Merge pull request #356 from nf-core/dev

Release v2.7.1

.github/workflows/ci.yml

@@ -16,7 +16,10 @@ on:
 
 env:
   NXF_ANSI_LOG: false
-  NFTEST_VER: "0.8.1"
+  NFT_VER: "0.9.0"
+  NFT_WORKDIR: "~"
+  NFT_DIFF: "pdiff"
+  NFT_DIFF_ARGS: "--line-numbers --expand-tabs=2"
 
 concurrency:
   group: "${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}"
@@ -42,29 +45,30 @@ jobs:
       - name: Check out pipeline code
         uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4
 
-      - name: Install Nextflow
-        uses: nf-core/setup-nextflow@v2
+      - uses: actions/setup-python@v4
         with:
-          version: "${{ matrix.NXF_VER }}"
+          python-version: "3.11"
+          architecture: "x64"
+
+      - name: Install pdiff to see diff between nf-test snapshots
+        run: |
+          python -m pip install --upgrade pip
+          pip install pdiff
 
-      - name: Cache nf-test installation
-        id: cache-software
-        uses: actions/cache@v3
+      - uses: nf-core/setup-nextflow@v2
         with:
-          path: |
-            /usr/local/bin/nf-test
-            /home/runner/.nf-test/nf-test.jar
-          key: ${{ runner.os }}-${{ env.NFTEST_VER }}-nftest
+          version: "${{ matrix.NXF_VER }}"
 
-      - name: Install nf-test
-        if: steps.cache-software.outputs.cache-hit != 'true'
-        run: |
-          wget -qO- https://code.askimed.com/install/nf-test | bash
-          sudo mv nf-test /usr/local/bin/
+      - uses: nf-core/setup-nf-test@v1
+        with:
+          version: ${{ env.NFT_VER }}
 
       - name: Run nf-test
         run: |
-          nf-test test tests/main_pipeline_${{ matrix.profile }}.test --junitxml=test.xml
+          nf-test test \
+            --ci \
+            --junitxml=test.xml \
+            tests/main_pipeline_${{ matrix.profile }}.nf.test
 
       - name: Output log on failure
         if: failure()

CHANGELOG.md

@@ -3,6 +3,14 @@
 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).
 
+## v2.7.1 - 2024-08-13
+
+- Fix that tests have not been executed with nf-test v0.9 ([#359](https://github.com/nf-core/scrnaseq/pull/359))
+- Add support for 10XV4 chemistry ([#348](https://github.com/nf-core/scrnaseq/pull/348))
+- Fix issues with predefined STAR index ([#350](https://github.com/nf-core/scrnaseq/pull/350))
+- Update modules ([#351](https://github.com/nf-core/scrnaseq/pull/351))
+- Fix resource specifications for `cellranger mkref`/`cellrangerarc mkref` ([#352](https://github.com/nf-core/scrnaseq/pull/352))
+
 ## v2.7.0 - 2024-06-03
 
 - Apply `check_max` to AlevinQC time limit ([#335](https://github.com/nf-core/scrnaseq/pull/335))

assets/multiqc_config.yml

@@ -1,7 +1,7 @@
 report_comment: >
-  This report has been generated by the <a href="https://github.com/nf-core/scrnaseq/releases/tag/2.7.0" target="_blank">nf-core/scrnaseq</a>
+  This report has been generated by the <a href="https://github.com/nf-core/scrnaseq/releases/tag/2.7.1" target="_blank">nf-core/scrnaseq</a>
   analysis pipeline. For information about how to interpret these results, please see the
-  <a href="https://nf-co.re/scrnaseq/2.7.0/docs/output" target="_blank">documentation</a>.
+  <a href="https://nf-co.re/scrnaseq/2.7.1/docs/output" target="_blank">documentation</a>.
 report_section_order:
   "nf-core-scrnaseq-methods-description":
     order: -1000

assets/protocols.json

@@ -12,6 +12,10 @@
             "protocol": "10xv3",
             "whitelist": "assets/whitelist/10x_V3_barcode_whitelist.txt.gz"
         },
+        "10XV4": {
+            "protocol": "10xv4",
+            "whitelist": "assets/whitelist/10x_V4_barcode_whitelist.txt.gz"
+        },
         "dropseq": {
             "protocol": "dropseq"
         }
@@ -28,6 +32,9 @@
         },
         "10XV3": {
             "protocol": "SC3Pv3"
+        },
+        "10XV4": {
+            "protocol": "SC3Pv4"
         }
     },
     "cellrangerarc": {
@@ -51,6 +58,11 @@
             "extra_args": "--soloUMIlen 12",
             "whitelist": "assets/whitelist/10x_V3_barcode_whitelist.txt.gz"
         },
+        "10XV4": {
+            "protocol": "CB_UMI_Simple",
+            "extra_args": "--soloUMIlen 12",
+            "whitelist": "assets/whitelist/10x_V4_barcode_whitelist.txt.gz"
+        },
         "dropseq": {
             "protocol": "CB_UMI_Simple"
         },
@@ -68,6 +80,9 @@
         "10XV3": {
             "protocol": "10XV3"
         },
+        "10XV4": {
+            "protocol": "10XV4"
+        },
         "dropseq": {
             "protocol": "DROPSEQ"
         },
@@ -88,6 +103,9 @@
         "10XV3": {
             "protocol": "10x-v3"
         },
+        "10XV4": {
+            "protocol": "10x-v4"
+        },
         "dropseq": {
             "protocol": "dropseq"
         }

