Merge pull request #2 from boulardlab/release-please--branches--main-…

…-components--3t-seq chore(main): release 1.1
boulardlab · Mar 11, 2024 · 06b3aae · 06b3aae
2 parents 4051f50 + 217962e
commit 06b3aae
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diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml
@@ -55,89 +55,10 @@ jobs:
           conda install -c conda-forge mamba
       - name: Setup snakemake
         run: |
-          mamba install -c conda-forge -c bioconda snakemake=7.28.3 singularity
-      - name: Run workflow
+          mamba install -c conda-forge -c bioconda snakemake=7.32.4 apptainer=1.2.5
+      - name: List tests
         run: |
-          ls -R tests/
-          snakemake --directory tests --configfile tests/config.yaml --profile tests/profile --snakefile workflow/Snakefile
-  run-workflow-no-te:
-    runs-on: ubuntu-latest
-    needs:
-      - linting
-      - formatting
-    steps:
-      - name: Checkout repository with submodules
-        uses: actions/checkout@v3
-        with:
-          submodules: recursive
-          lfs: true
-      - name: Setup Python 3.11
-        uses: actions/setup-python@v2
-        with:
-          python-version: 3.11
-      - name: Add Conda to system path
-        run: |
-          echo $CONDA/bin >> $GITHUB_PATH    
-      - name: Install dependencies
-        run: |
-          conda install -c conda-forge mamba
-      - name: Setup snakemake
-        run: |
-          mamba install -c conda-forge -c bioconda snakemake=7.28.3 singularity
+          ls -R tests
       - name: Run workflow
         run: |
-          snakemake --directory tests --configfile tests/config-no-te.yaml --profile tests/profile --snakefile workflow/Snakefile 
-  run-workflow-no-trna:
-    runs-on: ubuntu-latest
-    needs:
-      - linting
-      - formatting
-    steps:
-      - name: Checkout repository with submodules
-        uses: actions/checkout@v3
-        with:
-          submodules: recursive
-          lfs: true
-      - name: Setup Python 3.11
-        uses: actions/setup-python@v2
-        with:
-          python-version: 3.11
-      - name: Add Conda to system path
-        run: |
-          echo $CONDA/bin >> $GITHUB_PATH    
-      - name: Install dependencies
-        run: |
-          conda install -c conda-forge mamba
-      - name: Setup snakemake
-        run: |
-          mamba install -c conda-forge -c bioconda snakemake=7.28.3 singularity
-      - name: Run workflow
-        run: |
-          snakemake --directory tests --configfile tests/config-no-trna.yaml --profile tests/profile --snakefile workflow/Snakefile
-  run-workflow-no-trna-te:
-    runs-on: ubuntu-latest
-    needs:
-      - linting
-      - formatting
-    steps:
-      - name: Checkout repository with submodules
-        uses: actions/checkout@v3
-        with:
-          submodules: recursive
-          lfs: true
-      - name: Setup Python 3.11
-        uses: actions/setup-python@v2
-        with:
-          python-version: 3.11
-      - name: Add Conda to system path
-        run: |
-          echo $CONDA/bin >> $GITHUB_PATH    
-      - name: Install dependencies
-        run: |
-          conda install -c conda-forge mamba
-      - name: Setup snakemake
-        run: |
-          mamba install -c conda-forge -c bioconda snakemake=7.28.3 singularity
-      - name: Run workflow
-        run: |
-          snakemake --directory tests --configfile tests/config-no-trna-te.yaml --profile tests/profile --snakefile workflow/Snakefile
+          snakemake --directory tests --configfile tests/config.yaml --profile tests/profile --snakefile workflow/Snakefile
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -1,5 +1,38 @@
 # Changelog
 
