Merge pull request #91 from nf-core/dev

Bump versions to 1.1.0
nf-core · Nov 6, 2020 · ad5b2bb · ad5b2bb
2 parents 69dcb4e + d90c3d6
commit ad5b2bb
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diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
@@ -1,172 +1,172 @@
-name: nf-core CI
-# This workflow runs the pipeline with the minimal test dataset to check that it completes without any syntax errors
-on:
-  push:
-    branches:
-      - dev
-  pull_request:
-  release:
-    types: [published]
-
-jobs:
-  test:
-    name: Run workflow tests
-    # Only run on push if this is the nf-core dev branch (merged PRs)
-    if: ${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/nanoseq') }}
-    runs-on: ubuntu-latest
-    env:
-      NXF_VER: ${{ matrix.nxf_ver }}
-      NXF_ANSI_LOG: false
-    strategy:
-      matrix:
-        # Nextflow versions: check pipeline minimum and current latest
-        nxf_ver: ['19.10.0', '']
-    steps:
-      - name: Check out pipeline code
-        uses: actions/checkout@v2
-
-      - name: Check if Dockerfile or Conda environment changed
-        uses: technote-space/get-diff-action@v1
-        with:
-          PREFIX_FILTER: |
-            Dockerfile
-            environment.yml
-
-      - name: Build new docker image
-        if: env.GIT_DIFF
-        run: docker build --no-cache . -t nfcore/nanoseq:dev
-
-      - name: Pull docker image
-        if: ${{ !env.GIT_DIFF }}
-        run: |
-          docker pull nfcore/nanoseq:dev
-          docker tag nfcore/nanoseq:dev nfcore/nanoseq:dev
-
-      - name: Install Nextflow
-        run: |
-          wget -qO- get.nextflow.io | bash
-          sudo mv nextflow /usr/local/bin/
-
-      - name: Run pipeline with test data
-        run: |
-          nextflow run ${GITHUB_WORKSPACE} -profile test,docker
-
-  profile:
-    name: Run profile tests
-    if: ${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/nanoseq') }}
-    runs-on: ubuntu-latest
-    env:
-      NXF_VER: '19.10.0'
-      NXF_ANSI_LOG: false
-    strategy:
-      matrix:
-        profiles: [test_bc_nodx, test_nobc_dx, test_nobc_nodx, test_nobc_nodx_noaln]
-    steps:
-      - name: Check out pipeline code
-        uses: actions/checkout@v2
-
-      - name: Check if Dockerfile or Conda environment changed
-        uses: technote-space/get-diff-action@v1
-        with:
-          PREFIX_FILTER: |
-            Dockerfile
-            environment.yml
-
-      - name: Build new docker image
-        if: env.GIT_DIFF
-        run: docker build --no-cache . -t nfcore/nanoseq:dev
-
-      - name: Pull docker image
-        if: ${{ !env.GIT_DIFF }}
-        run: |
-          docker pull nfcore/nanoseq:dev
-          docker tag nfcore/nanoseq:dev nfcore/nanoseq:dev
-
-      - name: Install Nextflow
-        run: |
-          wget -qO- get.nextflow.io | bash
-          sudo mv nextflow /usr/local/bin/
-
-      - name: Run pipeline with different profiles
-        run: |
-          nextflow run ${GITHUB_WORKSPACE} -profile ${{ matrix.profiles }},docker
-
-  parameters:
-    name: Run parameter tests
-    if: ${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/nanoseq') }}
-    runs-on: ubuntu-latest
-    env:
-      NXF_VER: '19.10.0'
-      NXF_ANSI_LOG: false
-    strategy:
-      matrix:
-        parameters: [--aligner graphmap2, --skip_alignment, --skip_qc, --skip_quantification]
-    steps:
-      - name: Check out pipeline code
-        uses: actions/checkout@v2
-
-      - name: Check if Dockerfile or Conda environment changed
-        uses: technote-space/get-diff-action@v1
-        with:
-          PREFIX_FILTER: |
-            Dockerfile
-            environment.yml
-
-      - name: Build new docker image
-        if: env.GIT_DIFF
-        run: docker build --no-cache . -t nfcore/nanoseq:dev
-
-      - name: Pull docker image
-        if: ${{ !env.GIT_DIFF }}
-        run: |
-          docker pull nfcore/nanoseq:dev
-          docker tag nfcore/nanoseq:dev nfcore/nanoseq:dev
-
-      - name: Install Nextflow
-        run: |
-          wget -qO- get.nextflow.io | bash
-          sudo mv nextflow /usr/local/bin/
-
-      - name: Run pipeline with different parameters
-        run: |
-          nextflow run ${GITHUB_WORKSPACE} -profile test,docker ${{ matrix.parameters }}
-
-  quantification:
-    name: Run quantification tests
-    if: ${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/nanoseq') }}
-    runs-on: ubuntu-latest
-    env:
-      NXF_VER: '19.10.0'
-      NXF_ANSI_LOG: false
-    strategy:
-      matrix:
-        parameters: [--quantification_method 'stringtie2', --skip_quantification, --skip_differential_analysis]
-    steps:
-      - name: Check out pipeline code
-        uses: actions/checkout@v2
-
-      - name: Check if Dockerfile or Conda environment changed
-        uses: technote-space/get-diff-action@v1
-        with:
-          PREFIX_FILTER: |
-            Dockerfile
-            environment.yml
-
-      - name: Build new docker image
-        if: env.GIT_DIFF
-        run: docker build --no-cache . -t nfcore/nanoseq:dev
-
-      - name: Pull docker image
-        if: ${{ !env.GIT_DIFF }}
-        run: |
-          docker pull nfcore/nanoseq:dev
-          docker tag nfcore/nanoseq:dev nfcore/nanoseq:dev
-
-      - name: Install Nextflow
-        run: |
-          wget -qO- get.nextflow.io | bash
-          sudo mv nextflow /usr/local/bin/
-
-      - name: Run pipeline with different quantification parameters
-        run: |
