Fix the default rRNA

.github/workflows/apptainer.yml

@@ -5,6 +5,7 @@ on:
     branches:
       - main
       - dev
+  workflow_dispatch:
   pull_request:
     branches-ignore: []
   schedule:
@@ -49,9 +50,10 @@ jobs:
     - name: install package itself
       run: |
          pip install .
+         pip install "pulp==2.7.0" --no-deps
 
     - name: testing
       run: |
-        sequana_rnaseq --aligner bowtie2 --input-directory test/data/ --use-apptainer  --genome-directory test/data/Saccer3 && cd rnaseq && sh rnaseq.sh
+        sequana_rnaseq --aligner-choice bowtie2 --input-directory test/data/ --use-apptainer  --genome-directory test/data/Saccer3 && cd rnaseq && sh rnaseq.sh
 
 

.github/workflows/main.yml

@@ -31,28 +31,25 @@ jobs:
       uses: actions/checkout@v2
 
     - name: conda/mamba
-      uses: mamba-org/setup-micromamba@v1
+      uses: mamba-org/provision-with-micromamba@main
       with:
-          micromamba-version: '1.3.1-0'
           environment-file: environment.yml
-          create-args: |
+          extra-specs: |
             python=${{ matrix.python }}
-          cache-environment: true
-          cache-downloads: true
-
     - name: install package itself
-      shell: bash -el {0}
+      shell: bash -l {0}
       run: |
         pip install .
+        pip install "pulp==2.7.0" --no-deps
 
 
     - name: Install dependencies
-      shell: bash -el {0}
+      shell: bash -l {0}
       run: |
         pip install coveralls pytest-cov pytest pytest-xdist
 
     - name: testing
-      shell: bash -el {0}
+      shell: bash -l {0}
       run: |
         pytest -v --cov-report term-missing --cov=sequana_pipelines.rnaseq
 

README.rst

@@ -30,15 +30,17 @@ Installation
 
     pip install sequana_rnaseq --upgrade
 
-You will need third-party software such as bowtie2/star. Please see below for details.
+You will need third-party software such as bowtie2/star. However, if you choose to use aptainer/singularity,
+then nothing to install except singularity itself ! See below for details.
+
 
 Usage
 ~~~~~
 
 ::
 
     sequana_rnaseq --help
-    sequana_rnaseq --input-directory DATAPATH --genome-directory genome --aligner star
+    sequana_rnaseq --input-directory DATAPATH --genome-directory genome --aligner-choice star
 
 This creates a directory with the pipeline and configuration file. You will then need
 to execute the pipeline::
@@ -53,6 +55,28 @@ retrieve the pipeline itself and its configuration files and then execute the pi
 
 Or use `sequanix <https://sequana.readthedocs.io/en/main/sequanix.html>`_ interface.
 
+
+Usage with apptainer:
+~~~~~~~~~~~~~~~~~~~~~~~~~
+
+With apptainer, initiate the working directory as follows::
+
+    sequana_rnaseq --use-apptainer
+
+Images are downloaded in the working directory but you can store then in a directory globally (e.g.)::
+
+    sequana_rnaseq --use-apptainer --apptainer-prefix ~/.sequana/apptainers
+
+and then::
+
+    cd rnaseq
+    sh rnaseq.sh
+
+if you decide to use snakemake manually, do not forget to add apptainer options::
+
+    snakemake -s rnaseq.rules -c config.yaml --cores 4 --use-apptainer --apptainer-prefix ~/.sequana/apptainers --apptainer-args "-B /home:/home"
+
+
 Requirements
 ~~~~~~~~~~~~
 
@@ -67,8 +91,7 @@ may change. A Message will inform you would you be missing an executable:
 - multiqc
 - samtools
 
-Note that bowtie>=2.4.2 is set to ensure the pipeline can be used with python 3.7-3.8-3.9 and the sequana-wrappers
-that supports bowtie2 with option --threads only (not previous versions). See environment.yaml or conda.yaml for latest list of required third-party tools.
+Note that bowtie>=2.4.2 is set to ensure the pipeline can be used with python 3.7-3.8-3.9 and the sequana-wrappers that supports bowtie2 with option --threads only (not previous versions). See environment.yaml or conda.yaml for latest list of required third-party tools.
 
 You can install most of the tools using `damona <https://damona.readthedocs.io>`_::
 
@@ -89,10 +112,6 @@ all dependencies for you::
 
 For Linux users, we provide singularity images available through within the damona project (https://damona.readthedocs.io).
 
