Convert pipeline to DSL2

guigolab · Nov 25, 2021 · 8f04510 · 8f04510
1 parent af3d3e8
commit 8f04510
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Showing 12 changed files with 832 additions and 703 deletions.
diff --git a/.github/workflows/ci.sh b/.github/workflows/ci.sh
@@ -5,6 +5,8 @@ set -o pipefail
 DB_FILE=chipseq-pipeline.db
 VALIDATE_DIR=validate-ci
 
+export NXF_ANSI_LOG=false
+export NXF_DOCKER=${NXF_DOCKER-'with'}
 getPath() {
     if [ -n "$(type -a realpath)" ]; then
         realpath $@
@@ -17,16 +19,27 @@ case "$1" in
   run)
     shift
     echo "Running test pipeline..." >&2
-    ./nextflow run . $@
+    ./nextflow run . -${NXF_DOCKER}-docker $@
     ;;
   validate)
     shift
-    f=$(getPath ${1-data/md5s})
+    md5s=$(getPath ${1-data/md5s})
     echo "Validating test results..." >&2
     [[ -s ${DB_FILE} ]] || false
     mkdir -p ${VALIDATE_DIR} && cd ${VALIDATE_DIR}
-    cut -f 2 ../${DB_FILE} | xargs -I{} ln -fs {}
-    md5sum -c ${f}
+    cut -f 2 ../${DB_FILE} | while read f
+    do
+        name=$(basename $f)
+        ext=${name##*.}
+        case $ext in
+            bam)
+                samtools view ${f} > ${name%.*}.sam
+                ;;
+            *)
+                ln -fs ${f} .
+        esac
+    done
+    md5sum -c ${md5s}
     ;;
   cleanup)
     echo "Cleaning up test results..." >&2

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
@@ -24,7 +24,11 @@ jobs:
         curl -fsSL get.nextflow.io | bash -e
     - name: Run pipeline
       run: |
-        .github/workflows/ci.sh run -with-docker
+        .github/workflows/ci.sh run
     - name: Validate pipeline results
-      run: |
-        .github/workflows/ci.sh validate
+      uses: addnab/docker-run-action@v3
+      with:
+        image: guigolab/chip-nf:dev
+        options: -v ${{ github.workspace }}:${{ github.workspace }} -w ${{ github.workspace }}
+        run: |
+          .github/workflows/ci.sh validate