-          nextflow run ${GITHUB_WORKSPACE} -profile test_nobc_nodx,docker ${{ matrix.parameters }}
+name: nf-core CI
+# This workflow runs the pipeline with the minimal test dataset to check that it completes without any syntax errors
+on:
+  push:
+    branches:
+      - dev
+  pull_request:
+  release:
+    types: [published]
+
+jobs:
+  test:
+    name: Run workflow tests
+    # Only run on push if this is the nf-core dev branch (merged PRs)
+    if: ${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/nanoseq') }}
+    runs-on: ubuntu-latest
+    env:
+      NXF_VER: ${{ matrix.nxf_ver }}
+      NXF_ANSI_LOG: false
+    strategy:
+      matrix:
+        # Nextflow versions: check pipeline minimum and current latest
+        nxf_ver: ['19.10.0', '']
+    steps:
+      - name: Check out pipeline code
+        uses: actions/checkout@v2
+
+      - name: Check if Dockerfile or Conda environment changed
+        uses: technote-space/get-diff-action@v1
+        with:
+          PREFIX_FILTER: |
+            Dockerfile
+            environment.yml
+
+      - name: Build new docker image
+        if: env.GIT_DIFF
+        run: docker build --no-cache . -t nfcore/nanoseq:1.1.0
+
+      - name: Pull docker image
+        if: ${{ !env.GIT_DIFF }}
+        run: |
+          docker pull nfcore/nanoseq:dev
+          docker tag nfcore/nanoseq:dev nfcore/nanoseq:1.1.0
+
+      - name: Install Nextflow
+        run: |
+          wget -qO- get.nextflow.io | bash
+          sudo mv nextflow /usr/local/bin/
+
+      - name: Run pipeline with test data
+        run: |
+          nextflow run ${GITHUB_WORKSPACE} -profile test,docker
+
+  profile:
+    name: Run profile tests
+    if: ${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/nanoseq') }}
+    runs-on: ubuntu-latest
+    env:
+      NXF_VER: '19.10.0'
+      NXF_ANSI_LOG: false
+    strategy:
+      matrix:
+        profiles: [test_bc_nodx, test_nobc_dx, test_nobc_nodx, test_nobc_nodx_noaln]
+    steps:
+      - name: Check out pipeline code
+        uses: actions/checkout@v2
+
+      - name: Check if Dockerfile or Conda environment changed
+        uses: technote-space/get-diff-action@v1
+        with:
+          PREFIX_FILTER: |
+            Dockerfile
+            environment.yml
+
+      - name: Build new docker image
+        if: env.GIT_DIFF
+        run: docker build --no-cache . -t nfcore/nanoseq:1.1.0
+
+      - name: Pull docker image
+        if: ${{ !env.GIT_DIFF }}
+        run: |
+          docker pull nfcore/nanoseq:dev
+          docker tag nfcore/nanoseq:dev nfcore/nanoseq:1.1.0
+
+      - name: Install Nextflow
+        run: |
+          wget -qO- get.nextflow.io | bash
+          sudo mv nextflow /usr/local/bin/
+
+      - name: Run pipeline with different profiles
+        run: |
+          nextflow run ${GITHUB_WORKSPACE} -profile ${{ matrix.profiles }},docker
+
+  parameters:
+    name: Run parameter tests
+    if: ${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/nanoseq') }}
+    runs-on: ubuntu-latest
+    env:
+      NXF_VER: '19.10.0'
+      NXF_ANSI_LOG: false
+    strategy:
+      matrix:
+        parameters: [--aligner graphmap2, --skip_alignment, --skip_qc, --skip_quantification]
+    steps:
+      - name: Check out pipeline code
+        uses: actions/checkout@v2
+
+      - name: Check if Dockerfile or Conda environment changed
+        uses: technote-space/get-diff-action@v1
+        with:
+          PREFIX_FILTER: |
+            Dockerfile
+            environment.yml
+
+      - name: Build new docker image
+        if: env.GIT_DIFF
+        run: docker build --no-cache . -t nfcore/nanoseq:1.1.0
+
+      - name: Pull docker image
+        if: ${{ !env.GIT_DIFF }}
+        run: |
+          docker pull nfcore/nanoseq:dev
+          docker tag nfcore/nanoseq:dev nfcore/nanoseq:1.1.0
+
+      - name: Install Nextflow
+        run: |
+          wget -qO- get.nextflow.io | bash
+          sudo mv nextflow /usr/local/bin/
+
+      - name: Run pipeline with different parameters
+        run: |
+          nextflow run ${GITHUB_WORKSPACE} -profile test,docker ${{ matrix.parameters }}
+
+  quantification:
+    name: Run quantification tests
+    if: ${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/nanoseq') }}
+    runs-on: ubuntu-latest
+    env:
+      NXF_VER: '19.10.0'
+      NXF_ANSI_LOG: false
+    strategy:
+      matrix:
+        parameters: [--quantification_method 'stringtie2', --skip_quantification, --skip_differential_analysis]
+    steps:
+      - name: Check out pipeline code
+        uses: actions/checkout@v2
+
+      - name: Check if Dockerfile or Conda environment changed
+        uses: technote-space/get-diff-action@v1
+        with:
+          PREFIX_FILTER: |
+            Dockerfile
+            environment.yml
+
+      - name: Build new docker image
+        if: env.GIT_DIFF
+        run: docker build --no-cache . -t nfcore/nanoseq:1.1.0
+
+      - name: Pull docker image
+        if: ${{ !env.GIT_DIFF }}
+        run: |
+          docker pull nfcore/nanoseq:dev
+          docker tag nfcore/nanoseq:dev nfcore/nanoseq:1.1.0
+
+      - name: Install Nextflow
+        run: |
+          wget -qO- get.nextflow.io | bash
+          sudo mv nextflow /usr/local/bin/
+
+      - name: Run pipeline with different quantification parameters
+        run: |
+          nextflow run ${GITHUB_WORKSPACE} -profile test_nobc_nodx,docker ${{ matrix.parameters }}
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -3,7 +3,7 @@
 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).
 