-To use apptainer, initialise the pipeline with the --use-singularity option and everything should be downloaded automatically for you, which also guarantees reproducibility:
-
-    sequana_rnaseq --input-directory data --use-singularity --genome-directory ....
-
 
 .. image:: https://raw.githubusercontent.com/sequana/sequana_rnaseq/main/sequana_pipelines/rnaseq/dag.png
 
@@ -158,6 +177,7 @@ Changelog
 ========= ====================================================================
 Version   Description
 ========= ====================================================================
+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)
           * set genome directory default to None to enforce its usage

pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "poetry.core.masonry.api"
 
 [tool.poetry]
 name = "sequana-rnaseq"
-version = "0.19.2"
+version = "0.19.3"
 description = "A RNAseq pipeline from raw reads to feature counts"
 authors = ["Sequana Team"]
 license = "BSD-3"

sequana_pipelines/rnaseq/main.py

@@ -31,7 +31,7 @@
     NAME,
     groups={
         "Pipeline Specific": [
-            "--aligner",
+            "--aligner-choice",
             "--contaminant-file",
             "--do-igvtools",
             "--do-bam-coverage",
@@ -65,7 +65,7 @@
     required=True,
 )
 @click.option(
-    "--aligner",
+    "--aligner-choice",
     "aligner",
     required=True,
     type=click.Choice(["bowtie2", "bowtie1", "star", "salmon"]),
@@ -74,6 +74,7 @@
 @click.option(
     "--rRNA-feature",
     "rRNA",
+    default="rRNA",
     help="""Feature name corresponding to the rRNA to be identified in
 the input GFF/GTF files. Must exist and be valid. If you do not have any,
 you may skip this step using --skip-rRNA or provide a fasta file using --contaminant-file""",

sequana_pipelines/rnaseq/rnaseq.rules

@@ -1218,7 +1218,6 @@ onsuccess:
     </p>
     """
 
-
     # Now the final report. add the original command in the HTML report
     data = manager.getmetadata()
     s = SequanaReport(data, intro)

test/test_main.py

@@ -34,7 +34,7 @@ def test_standalone_script():
             "--genome-directory",
             saccer3,
             "--force",
-            "--aligner",
+            "--aligner-choice",
             "bowtie2",
             "--feature-counts-feature-type",
             "gene,tRNA",
@@ -58,7 +58,7 @@ def test_standalone_script_contaminant():
             "--genome-directory",
             saccer3,
             "--force",
-            "--aligner",
+            "--aligner-choice",
             "bowtie2",
             "--feature-counts-feature-type",
             "gene",
@@ -89,7 +89,7 @@ def test_standalone_script_wrong_feature():
         "--genome-directory",
         saccer3,
         "--force",
-        "--aligner",
+        "--aligner-choice",
         "bowtie2",
         "--feature-counts-feature-type",
         "dummy",
@@ -117,7 +117,7 @@ def test_standalone_script_wrong_reference():
         "--genome-directory",
         "dummy",
         "--force",
-        "--aligner",
+        "--aligner-choice",
         "bowtie2",
         "--working-directory",
         directory.name,
@@ -143,7 +143,7 @@ def test_standalone_script_wrong_triming():
         "--genome-directory",
         saccer3,
         "--force",
-        "--aligner",
+        "--aligner-choice",
         "bowtie2",
         "--software-choice",
         "dummy",
@@ -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 bowtie2 --working-directory {wk} --force"
+        cmd = f"sequana_rnaseq --input-directory {sharedir} --genome-directory {saccer3} --aligner-choice bowtie2 --working-directory {wk} --force"
         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 star --working-directory {wk} --force"
+        cmd = f"sequana_rnaseq --input-directory {sharedir} --genome-directory {saccer3} --aligner-choice star --working-directory {wk} --force"
         subprocess.call(cmd.split())
 
         cmd = "snakemake -s rnaseq.rules --wrapper-prefix https://raw.githubusercontent.com/sequana/sequana-wrappers/  -p --cores 2 "
@@ -199,7 +199,7 @@ def __test_full_salmon():
     with tempfile.TemporaryDirectory() as directory:
         wk = directory
 
-        cmd = f"sequana_rnaseq --input-directory {sharedir} --genome-directory {saccer3} --aligner salmon --working-directory {wk} --force"
+        cmd = f"sequana_rnaseq --input-directory {sharedir} --genome-directory {saccer3} --aligner-choice salmon --working-directory {wk} --force"
         subprocess.call(cmd.split())
 
         cmd = "snakemake -s rnaseq.rules --wrapper-prefix https://raw.githubusercontent.com/sequana/sequana-wrappers/  -p --cores 2 "