Merge branch 'main' into iss-120

.github/workflows/draft-release.yml

@@ -115,7 +115,12 @@ jobs:
           citation._implementation.cffobj['version'] = "${{ env.NEXT_VERSION }}"
           citation._implementation.cffobj['date-released'] = "${{ env.DATE }}"
           with open('CITATION.cff', 'w') as outfile:
-            outfile.write(yaml.dump(citation._implementation.cffobj, sort_keys=False))
+            outfile.write(yaml.dump(citation._implementation.cffobj, sort_keys=False, indent=2))
+
+      - uses: pre-commit/[email protected]
+        with:
+          extra_args: --files CITATION.cff CHANGELOG.md VERSION
+        continue-on-error: true
 
       - name: Commit & push to branch
         run: |

.github/workflows/main.yaml

@@ -12,12 +12,12 @@ jobs:
   Dryrun_Lint:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v4
       - uses: docker://snakemake/snakemake:v5.24.2
       - name: Dry-run pipeline
         run: |
           docker run -v $PWD:/opt2 -w /opt2 snakemake/snakemake:v5.24.2 \
-            python ./renee run \
+            python src/renee/__main__.py run \
               --input .tests/KO_S3.R1.fastq.gz .tests/KO_S3.R2.fastq.gz .tests/KO_S4.R1.fastq.gz .tests/KO_S4.R2.fastq.gz .tests/WT_S1.R1.fastq.gz .tests/WT_S1.R2.fastq.gz .tests/WT_S2.R1.fastq.gz .tests/WT_S2.R2.fastq.gz \
               --output output \
               --genome config/genomes/biowulf/hg38_30.json \
@@ -29,3 +29,49 @@ jobs:
         run: |
           docker run -v $PWD:/opt2 snakemake/snakemake:v5.24.2 snakemake --lint -s /opt2/output/workflow/Snakefile -d /opt2/output || \
           echo 'There may have been a few warnings or errors. Please read through the log to determine if its harmless.'
+
+  Test:
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: ["3.11"]
+        snakemake-version: ["7.32.3"]
+    steps:
+      - uses: actions/checkout@v4
+      - uses: mamba-org/setup-micromamba@v1
+        with:
+          environment-name: test
+          cache-environment: true
+          condarc: |
+            channels:
+              - conda-forge
+              - bioconda
+          create-args: >-
+            python=${{ matrix.python-version }}
+            snakemake=${{ matrix.snakemake-version }}
+            setuptools
+            pip
+            pytest
+      - name: check CLI basics
+        run: |
+          ./bin/renee --help
+          ./bin/renee --version
+        shell: micromamba-shell {0}
+      - name: Test
+        run: |
+          python -m pytest
+        env:
+          TMPDIR: ${{ runner.temp }}
+        shell: micromamba-shell {0}
+
+  build-status: # https://github.com/orgs/community/discussions/4324#discussioncomment-3477871
+    runs-on: ubuntu-latest
+    needs: [Dryrun_Lint, Test]
+    if: always()
+    steps:
+      - name: Successful build
+        if: ${{ !(contains(needs.*.result, 'failure')) }}
+        run: exit 0
+      - name: Failing build
+        if: ${{ contains(needs.*.result, 'failure') }}
+        run: exit 1

.github/workflows/post-release.yml

@@ -36,14 +36,20 @@ jobs:
           with open('VERSION', 'w') as outfile:
             outfile.write(f"{version}-dev\n")
 
+      - uses: pre-commit/[email protected]
+        with:
+          extra_args: --files CITATION.cff CHANGELOG.md VERSION
+        continue-on-error: true
+
       - name: Open pull request
         run: |
           git add CHANGELOG.md VERSION
           git commit -m "chore: bump changelog & version after release of ${{ github.ref_name }}"
           git push --set-upstream origin ${{ env.BRANCH }}
 
           gh pr create \
-            --fill-first
+            --fill-first \
+            --reviewer ${{ github.triggering_actor }}
 
       - name: Clean up release-draft branch
         run: |

.gitignore

@@ -159,4 +159,4 @@ site/
 
 # other
 
-**/.koparde*
+**/.koparde*

CHANGELOG.md

@@ -1,5 +1,9 @@
-## development version
 
+## RENEE development version
+
+- Minor documentation improvements. (#100, @kelly-sovacool)
+- Fix RNA report bug, caused by hard-coding of PC1-3, when only PC1-2 were generated. (#104, @slsevilla)
+- Allow printing the version or help message even if singularity is not in the path. (#110, @kelly-sovacool)
 - Set RSeQC envmodule version to 4.0.0, which synchronizes it with the version in the docker container used by singularity. (#122, @kelly-sovacool)
 