+## [1.0.1](https://github.com/boulardlab/3t-seq/compare/v1.0.0...v1.0.1) (2024-03-06)
+
+
+### Features
+
+* add example Slurm configuration ([96ce038](https://github.com/boulardlab/3t-seq/commit/96ce0383c48844a7691342dca721a9a1bb64440f))
+* decouple TE, tRNA and single copy genes pipelines. Allow users to decide which branches to run.[#3](https://github.com/boulardlab/3t-seq/issues/3) ([d3b12e4](https://github.com/boulardlab/3t-seq/commit/d3b12e4017c69df6a91c929088cd6641c8790bbb))
+* describe how to run tests ([46e023f](https://github.com/boulardlab/3t-seq/commit/46e023f37e9cfbd96b669695027587fa4888d1f4))
+* DESeq2 reference is now separate for each sequencing library ([b4cf102](https://github.com/boulardlab/3t-seq/commit/b4cf10264ffd7bc33ad01ef3e4ae1d12482e3718))
+
+
+### Bug Fixes
+
+* allow deseq2 ananlysi with different variables and different levels ([76c2562](https://github.com/boulardlab/3t-seq/commit/76c2562501c091b615640a0ec3973a814ec6cca3))
+* fix deseq2 scripts to look for correct column names ([ffc4537](https://github.com/boulardlab/3t-seq/commit/ffc4537558e28ba5ee278975d63fb7958d8f3384))
+* fix problem with SalmonTE quant input array on single-end libraries ([3fd51ff](https://github.com/boulardlab/3t-seq/commit/3fd51fff87474b1243f7844d4699eb34e445e352))
+* fix Snakemake version to be below 8 ([5fa9be3](https://github.com/boulardlab/3t-seq/commit/5fa9be31940270c93024a8cf6a5190215a58ea7d))
+* look for correct column name in edit_conditions_file.py ([e60456e](https://github.com/boulardlab/3t-seq/commit/e60456ed4c3e471b21417c2dc4126c46b6d91382))
+* make test dataset smaller to let it run in GH Actions ([17ac70d](https://github.com/boulardlab/3t-seq/commit/17ac70d120fd772f369c76d9514e260b2a31746d))
+* pin all conda packages versions ([feddd48](https://github.com/boulardlab/3t-seq/commit/feddd48cd06365923fbee22ffc5385a6ec7bebfb))
+* remove params.mem_mb from starTE rules ([b6f1848](https://github.com/boulardlab/3t-seq/commit/b6f18484851a60224d1520166b68ed0df9c2c5f0))
+* restore test profile ([c50b75e](https://github.com/boulardlab/3t-seq/commit/c50b75ebb4e27459c58e298b1546729b651efc83))
+* revert alpine base for SalmonTE Docker ([bfb4a48](https://github.com/boulardlab/3t-seq/commit/bfb4a48f156494a8605dd385c34da6b468c60d1c))
+* switch to miniconda3-alpine as base ([7ac38c7](https://github.com/boulardlab/3t-seq/commit/7ac38c79ed9f88fb2a0d93d0cae99302cc752563))
+* test config now has library-specific deseq2 reference level ([44d4b43](https://github.com/boulardlab/3t-seq/commit/44d4b43565939785370fa4b1233ec025c1c08614))
+* typo ([6e64c84](https://github.com/boulardlab/3t-seq/commit/6e64c848bd9b1765329bac1d8a0a075b98546878))
+* update docs ([c811991](https://github.com/boulardlab/3t-seq/commit/c811991b8186ae6aba348964fbbb1c01096292b8))
+
+
+### Miscellaneous Chores
+
+* release 1.0.1 ([25c11bc](https://github.com/boulardlab/3t-seq/commit/25c11bc0886cf580768fd61ac373ceaca97b997c))
+
 ## 1.0.0 (2023-11-17)
 
 

diff --git a/Dockerfile → tests/Dockerfile b/Dockerfile → tests/Dockerfile
@@ -1,6 +1,6 @@
 FROM condaforge/mambaforge:latest
 LABEL io.github.snakemake.containerized="true"
-LABEL io.github.snakemake.conda_env_hash="ad0a8b2d2a30232f4f3a00bd4dfd3890f43389fc1ad22fa308fc04cc0d85c5eb"
+LABEL io.github.snakemake.conda_env_hash="513bdb2b4084511fb27cc35dd917700337f86ce6b26566dfe6049b47ebc4a3f7"
 
 # Step 1: Retrieve conda environments
 
@@ -79,13 +79,14 @@ COPY ../workflow/env/deeptools.yml /conda-envs/2f716f46231f821a5e905c39c6060cff/
 
 # Conda environment:
 #   source: ../workflow/env/pandas.yml
-#   prefix: /conda-envs/4cbe6e4a8fd33debbcca31573b178d17
+#   prefix: /conda-envs/50d812d8ce9078db884e008cdd1ec8ab
 #   channels:
+#     - conda-forge
 #     - anaconda
 #   dependencies:
-#     - pandas
-RUN mkdir -p /conda-envs/4cbe6e4a8fd33debbcca31573b178d17
-COPY ../workflow/env/pandas.yml /conda-envs/4cbe6e4a8fd33debbcca31573b178d17/environment.yaml
+#     - pandas=2.2.1
+RUN mkdir -p /conda-envs/50d812d8ce9078db884e008cdd1ec8ab
+COPY ../workflow/env/pandas.yml /conda-envs/50d812d8ce9078db884e008cdd1ec8ab/environment.yaml
 
