Docs

.github/dependabot.yaml

@@ -1,6 +1,11 @@
 version: 2
+name: dependabot
+on:
+  push:
+    branches:
+      - master
 updates:
   - package-ecosystem: "github-actions"
     directory: "/"
     schedule:
-      interval: "weekly"
+      interval: "weekly"

.github/workflows/main.yaml

@@ -0,0 +1,143 @@
+name: mosaicatcher-pipeline workflow checks
+
+on:
+  push:
+    branches:
+      - master
+      - smk_wf_catalog
+      - ref_genomes
+
+jobs:
+  # WORK
+  Formatting:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v2
+
+      - name: Formatting
+        uses: github/super-linter@v4
+        env:
+          VALIDATE_ALL_CODEBASE: false
+          DEFAULT_BRANCH: master
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+          VALIDATE_SNAKEMAKE_SNAKEFMT: true
+
+  Linting:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v2
+      - name: Linting
+        uses: snakemake/snakemake-github-action@v1.23.0
+        with:
+          directory: .
+          snakefile: ./workflow/Snakefile
+          args: "--lint"
+  Testing:
+    runs-on: ubuntu-latest
+    # needs:
+    #   - Linting
+    #   - Formatting
+    steps:
+      - uses: actions/checkout@v2
+      - name: Testing data
+        uses: snakemake/snakemake-github-action@v1.23.0
+        with:
+          directory: .
+          snakefile: ./workflow/Snakefile
+          args: "--cores 1 --use-conda --configfile .tests/config/simple_config.yaml --conda-frontend mamba -p --verbose --debug"
+      - name: Testing report
+        uses: snakemake/snakemake-github-action@v1.23.0
+        with:
+          directory: .
+          snakefile: ./workflow/Snakefile
+          args: "--cores 1 --use-conda --configfile .tests/config/simple_config.yaml --conda-frontend mamba --report report.zip"
+
+  Linting_ashleys:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v2
+      - name: Linting
+        uses: snakemake/snakemake-github-action@v1.23.0
+        with:
+          directory: .
+          snakefile: ./workflow/Snakefile
+          args: "--lint --config ashleys_pipeline=True"
+  Testing_ashleys:
+    runs-on: ubuntu-latest
+    # needs:
+    #   - Linting
+    #   - Formatting
+    steps:
+      - uses: actions/checkout@v2
+      - name: Testing data
+        uses: snakemake/snakemake-github-action@v1.23.0
+        with:
+          directory: .
+          snakefile: ./workflow/Snakefile
+          stagein: "conda config --set channel_priority flexible"
+          args: "--cores 1 --use-conda --configfile .tests/config/simple_config.yaml --config ashleys_pipeline=True use_light_data=True --conda-frontend mamba -p --verbose --debug"
+      - name: Testing report
+        uses: snakemake/snakemake-github-action@v1.23.0
+        with:
+          directory: .
+          snakefile: ./workflow/Snakefile
+          args: "--cores 1 --use-conda --configfile .tests/config/simple_config.yaml --config ashleys_pipeline=True use_light_data=True --conda-frontend mamba --report report.zip"
+  Testing_jup_nb:
+    runs-on: ubuntu-latest
+    # needs:
+    #   - Linting
+    #   - Formatting
+    steps:
+      - uses: actions/checkout@v2
+      - name: Testing data
+        uses: snakemake/snakemake-github-action@v1.23.0
+        with:
+          directory: .
+          snakefile: ./workflow/Snakefile
+          stagein: "conda config --set channel_priority flexible"
+          args: "--cores 1 --use-conda --configfile .tests/config/simple_config.yaml --config ashleys_pipeline=True use_light_data=True hand_selection=True --conda-frontend mamba -p --verbose --debug"
+      - name: Testing report
+        uses: snakemake/snakemake-github-action@v1.23.0
+        with:
+          directory: .
+          snakefile: ./workflow/Snakefile
+          args: "--cores 1 --use-conda --configfile .tests/config/simple_config.yaml --config ashleys_pipeline=True use_light_data=True hand_selection=True  --conda-frontend mamba --report report.zip"
+  Downloading_example_data:
+    runs-on: ubuntu-latest
+    # needs:
+    #   - Linting
+    #   - Formatting
+    steps:
+      - uses: actions/checkout@v2
+      - name: Testing data
+        uses: snakemake/snakemake-github-action@v1.23.0
+        with:
+          directory: .
+          snakefile: ./workflow/Snakefile
+          args: "--cores 1 --config dl_bam_example=True input_bam_location=TEST_EXAMPLE_DATA -p --verbose --debug"
+  Downloading_hg19:
+    runs-on: ubuntu-latest
+    # needs:
+    #   - Linting
+    #   - Formatting
+    steps:
+      - uses: actions/checkout@v2
+      - name: Testing data
+        uses: snakemake/snakemake-github-action@v1.23.0
+        with:
+          directory: .
+          snakefile: ./workflow/Snakefile
+          args: "--cores 1 --config dl_external_files=True reference=hg19 -p --verbose --debug"
+  Downloading_hg38:
+    runs-on: ubuntu-latest
+    # needs:
+    #   - Linting
+    #   - Formatting
+    steps:
+      - uses: actions/checkout@v2
+      - name: Testing data
+        uses: snakemake/snakemake-github-action@v1.23.0
+        with:
+          directory: .
+          snakefile: ./workflow/Snakefile
+          args: "--cores 1 --config dl_external_files=True reference=hg38 -p --verbose --debug"

.gitignore

@@ -66,6 +66,8 @@ workflow/test.txt
 .snakemake
 
 # Exceptions
+!docs/images/plots/
+!docs/images/plots/*.png
 !docs/images/*.png
 !workflow/data/segdups/segDups_hg38_UCSCtrack.bed.gz
 !workflow/data/bin_200kb_all.bed

.snakemake-workflow-catalog.yml

@@ -1,16 +1,6 @@
 usage:
-  mandatory-flags: # optional definition of additional flags
-    desc: # describe your flags here in a few sentences (they will be inserted below the example commands)
-    flags:
-      - "snakemake"
-      - "mosaicatcher"
-      - "single-cell-genomics"
-      - "strand-seq"
-      - "structural-variants"
-      - "sv-calling"
-        # put your flags here
-  software-stack-deployment: # definition of software deployment method (at least one of conda, singularity, or singularity+conda)
-    conda: true # whether pipeline works with --use-conda
-    singularity: false # whether pipeline works with --use-singularity
-    singularity+conda: true # whether pipeline works with --use-singularity --use-conda
-  report: true # add this to confirm that the workflow allows to use 'snakemake --report report.zip' to generate a report containing all results and explanations
+  software-stack-deployment:
+    conda: true
+    singularity: false
+    singularity+conda: true
+  report: true