Merge branch 'main' into dev

NBISweden · Oct 12, 2023 · f1865a9 · f1865a9
2 parents feaa78f + e355898
commit f1865a9
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diff --git a/.github/workflows/gerp.yaml b/.github/workflows/gerp.yaml
@@ -0,0 +1,62 @@
+name: gerp
+
+on:
+  push:
+    paths-ignore:
+      - 'README.md'
+      - 'LICENSE.md'
+      - 'workflow/rules/1.2_map_to_mitogenomes.smk'
+      - 'workflow/rules/7_mlRho.smk'
+      - 'workflow/rules/10_pca.smk'
+      - 'workflow/rules/11_ROH.smk'
+      - 'workflow/rules/12_snpEff.smk'
+    branches:
+      - main
+  pull_request:
+    paths-ignore:
+      - 'README.md'
+      - 'LICENSE.md'
+      - 'workflow/docker'
+      - 'workflow/rules/1.2_map_to_mitogenomes.smk'
+      - 'workflow/rules/7_mlRho.smk'
+      - 'workflow/rules/10_pca.smk'
+      - 'workflow/rules/11_ROH.smk'
+      - 'workflow/rules/12_snpEff.smk'
+    branches:
+      - main
+      - dev
+
+jobs:
+  test:
+    runs-on: ubuntu-latest
+
+    steps:
+      - uses: actions/checkout@v3
+
+      - uses: eWaterCycle/setup-apptainer@v2
+        with:
+          apptainer-version: 1.1.4
+
+      - uses: conda-incubator/setup-miniconda@v2
+        with:
+          miniforge-variant: Mambaforge
+          channels: conda-forge,bioconda
+          activate-environment: generode
+          environment-file: environment.yml
+          auto-activate-base: false
+
+      - name: conda_environment
+        shell: bash -l {0}
+        run: |
+          conda info
+          conda list
+
+      - name: gerp_dry
+        shell: bash -l {0}
+        run: |
+          snakemake -npr --configfile .test/config/config_gerp.yaml -j 4 --cores 1 --use-singularity
+
+      - name: gerp
+        shell: bash -l {0}
+        run: |
+          snakemake --configfile .test/config/config_gerp.yaml -j 4 --cores 1 --use-singularity
diff --git a/.github/workflows/mitogenome_mapping.yaml b/.github/workflows/mitogenome_mapping.yaml
@@ -0,0 +1,87 @@
+name: mitogenome_mapping
+
+on:
+  push:
+    paths-ignore:
+      - 'README.md'
+      - 'LICENSE.md'
+      - 'workflow/rules/0.1_reference_genome_preps.smk'
+      - 'workflow/rules/0.2_repeat_identification.smk'
+      - 'workflow/rules/2_mapping.smk'
+      - 'workflow/rules/3.1_bam_rmdup_realign_indels.smk'
+      - 'workflow/rules/3.2_historical_bam_mapDamage.smk'
+      - 'workflow/rules/3.3_bam_subsampling.smk'
+      - 'workflow/rules/4_genotyping.smk'
+      - 'workflow/rules/5_CpG_identification.smk'
+      - 'workflow/rules/6_autosome_sexchromosome_bed_files.smk'
+      - 'workflow/rules/7_mlRho.smk'
+      - 'workflow/rules/8.1_vcf_CpG_filtering.smk'
+      - 'workflow/rules/8.2_vcf_qual_repeat_filtering.smk'
+      - 'workflow/rules/9_merge_vcfs.smk'
+      - 'workflow/rules/10_pca.smk'
+      - 'workflow/rules/11_ROH.smk'
+      - 'workflow/rules/12_snpEff.smk'
+      - 'workflow/rules/13_GERP.smk'
+    branches:
+      - main
+  pull_request:
+    paths-ignore:
+      - 'README.md'
+      - 'LICENSE.md'
+      - 'workflow/docker'
+      - 'workflow/rules/0.1_reference_genome_preps.smk'
+      - 'workflow/rules/0.2_repeat_identification.smk'
+      - 'workflow/rules/2_mapping.smk'
+      - 'workflow/rules/3.1_bam_rmdup_realign_indels.smk'
+      - 'workflow/rules/3.2_historical_bam_mapDamage.smk'
+      - 'workflow/rules/3.3_bam_subsampling.smk'
+      - 'workflow/rules/4_genotyping.smk'
+      - 'workflow/rules/5_CpG_identification.smk'
+      - 'workflow/rules/6_autosome_sexchromosome_bed_files.smk'
+      - 'workflow/rules/7_mlRho.smk'
+      - 'workflow/rules/8.1_vcf_CpG_filtering.smk'