docs/usage.md

@@ -85,7 +85,7 @@ The single-cell protocol used in the experiment can be specified using the `--pr
 For cellranger, it is recommended to stick with the default value `'auto'` for automatic detection of the protocol.
 For all other aligner, you need to specify the protocol manually.
 
-The three 10x Genomics protocols 3' v1 (`10XV1`), 3' v2 (`10XV2`) and 3' v3 (`10XV3`) are universally supported
+The three 10x Genomics protocols 3' v1 (`10XV1`), 3' v2 (`10XV2`), 3' v3 (`10XV3`), and 3' v4 (`10XV4`) are universally supported
 by all aligners in the pipeline and mapped to the correct options automatically. If the protocol is unknown to the
 nf-core pipeline, the value specified to `--protocol` is passed to the aligner _in verbatim_ to support additional protocols.
 

modules.json

@@ -7,17 +7,17 @@
                 "nf-core": {
                     "cellranger/count": {
                         "branch": "master",
-                        "git_sha": "e66183d2ab6a5c2f3fd66b2bee942287cf65536c",
+                        "git_sha": "90dad5491658049282ceb287a3d7732c1ce39837",
                         "installed_by": ["modules"]
                     },
                     "cellranger/mkgtf": {
                         "branch": "master",
-                        "git_sha": "e66183d2ab6a5c2f3fd66b2bee942287cf65536c",
+                        "git_sha": "90dad5491658049282ceb287a3d7732c1ce39837",
                         "installed_by": ["modules"]
                     },
                     "cellranger/mkref": {
                         "branch": "master",
-                        "git_sha": "e66183d2ab6a5c2f3fd66b2bee942287cf65536c",
+                        "git_sha": "3549a361ce3401b6afd238a266389d78392a53f6",
                         "installed_by": ["modules"]
                     },
                     "cellranger/mkvdjref": {
@@ -27,7 +27,7 @@
                     },
                     "cellranger/multi": {
                         "branch": "master",
-                        "git_sha": "5f12fc2128f419a8750c5b0620e4b54d7aa33fec",
+                        "git_sha": "90dad5491658049282ceb287a3d7732c1ce39837",
                         "installed_by": ["modules"]
                     },
                     "cellrangerarc/count": {
@@ -42,12 +42,12 @@
                     },
                     "cellrangerarc/mkref": {
                         "branch": "master",
-                        "git_sha": "4196b1b2e7ce265892f3979eabf7a9ddc030702f",
+                        "git_sha": "3549a361ce3401b6afd238a266389d78392a53f6",
                         "installed_by": ["modules"]
                     },
                     "fastqc": {
                         "branch": "master",
-                        "git_sha": "285a50500f9e02578d90b3ce6382ea3c30216acd",
+                        "git_sha": "46eca555142d6e597729fcb682adcc791796f514",
                         "installed_by": ["modules"]
                     },
                     "gffread": {
@@ -57,7 +57,7 @@
                     },
                     "gunzip": {
                         "branch": "master",
-                        "git_sha": "3a5fef109d113b4997c9822198664ca5f2716208",
+                        "git_sha": "4e5f4687318f24ba944a13609d3ea6ebd890737d",
                         "installed_by": ["modules"]
                     },
                     "kallistobustools/count": {
@@ -72,12 +72,12 @@
                     },
                     "multiqc": {
                         "branch": "master",
-                        "git_sha": "b7ebe95761cd389603f9cc0e0dc384c0f663815a",
+                        "git_sha": "b80f5fd12ff7c43938f424dd76392a2704fa2396",
                         "installed_by": ["modules"]
                     },
                     "star/genomegenerate": {
                         "branch": "master",
-                        "git_sha": "a21faa6a3481af92a343a10926f59c189a2c16c9",
+                        "git_sha": "46eca555142d6e597729fcb682adcc791796f514",
                         "installed_by": ["modules"]
                     },
                     "universc": {
@@ -87,7 +87,7 @@
                     },
                     "unzip": {
                         "branch": "master",
-                        "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5",
+                        "git_sha": "b0c3ff2485534c09d9debbf20125d9c6b72ce118",
                         "installed_by": ["modules"]
                     }
                 }