feat: added pixi env, test tasks, and updated apptainer workflow to handle new --containerize args

.gitattributes

@@ -0,0 +1,2 @@
+# SCM syntax highlighting & preventing 3-way merges
+pixi.lock merge=binary linguist-language=YAML linguist-generated=true -diff

.github/workflows/deploy-apptainer.yml

@@ -11,27 +11,19 @@ jobs:
       packages: write
     steps:
       - name: checkout repo
-        uses: actions/checkout@v4
+        uses: actions/checkout@v6
         with:
           fetch-depth: 0
 
-      - name: create dockerfile
+      - name: create apptainer recipe
         uses: snakemake/snakemake-github-action@v2
         with:
           directory: .
           snakefile: workflow/Snakefile
           install-apptainer: true
           args: "--cores 1"
           task: containerize
-
-      - name: create apptainer recipe
-        shell: bash
-        run: |
-          pip install spython
-          sed -i "2i RUN apt-get update && apt-get install -y curl" Dockerfile
-          spython recipe Dockerfile > apptainer.def
-          sed -i 's/\/environment.yaml\/environment.yaml$/\/environment.yaml/' apptainer.def
-          sed -i 's/^curl /curl -L /' apptainer.def
+          containerize-args: apptainer
 
       - name: create apptainer image
         shell: bash

.github/workflows/snakemake-tests.yml

@@ -18,7 +18,7 @@ jobs:
   Formatting:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v6
         with:
           fetch-depth: 0
       - name: Formatting
@@ -33,7 +33,7 @@ jobs:
   Linting:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v6
       - name: Lint workflow
         uses: snakemake/snakemake-github-action@v2
         with:
@@ -47,7 +47,7 @@ jobs:
       - Linting
       - Formatting
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v6
 
       - name: Test workflow
         uses: snakemake/snakemake-github-action@v2

.github/workflows/yaml-formatting.yml

@@ -8,7 +8,7 @@ jobs:
   Formatting:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v6
         with:
           fetch-depth: 0
       - name: Formatting

.gitignore

@@ -0,0 +1,8 @@
+# workspace
+.snakemake
+.test/result.*
+.test/apptainer.*
+
+# pixi environments
+.pixi/*
+!.pixi/config.toml

.test/Snakefile

@@ -0,0 +1,26 @@
+rule all:
+    input:
+        "result.txt",
+        "result.html",
+
+
+rule test:
+    output:
+        "result.txt",
+    conda:
+        "test_env.yaml"
+    shell:
+        "echo 'This is just a test.' > {output}"
+
+
+rule test_wrapper:
+    input:
+        sample=["input.fastq"],
+    output:
+        html="result.html",
+        json="result.json",
+    log:
+        "result.log",
+    threads: 1
+    wrapper:
+        "v9.5.0/bio/fastp"

.test/input.fastq

@@ -0,0 +1,40 @@
+@read1
+ACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@read2
+TGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@read3
+AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@read4
+TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@read5
+GCGCGCGCGCGCGCGCGCGCGCGCGCGCGCGCGCGCGCGCGCGCGCGC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@read6
+ATATATATATATATATATATATATATATATATATATATATATATATAT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@read7
+ACACACACACACACACACACACACACACACACACACACACACACACAC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@read8
+GTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@read9
+AGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@read10
+CTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII

.test/test_env.yaml

@@ -0,0 +1,6 @@
+name: test_env
+channels:
+  - conda-forge
+  - bioconda
+dependencies:
+  - pyyaml=6.0.3

pixi.toml

@@ -0,0 +1,16 @@
+[workspace]
+authors = ["m-jahn <jahn@mpusp.mpg.de>"]
+channels = ["conda-forge", "bioconda"]
+name = "mpusp-github-actions"
+platforms = ["linux-64"]
+version = "0.1.0"
+
+[tasks]
+test-workflow = { cmd = "snakemake -d .test -s .test/Snakefile -c 1 --sdm conda" }
+test-containerize = { cmd = "snakemake -d .test -s .test/Snakefile -c 1 --show-failed-logs --containerize apptainer > .test/apptainer.def" }
+test-uidmap = { cmd = "dpkg -l uidmap 2>/dev/null" }
+test-apptainer = { cmd = "cd .test; apptainer build --fakeroot apptainer.sif apptainer.def" }
+
+[dependencies]
+snakemake = ">=9.19.0,<10"
+apptainer = ">=1.4.5,<2"