+      - 'workflow/rules/8.2_vcf_qual_repeat_filtering.smk'
+      - 'workflow/rules/9_merge_vcfs.smk'
+      - 'workflow/rules/10_pca.smk'
+      - 'workflow/rules/11_ROH.smk'
+      - 'workflow/rules/12_snpEff.smk'
+      - 'workflow/rules/13_GERP.smk'
+    branches:
+      - main
+      - dev
+
+jobs:
+  test:
+    runs-on: ubuntu-latest
+
+    steps:
+      - uses: actions/checkout@v3
+
+      - uses: eWaterCycle/setup-apptainer@v2
+        with:
+          apptainer-version: 1.1.4
+
+      - uses: conda-incubator/setup-miniconda@v2
+        with:
+          miniforge-variant: Mambaforge
+          channels: conda-forge,bioconda
+          activate-environment: generode
+          environment-file: environment.yml
+          auto-activate-base: false
+
+      - name: conda_environment
+        shell: bash -l {0}
+        run: |
+          conda info
+          conda list
+
+      - name: mitogenome_mapping_dry
+        shell: bash -l {0}
+        run: |
+          snakemake -npr --configfile .test/config/config_mitogenomes.yaml -j 4 --cores 1 --use-singularity
+
+      - name: mitogenome_mapping
+        shell: bash -l {0}
+        run: |
+          snakemake --configfile .test/config/config_mitogenomes.yaml -j 4 --cores 1 --use-singularity
+
diff --git a/.github/workflows/main.yaml → .github/workflows/mlRho_options.yaml b/.github/workflows/main.yaml → .github/workflows/mlRho_options.yaml
@@ -1,17 +1,33 @@
-name: CI
+name: mlRho_options
 
 on:
   push:
     paths-ignore:
       - 'README.md'
       - 'LICENSE.md'
+      - 'workflow/rules/1.2_map_to_mitogenomes.smk'
+      - 'workflow/rules/8.1_vcf_CpG_filtering.smk'
+      - 'workflow/rules/8.2_vcf_qual_repeat_filtering.smk'
+      - 'workflow/rules/9_merge_vcfs.smk'
+      - 'workflow/rules/10_pca.smk'
+      - 'workflow/rules/11_ROH.smk'
+      - 'workflow/rules/12_snpEff.smk'
+      - 'workflow/rules/13_GERP.smk'
     branches:
       - main
   pull_request:
     paths-ignore:
       - 'README.md'
       - 'LICENSE.md'
       - 'workflow/docker'
+      - 'workflow/rules/1.2_map_to_mitogenomes.smk'
+      - 'workflow/rules/8.1_vcf_CpG_filtering.smk'
+      - 'workflow/rules/8.2_vcf_qual_repeat_filtering.smk'
+      - 'workflow/rules/9_merge_vcfs.smk'
+      - 'workflow/rules/10_pca.smk'
+      - 'workflow/rules/11_ROH.smk'
+      - 'workflow/rules/12_snpEff.smk'
+      - 'workflow/rules/13_GERP.smk'
     branches:
       - main
       - dev
@@ -41,16 +57,6 @@ jobs:
           conda info
           conda list
 
-      - name: mitogenome_mapping_dry
-        shell: bash -l {0}
-        run: |
-          snakemake -npr --configfile .test/config/config_mitogenomes.yaml -j 4 --cores 1 --use-singularity
-
-      - name: mitogenome_mapping
-        shell: bash -l {0}
-        run: |
-          snakemake --configfile .test/config/config_mitogenomes.yaml -j 4 --cores 1 --use-singularity
-
       - name: mlRho_options_dry
         shell: bash -l {0}
         run: |
@@ -60,23 +66,3 @@ jobs:
         shell: bash -l {0}
         run: |
           snakemake --configfile .test/config/config_mlRho_options.yaml -j 4 --cores 1 --use-singularity
-
-      - name: pca_roh_dry
-        shell: bash -l {0}
-        run: |
-          snakemake -npr --configfile .test/config/config_pca_roh.yaml -j 4 --cores 1 --use-singularity
-
-      - name: pca_roh
-        shell: bash -l {0}
-        run: |
-          snakemake --configfile .test/config/config_pca_roh.yaml -j 4 --cores 1 --use-singularity
-
-      - name: snpeff_gerp_dry
-        shell: bash -l {0}
-        run: |
