🔀 Merge pull request #78 from cnr-ibba/issue-77

⬆️ upgrade markduplicate step

.github/workflows/linting.yml

@@ -14,13 +14,12 @@ jobs:
   pre-commit:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 # v4
+      - uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4
 
-      - name: Set up Python 3.11
-        uses: actions/setup-python@0a5c61591373683505ea898e09a3ea4f39ef2b9c # v5
+      - name: Set up Python 3.12
+        uses: actions/setup-python@82c7e631bb3cdc910f68e0081d67478d79c6982d # v5
         with:
-          python-version: 3.11
-          cache: "pip"
+          python-version: "3.12"
 
       - name: Install pre-commit
         run: pip install pre-commit
@@ -32,14 +31,14 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Check out pipeline code
-        uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 # v4
+        uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4
 
       - name: Install Nextflow
-        uses: nf-core/setup-nextflow@v1
+        uses: nf-core/setup-nextflow@v2
 
-      - uses: actions/setup-python@0a5c61591373683505ea898e09a3ea4f39ef2b9c # v5
+      - uses: actions/setup-python@82c7e631bb3cdc910f68e0081d67478d79c6982d # v5
         with:
-          python-version: "3.11"
+          python-version: "3.12"
           architecture: "x64"
 
       - name: Install dependencies
@@ -60,7 +59,7 @@ jobs:
 
       - name: Upload linting log file artifact
         if: ${{ always() }}
-        uses: actions/upload-artifact@5d5d22a31266ced268874388b861e4b58bb5c2f3 # v4
+        uses: actions/upload-artifact@65462800fd760344b1a7b4382951275a0abb4808 # v4
         with:
           name: linting-logs
           path: |

.github/workflows/linting_comment.yml

@@ -11,7 +11,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Download lint results
-        uses: dawidd6/action-download-artifact@f6b0bace624032e30a85a8fd9c1a7f8f611f5737 # v3
+        uses: dawidd6/action-download-artifact@09f2f74827fd3a8607589e5ad7f9398816f540fe # v3
         with:
           workflow: linting.yml
           workflow_conclusion: completed

.nf-core.yml

@@ -10,3 +10,4 @@ lint:
   multiqc_config: False
   pipeline_name_conventions: False
 repository_type: pipeline
+nf_core_version: "2.14.1"

CHANGELOG.md

@@ -3,6 +3,16 @@
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/)
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
+## 0.6.2 - dev
+
+- Fixed issue with `picard/markduplicates` ([#77](https://github.com/cnr-ibba/nf-resequencing-mem/issues/77))
+- Display current chromosome in `samtools/depth`
+
+### `Fixed`
+
+- `picard/markduplicates` was updated to the latest release in order to work
+  with `*.cram` files
+
 ## 0.6.1 - [2024-04-11]
 
 - Calculate `samtools/depth` on each chromosomes ([#73](https://github.com/cnr-ibba/nf-resequencing-mem/issues/73))

modules.json

@@ -68,7 +68,7 @@
           },
           "picard/markduplicates": {
             "branch": "master",
-            "git_sha": "1943aa60f7490c3d6740e8872e6e69122ccc8087",
+            "git_sha": "0dee12b56ccecc416d6f7a1ccd85fd571eab3307",
             "installed_by": ["modules"]
           },
           "samtools/coverage": {

nextflow.config

@@ -162,7 +162,7 @@ manifest {
     description     = 'Nextflow Resequencing with BWA MEM'
     mainScript      = 'main.nf'
     nextflowVersion = '!>=23.04.0'
-    version         = '0.6.1'
+    version         = '0.6.2-dev'
 }
 
 // Load modules.config for DSL2 module specific options