-## [1.1.0] - 2020-11-13
+## [1.1.0] - 2020-11-06
 
 ### Major enhancements
 

diff --git a/Dockerfile b/Dockerfile
@@ -7,10 +7,10 @@ COPY environment.yml /
 RUN conda env create --quiet -f /environment.yml && conda clean -a
 
 # Add conda installation dir to PATH (instead of doing 'conda activate')
-ENV PATH /opt/conda/envs/nf-core-nanoseq-1.1.0dev/bin:$PATH
+ENV PATH /opt/conda/envs/nf-core-nanoseq-1.1.0/bin:$PATH
 
 # Dump the details of the installed packages to a file for posterity
-RUN conda env export --name nf-core-nanoseq-1.1.0dev > nf-core-nanoseq-1.1.0dev.yml
+RUN conda env export --name nf-core-nanoseq-1.1.0 > nf-core-nanoseq-1.1.0.yml
 
 # Instruct R processes to use these empty files instead of clashing with a local version
 RUN touch .Rprofile

diff --git a/environment.yml b/environment.yml
@@ -1,6 +1,6 @@
 # You can use this file to create a conda environment for this pipeline:
 #   conda env create -f environment.yml
-name: nf-core-nanoseq-1.1.0dev
+name: nf-core-nanoseq-1.1.0
 channels:
   - conda-forge
   - bioconda

diff --git a/main.nf b/main.nf
@@ -1011,7 +1011,7 @@ if (!params.skip_quantification && (params.protocol == 'cDNA' || params.protocol
          * Quantification and novel isoform detection with bambu
          */
         process BAMBU {
-            label 'process_medium'
+            label 'process_high'
             publishDir "${params.outdir}/${params.quantification_method}", mode: params.publish_dir_mode,
                 saveAs: { filename ->
                             if (!filename.endsWith("bambu.txt")) filename