 # Conda environment:
 #   source: ../workflow/env/picard.yml
@@ -112,16 +113,16 @@ COPY ../workflow/env/qc.yml /conda-envs/c9db25f4fb5a47a64d4be70e476fd582/environ
 
 # Conda environment:
 #   source: ../workflow/env/samtools.yml
-#   prefix: /conda-envs/0b7012a9a9c4bff84185eb9d96cb0332
+#   prefix: /conda-envs/9a7384898f8f9aa25cd1d29f531a7f7d
 #   channels:
 #     - conda-forge
 #     - bioconda
 #   dependencies:
 #     - samtools=1.16.1
-#     - ucsc-gtftogenepred
-#     - ucsc-genepredtobed
-RUN mkdir -p /conda-envs/0b7012a9a9c4bff84185eb9d96cb0332
-COPY ../workflow/env/samtools.yml /conda-envs/0b7012a9a9c4bff84185eb9d96cb0332/environment.yaml
+#     - ucsc-gtftogenepred=447
+#     - ucsc-genepredtobed=447
+RUN mkdir -p /conda-envs/9a7384898f8f9aa25cd1d29f531a7f7d
+COPY ../workflow/env/samtools.yml /conda-envs/9a7384898f8f9aa25cd1d29f531a7f7d/environment.yaml
 
 # Conda environment:
 #   source: ../workflow/env/trimmomatic.yml
@@ -173,10 +174,10 @@ RUN mamba env create --prefix /conda-envs/40cdd57d2470dfd817a34e1ec7edeaa4 --fil
     mamba env create --prefix /conda-envs/16e1dc5e3e5976d71e955eaf12ac9181 --file /conda-envs/16e1dc5e3e5976d71e955eaf12ac9181/environment.yaml && \
     mamba env create --prefix /conda-envs/7548059a7c044c6fa179ed2c582570cb --file /conda-envs/7548059a7c044c6fa179ed2c582570cb/environment.yaml && \
     mamba env create --prefix /conda-envs/2f716f46231f821a5e905c39c6060cff --file /conda-envs/2f716f46231f821a5e905c39c6060cff/environment.yaml && \
-    mamba env create --prefix /conda-envs/4cbe6e4a8fd33debbcca31573b178d17 --file /conda-envs/4cbe6e4a8fd33debbcca31573b178d17/environment.yaml && \
+    mamba env create --prefix /conda-envs/50d812d8ce9078db884e008cdd1ec8ab --file /conda-envs/50d812d8ce9078db884e008cdd1ec8ab/environment.yaml && \
     mamba env create --prefix /conda-envs/5802f2d84ae022c00e054e6c16564f06 --file /conda-envs/5802f2d84ae022c00e054e6c16564f06/environment.yaml && \
     mamba env create --prefix /conda-envs/c9db25f4fb5a47a64d4be70e476fd582 --file /conda-envs/c9db25f4fb5a47a64d4be70e476fd582/environment.yaml && \
-    mamba env create --prefix /conda-envs/0b7012a9a9c4bff84185eb9d96cb0332 --file /conda-envs/0b7012a9a9c4bff84185eb9d96cb0332/environment.yaml && \
+    mamba env create --prefix /conda-envs/9a7384898f8f9aa25cd1d29f531a7f7d --file /conda-envs/9a7384898f8f9aa25cd1d29f531a7f7d/environment.yaml && \
     mamba env create --prefix /conda-envs/b93daf96b2454232db6380819bb61725 --file /conda-envs/b93daf96b2454232db6380819bb61725/environment.yaml && \
     mamba env create --prefix /conda-envs/8deaf44f9ffd29816443812db4b8bb83 --file /conda-envs/8deaf44f9ffd29816443812db4b8bb83/environment.yaml && \
     mamba env create --prefix /conda-envs/3674dd77e0957c12c05158a88113106a --file /conda-envs/3674dd77e0957c12c05158a88113106a/environment.yaml && \

diff --git a/tests/profile/config.yaml b/tests/profile/config.yaml
@@ -4,3 +4,4 @@ singularity-args: ""
 show-failed-logs: True
 cores: 2
 conda-cleanup-pkgs: cache
+all-temp: True
diff --git a/workflow/env/pandas.yml b/workflow/env/pandas.yml
@@ -1,4 +1,5 @@
 channels:
+  - conda-forge
   - anaconda
 dependencies:
-  - pandas=2.1.1
+  - pandas=2.2.1