Merge pull request #30 from pdimens/dev

Dev

.github/workflows/createrelease.yml

@@ -0,0 +1,38 @@
+name: Create Release
+
+on:
+  push:
+    branches:
+      - 'main'
+    tags:
+      - v*
+
+permissions:
+  contents: write
+
+jobs:
+  release:
+    name: Release pushed tag
+    runs-on: ubuntu-22.04
+    steps:
+      - name: Create release
+        id: create_release
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+          tag: ${{ github.ref_name }}
+        run: |
+          gh release create "$tag" \
+              --repo="$GITHUB_REPOSITORY" \
+              --title="${GITHUB_REPOSITORY#*/} ${tag#v}" \
+              --generate-notes
+      - name: build artifacts
+        run: tar --exclude="test" --exclude=".git" --exclude=".github" --exclude=".snakemake" -zcvf harpy.${{tag#v}}.tar.gz .
+      - name: upload tarball
+        uses: actions/upload-release-asset@v1
+        env:
+          GITHUB_TOKEN: ${{ github.token }}
+        with:
+          upload_url: ${{ steps.create_release.outputs.upload_url }}
+          asset_path: ./harpy.${{tag#v}}.tar.gz
+          asset_name: harpy.${{tag#v}}.tar.gz
+          asset_content_type: application/gzip

.github/workflows/impute.yml

@@ -65,11 +65,11 @@ jobs:
 
       - name: impute
         shell: micromamba-shell {0}
-        run: harpy impute --vcf test/vcf/test.bcf -d test/bam -p test/stitch.params -q -s "--show-failed-logs"
+        run: harpy impute --vcf test/vcf/test.bcf -d test/bam -p test/stitch.params -s "--show-failed-logs"
 
       - name: impute from vcf
         shell: micromamba-shell {0}
         if: always()
         run: |
           rm -rf Impute
-          harpy impute --vcf-samples --vcf test/vcf/test.bcf -d test/bam -p test/stitch.params -q -s "--show-failed-logs"
+          harpy impute --vcf-samples --vcf test/vcf/test.bcf -d test/bam -p test/stitch.params -s "--show-failed-logs"

resources/build.sh

@@ -3,13 +3,13 @@
 mkdir -p ${PREFIX}/bin
 
 # install harpy proper
-${PREFIX}/bin/python -m pip install . --no-deps -vv
+${PYTHON} -m pip install . --no-deps -vvv
 
 # rules
 cp workflow/rules/*.smk ${PREFIX}/bin/
 
 # associated scripts
-chmod +x workdflow/scripts/* 
+chmod +x workflow/scripts/* 
 cp workflow/scripts/* ${PREFIX}/bin/
 
 # reports

resources/meta.yaml

@@ -35,8 +35,17 @@ test:
     - "harpy --version"
 about:
   home: "https://github.com/pdimens/harpy/"
-  license: MIT
+  license: GPL-3.0-or-later
+  license_family: GPL3
+  license_file: LICENSE
   summary: "Process raw haplotagging data, from raw sequences to phased haplotypes."
+  description: |
+    Harpy is a command-line tool to easily process haplotag or 10x linked-read data. It uses
+    Snakemake under the hood to execute different workflows (quality control, trimming, 
+    alignment, variant calling, phasing, etc.), but the user is rarely, if ever, exposed
+    to Snakemake directly. With an emphasis on user-friendliness, parallelization, transparency,
+    and reproducibility, Harpy aims to quickly handle data processing so that you can focus more
+    on analyzing your data. 
   doc_url: https://pdimens.github.io/harpy/
   dev_url: https://github.com/pdimens/harpy
 
@@ -46,4 +55,4 @@ extra:
   recipe-maintainers:
     - pdimens
 #  skip-lints:
-#    - should_be_noarch_generic
+#    - should_be_noarch_generic

workflow/envs/harpy.yaml

@@ -6,10 +6,11 @@ dependencies:
   - bcftools =1.19
   - mamba
   - multiqc
+  - pandas
   - pysam =0.22
   - python
   - rich-click
-  - snakemake
+  - snakemake-minimal
   - samtools
   - seqtk
   - tabix