probably. If this is too much,
+you can try to restrict the memory. Check out the config.yaml file in the star section.
+
+
+
 Changelog
 ~~~~~~~~~
 
 ========= ====================================================================
 Version   Description
 ========= ====================================================================
+0.17.2    * CHANGES: in star section, added --limitBAMsortRAM and set to 30G
+          * BUG: Fix missing params (options) in star_mapping rule not taken
+            into account
 0.17.1    * use new rulegraph / graphviz apptainer
 0.17.0    * fastp step changed to use sequana-wrappers. Slight change in 
             config file. The reverse and forward adapter options called

sequana_pipelines/rnaseq/config.yaml

@@ -169,17 +169,18 @@ bowtie1_mapping_rna:
 # :Parameters:
 #
 # - do: if unchecked, this rule is ignored
-# - options: any options recognised by rna-star tool
+# - options: any options recognised by rna-star tool. Set limitBAMsortRAM to 30G
 # - threads: number of threads to be used
 # - legacy: if set to True will use the old 2-pass version from STAR
 #      used in this pipeline until v0.15.3. If you want to use the
 #      2-pass mode available in star, you will need star 2.7 and above
+# 
 star_mapping:
-    options: --outFilterMismatchNoverLmax 0.05 --seedSearchStartLmax 20
+    options: " --limitBAMsortRAM 30000000000 --outFilterMismatchNoverLmax 0.05 --seedSearchStartLmax 20 "
     legacy: True
     threads: 4
     resources:
-      mem: 34G
+      mem: 32G
 
 ##############################################################################
 # STAR indexing section

sequana_pipelines/rnaseq/rnaseq.rules

@@ -559,6 +559,10 @@ elif manager.config.general.aligner == "star":
         output:
             bam = "{sample}/star_mapping/{sample}_Aligned.sortedByCoord.out.bam"
         params:
+            options=config['star_mapping']['options'],
+            # for legacy mapping, set the first and second pass options
+            options_first_pass=config['star_mapping']['options'],
+            options_second_pass=config['star_mapping']['options'],
             prefix = "{sample}/star_mapping/{sample}",
             legacy=True,
         threads:

setup.py

@@ -5,7 +5,7 @@
 
 _MAJOR = 0
 _MINOR = 17
-_MICRO = 1
+_MICRO = 2
 version = "%d.%d.%d" % (_MAJOR, _MINOR, _MICRO)
 release = "%d.%d" % (_MAJOR, _MINOR)
 
@@ -25,9 +25,9 @@
         "Intended Audience :: Science/Research",
         "License :: OSI Approved :: BSD License",
         "Operating System :: OS Independent",
-        "Programming Language :: Python :: 3.7",
         "Programming Language :: Python :: 3.8",
         "Programming Language :: Python :: 3.9",
+        "Programming Language :: Python :: 3.10",
         "Topic :: Software Development :: Libraries :: Python Modules",
         "Topic :: Scientific/Engineering :: Bio-Informatics",
         "Topic :: Scientific/Engineering :: Information Analysis",