 ## RENEE 2.5.11

CITATION.cff

@@ -27,5 +27,9 @@ url: https://ccbr.github.io/RENEE
 repository-code: https://github.com/CCBR/RENEE
 license: MIT
 type: software
+identifiers:
+  - description: Archived snapshots of all versions
+    type: doi
+    value: 10.5281/zenodo.10553198
 version: v2.5.11
-date-released: '2024-01-22'
+date-released: 2024-01-22

VERSION

@@ -1 +1 @@
-2.5.11
+2.5.11-dev

bin/redirect

@@ -67,13 +67,4 @@ elif [[ $ISFRCE == true ]];then
 	export PATH="/mnt/projects/CCBR-Pipelines/bin:$PATH"
 fi
 
-# check if singularity, snakemake are in PATH
-for tool in singularity snakemake;do
-	x=$(type -P $tool)
-	if [[ -z $x ]]; then # is $x blank
-		echo "$tool is not it path! Exiting."
-		exit
-	fi
-done
-
-${TOOLDIR}/${TOOLNAME} "$@" || true
+${TOOLDIR}/src/renee/__main__.py "$@" || true

config/genomes/biowulf/hg19_19.json

@@ -22,4 +22,4 @@
             "FUSIONPROTDOMAIN": "s3://nciccbr/Resources/RNA-seq/arriba/protein_domains_hg19_hs37d5_GRCh37_v2.0.0.gff3"
         }
     }
-}
+}

config/genomes/biowulf/hg38_30.json

@@ -22,4 +22,4 @@
             "FUSIONPROTDOMAIN": "s3://nciccbr/Resources/RNA-seq/arriba/protein_domains_hg38_GRCh38_v2.0.0.gff3"
         }
     }
-}
+}

config/genomes/biowulf/hg38_34.json

@@ -22,4 +22,4 @@
             "FUSIONPROTDOMAIN": "s3://nciccbr/Resources/RNA-seq/arriba/protein_domains_hg38_GRCh38_v2.0.0.gff3"
         }
     }
-}
+}

config/genomes/biowulf/hg38_36.json

@@ -22,4 +22,4 @@
             "FUSIONPROTDOMAIN": "s3://nciccbr/Resources/RNA-seq/arriba/protein_domains_hg38_GRCh38_v2.0.0.gff3"
         }
     }
-}
+}

config/genomes/biowulf/hg38_38.json

@@ -22,4 +22,4 @@
             "FUSIONPROTDOMAIN": "s3://nciccbr/Resources/RNA-seq/arriba/protein_domains_hg38_GRCh38_v2.0.0.gff3"
         }
     }
-}
+}

config/genomes/biowulf/mm10_M23.json

@@ -22,4 +22,4 @@
             "FUSIONPROTDOMAIN": "s3://nciccbr/Resources/RNA-seq/arriba/protein_domains_mm10_GRCm38_v2.0.0.gff3"
         }
     }
-}
+}

docker/multiqc/Dockerfile

@@ -13,19 +13,19 @@ LABEL [email protected]
 #    - matplotlib     (pypi)
 #    - XlsxWriter     (pypi)
 
-# Create Container filesystem specific 
+# Create Container filesystem specific
 # working directory and opt directories
-# to avoid collisions with host filesyetem 
+# to avoid collisions with host filesyetem
 RUN mkdir -p /opt2 && mkdir -p /data2
-WORKDIR /opt2 
+WORKDIR /opt2
 
-# Set time zone to US east coast 
+# Set time zone to US east coast
 ENV TZ=America/New_York
 RUN ln -snf /usr/share/zoneinfo/$TZ /etc/localtime \
     && echo $TZ > /etc/timezone
 
-# This section installs system packages 
-# required for your project. If you need 
+# This section installs system packages
+# required for your project. If you need
 # extra system packages add them here.
 # Installs python/3.8.10
 RUN apt-get update \
@@ -55,6 +55,6 @@ RUN pip3 install --upgrade pip \
 
 # Add Dockerfile and export env variables
 ADD Dockerfile /opt2/Dockerfile
-RUN chmod -R a+rX /opt2 
+RUN chmod -R a+rX /opt2
 ENV PATH="/opt2:$PATH"
-WORKDIR /data2
+WORKDIR /data2