convert old pipeline workflow to just sra

.github/workflows/pipeline_sra.yaml

@@ -0,0 +1,144 @@
+name: Pipeline
+#This is a workflow for full pipeline testing.
+
+# Global workflow environment variables
+env:
+    PHYLO_NF_REV: "master"
+    EAGER_NF_REV: "7b51863957"
+    PHYLO_CONDA_ENV: "plague-phylogeography-0.1.4dev"
+    EAGER_CONDA_ENV: "nf-core-eager-2.2.0dev"
+
+on:
+  # Triggered on Push for any branch
+  push:
+    branches:
+      - '*'
+    # On change to workflow, pipeline
+    paths:
+      - '.github/workflows/pipeline_sra.yaml'
+      - 'main.nf'
+      - 'nextflow.config'
+      - 'environment.yaml'
+
+  # Triggered on PR for all branches, pipeline
+  pull_request:
+    branches:
+      - '*'
+  # Also on a published release
+  release:
+    types: [published]
+
+jobs:
+
+  # Install the pipeline and dependencies
+  pipeline:
+    runs-on: ubuntu-latest
+    steps:
+
+      # 1. Install nextflow
+      - name: install nextflow
+        run: |
+          wget -qO- get.nextflow.io | bash
+          sudo mv nextflow /usr/local/bin/
+
+      # 2. Setup conda
+      - name: setup conda
+        uses: goanpeca/setup-miniconda@v1
+        with:
+          auto-update-conda: true
+
+      # 3a. Install ktmeaton/plague-phylogeography
+      - name: install nf ktmeaton/plague-phylogeography
+        shell: bash -l {0}
+        run: |
+          nextflow pull ktmeaton/plague-phylogeography
+          nextflow pull ktmeaton/plague-phylogeography -r ${PHYLO_NF_REV}
+          nextflow run ktmeaton/plague-phylogeography --version
+
+      # 3b. Install ktmeaton/plague-phylogeography
+      - name: install conda ktmeaton/plague-phylogeography
+        shell: bash -l {0}
+        run: |
+          conda env create -f  ~/.nextflow/assets/ktmeaton/plague-phylogeography/environment.yaml
+          conda activate ${PHYLO_CONDA_ENV}
+          conda deactivate
+
+      # 4a. Install nf-core/eager
+      - name: install nf nf-core/eager
+        shell: bash -l {0}
+        run: |
+          nextflow pull nf-core/eager
+          nextflow pull nf-core/eager -r ${EAGER_NF_REV}
+          nextflow run nf-core/eager -r ${EAGER_NF_REV} --help
+
+      # 4b. Install nf-core/eager
+      - name: install conda nf-core/eager
+        shell: bash -l {0}
+        run: |
+          conda env create -f ~/.nextflow/assets/nf-core/eager/environment.yml
+          conda install -n ${EAGER_CONDA_ENV} -c bioconda nextflow
+          conda install -n ${EAGER_CONDA_ENV} -c anaconda graphviz
+          conda activate ${EAGER_CONDA_ENV}
+          dot -v
+          nextflow -v
+          conda deactivate
+
+      - name: example pipeline
+        shell: bash -l {0}
+        run: |
+          conda info --envs
+          conda activate ${PHYLO_CONDA_ENV}
+          nextflow run ktmeaton/plague-phylogeography \
+            --skip_assembly_download \
+            --sqlite_select_command_sra "\"SELECT BioSampleAccession,SRARunAccession,SRALibraryLayout,SRAFileURL FROM Master WHERE (SRARunAccession = 'SRR1048902' OR SRARunAccession = 'SRR1048905')\"" \
+            --skip_eager \
+            --skip_outgroup_download \
+            --outdir test
+
+      - name: example eager
+        shell: bash -l {0}
+        run: |
+          conda activate ${EAGER_CONDA_ENV}
+          mkdir -p test/eager
+          nextflow -C ~/.nextflow/assets/nf-core/eager/nextflow.config \
+            run nf-core/eager \
+            -r ${EAGER_NF_REV} \
+            --input test/sqlite_import/metadata_sra_eager.tsv \
+            --outdir test/eager \
+            --fasta test/reference_genome/GCF_000009065.1_ASM906v1_genomic.fna \
+            --clip_readlength 35 \
+            --preserve5p \
+            --mergedonly \
+            --mapper bwaaln \
+            --bwaalnn 0.01 \
+            --bwaalnl 16 \
+            --run_bam_filtering \
+            --bam_mapping_quality_threshold 30 \
+            --bam_discard_unmapped \
+            --bam_unmapped_type discard \
+            --max_memory "6.GB" \
+            --max_cpus 2
+
+      - name: artifact sqlite-import
+        uses: actions/upload-artifact@v2
+        with:
+          name: sqlite-import
+          path: test/sqlite_import/
+
+      - name: artifact iqtree
+        uses: actions/upload-artifact@v2
+        with:
+          name: iqtree
+          path: test/iqtree/
+
+      - name: artifact multiqc
+        uses: actions/upload-artifact@v2
+        with:
+          name: multiqc
+          path: test/eager/MultiQC
+
+      - name: artifact trace
+        uses: actions/upload-artifact@v2
+        with:
+          name: trace
+          path: test/trace/