Converting Galaxy wf to Nextflow wf

.github/workflows/ci.config

@@ -0,0 +1,15 @@
+
+process {
+    executor='slurm'
+    time = '7 d'
+    memory = '4 GB'
+}
+
+singularity {
+    enabled = true
+}
+
+conda {
+    createTimeout = "30 min"
+    useMamba = true
+}

.github/workflows/nextflow-linter.yaml

@@ -0,0 +1,55 @@
+name: nf-core linting
+on:
+  push:
+    branches:
+      - main
+  pull_request:
+    branches:
+      - main
+
+jobs:
+  lint:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v2
+      - uses: actions/setup-java@v2
+        with:
+          distribution: 'adopt'
+          java-version: '11'
+
+      - name: install Nextflow
+        run: |
+          wget -qO- https://get.nextflow.io | bash
+          chmod +x nextflow
+          mkdir -p $HOME/.local/bin
+          mv nextflow $HOME/.local/bin/
+          echo "$HOME/.local/bin" >> $GITHUB_PATH
+
+      - name: set up Python
+        uses: actions/setup-python@v2
+        with:
+          python-version: '3.x'
+
+      - name: install nf-core tools
+        run: |
+          python -m pip install --upgrade pip
+          pip install nf-core
+
+      - name: check Nextflow version
+        run: nextflow -version
+
+      # https://nf-co.re/tools/docs/latest/pipeline_lint_tests/
+      - name: create .nf-core.yml
+        run: |
+          cat << EOF > .nf-core.yml
+          repository_type: pipeline
+          lint:
+            actions_awsfulltest: False
+            actions_awstest: False
+            multiqc_config: False
+            schema_lint: False
+            schema_params: False
+          EOF
+
+      - name: run nf-core lint
+        run: nf-core pipelines lint --dir .

README.md

@@ -1,2 +1,18 @@
 # scxa-tertiary-workflow
 Tertiary component for SCXA workflows
+
+# How to run workflow for tertiary analysis 
+## Prepare data
+```
+bash scripts/data_prep.sh <EXP-ID> [output path]
+```
+## Run for plate
+```
+nextflow run main.nf --slurm -resume --dir_path <EXP-ID with path> [--output_path <PATH>]  [--scanpy_scripts_container <container_id>]
+```
+## Run for droplet
+```
+nextflow run main.nf --slurm -resume --dir_path <EXP-ID with path> --technology droplet [--output_path <PATH>] [--scanpy_scripts_container <container_id>]
+```
+
+If `[--output_path <PATH>]` is not specified results will be `<EXP-ID with path>/results` dir.