-          snakemake -npr --configfile .test/config/config_snpeff_gerp.yaml -j 4 --cores 1 --use-singularity
-
-      - name: snpeff_gerp
-        shell: bash -l {0}
-        run: |
-          snakemake --configfile .test/config/config_snpeff_gerp.yaml -j 4 --cores 1 --use-singularity
diff --git a/.github/workflows/pca_roh.yaml b/.github/workflows/pca_roh.yaml
@@ -0,0 +1,60 @@
+name: pca_roh
+
+on:
+  push:
+    paths-ignore:
+      - 'README.md'
+      - 'LICENSE.md'
+      - 'workflow/rules/1.2_map_to_mitogenomes.smk'
+      - 'workflow/rules/7_mlRho.smk'
+      - 'workflow/rules/12_snpEff.smk'
+      - 'workflow/rules/13_GERP.smk'
+    branches:
+      - main
+  pull_request:
+    paths-ignore:
+      - 'README.md'
+      - 'LICENSE.md'
+      - 'workflow/docker'
+      - 'workflow/rules/1.2_map_to_mitogenomes.smk'
+      - 'workflow/rules/7_mlRho.smk'
+      - 'workflow/rules/12_snpEff.smk'
+      - 'workflow/rules/13_GERP.smk'
+    branches:
+      - main
+      - dev
+
+jobs:
+  test:
+    runs-on: ubuntu-latest
+
+    steps:
+      - uses: actions/checkout@v3
+
+      - uses: eWaterCycle/setup-apptainer@v2
+        with:
+          apptainer-version: 1.1.4
+
+      - uses: conda-incubator/setup-miniconda@v2
+        with:
+          miniforge-variant: Mambaforge
+          channels: conda-forge,bioconda
+          activate-environment: generode
+          environment-file: environment.yml
+          auto-activate-base: false
+
+      - name: conda_environment
+        shell: bash -l {0}
+        run: |
+          conda info
+          conda list
+
+      - name: pca_roh_dry
+        shell: bash -l {0}
+        run: |
+          snakemake -npr --configfile .test/config/config_pca_roh.yaml -j 4 --cores 1 --use-singularity
+
+      - name: pca_roh
+        shell: bash -l {0}
+        run: |
+          snakemake --configfile .test/config/config_pca_roh.yaml -j 4 --cores 1 --use-singularity
diff --git a/.github/workflows/snpeff.yaml b/.github/workflows/snpeff.yaml
@@ -0,0 +1,62 @@
+name: snpeff
+
+on:
+  push:
+    paths-ignore:
+      - 'README.md'
+      - 'LICENSE.md'
+      - 'workflow/rules/1.2_map_to_mitogenomes.smk'
+      - 'workflow/rules/7_mlRho.smk'
+      - 'workflow/rules/10_pca.smk'
+      - 'workflow/rules/11_ROH.smk'
+      - 'workflow/rules/13_GERP.smk'
+    branches:
+      - main
+  pull_request:
+    paths-ignore:
+      - 'README.md'
+      - 'LICENSE.md'
+      - 'workflow/docker'
+      - 'workflow/rules/1.2_map_to_mitogenomes.smk'
+      - 'workflow/rules/7_mlRho.smk'
+      - 'workflow/rules/10_pca.smk'
+      - 'workflow/rules/11_ROH.smk'
+      - 'workflow/rules/13_GERP.smk'
+    branches:
+      - main
+      - dev
+
+jobs:
+  test:
+    runs-on: ubuntu-latest
+
+    steps:
+      - uses: actions/checkout@v3
+
+      - uses: eWaterCycle/setup-apptainer@v2
+        with:
+          apptainer-version: 1.1.4
+
+      - uses: conda-incubator/setup-miniconda@v2
+        with:
+          miniforge-variant: Mambaforge
+          channels: conda-forge,bioconda
+          activate-environment: generode
+          environment-file: environment.yml
+          auto-activate-base: false
+
+      - name: conda_environment
+        shell: bash -l {0}
+        run: |
+          conda info
+          conda list
+
+      - name: snpeff_dry
+        shell: bash -l {0}
+        run: |
+          snakemake -npr --configfile .test/config/config_snpeff.yaml -j 4 --cores 1 --use-singularity
+
+      - name: snpeff
+        shell: bash -l {0}
+        run: |
+          snakemake --configfile .test/config/config_snpeff.yaml -j 4 --cores 1 --use-singularity