Merge pull request #213 from nf-core/dev

`dev` -> `master` for release `1.6.1`

Author: ewels

.github/workflows/ci.yml

@@ -10,7 +10,7 @@ on:
 
 jobs:
   test:
-    name: Run workflow tests
+    name: workflow
     # 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/methylseq') }}
     runs-on: ubuntu-latest
@@ -20,7 +20,7 @@ jobs:
     strategy:
       matrix:
         # Nextflow versions: check pipeline minimum and current latest
-        nxf_ver: ['20.07.1', '21.03.0-edge']
+        nxf_ver: ['20.07.1', '']
         aligner: ['bismark', 'bismark_hisat', 'bwameth']
         include:
           - aligner: 'bismark'
@@ -42,13 +42,13 @@ jobs:
 
       - name: Build new docker image
         if: env.MATCHED_FILES
-        run: docker build --no-cache . -t nfcore/methylseq:1.6
+        run: docker build --no-cache . -t nfcore/methylseq:1.6.1
 
       - name: Pull docker image
         if: ${{ !env.MATCHED_FILES }}
         run: |
           docker pull nfcore/methylseq:dev
-          docker tag nfcore/methylseq:dev nfcore/methylseq:1.6
+          docker tag nfcore/methylseq:dev nfcore/methylseq:1.6.1
 
       - name: Install Nextflow
         env:
@@ -57,8 +57,14 @@ jobs:
           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 --aligner ${{matrix.aligner}} --save_reference
-          nextflow run ${GITHUB_WORKSPACE} -profile test,docker --aligner ${{matrix.aligner}} ${{matrix.ref_index}}
-          nextflow run ${GITHUB_WORKSPACE} -profile test,docker --aligner ${{matrix.aligner}} --skip_trimming --rrbs
+      - name: Test - Single End
+        run: nextflow run ${GITHUB_WORKSPACE} -profile test,docker --aligner ${{matrix.aligner}} --save_reference
+
+      - name: Test - Single End with index
+        run: nextflow run ${GITHUB_WORKSPACE} -profile test,docker --aligner ${{matrix.aligner}} ${{matrix.ref_index}}
+
+      - name: Test - Single End RRBS
+        run: nextflow run ${GITHUB_WORKSPACE} -profile test,docker --aligner ${{matrix.aligner}} --skip_trimming --rrbs
+
+      - name: Test - Paired End with index
+        run: nextflow run ${GITHUB_WORKSPACE} -profile test_paired,docker --aligner ${{matrix.aligner}} ${{matrix.ref_index}}

.nf-core-lint.yaml

@@ -0,0 +1,2 @@
+files_unchanged:
+  - lib/NfcoreSchema.groovy

CHANGELOG.md

@@ -1,5 +1,20 @@
 # nf-core/methylseq
 
+## [v1.6.1](https://github.com/nf-core/methylseq/releases/tag/1.6.1) - 2021-05-08
+
+### Pipeline Updates
+
+* Added new config profile to run minimal test paired-end dataset, with `-profile test_paired`. Added to the CI tests.
+
+### Bug fixes
+
+* Fixed silent bug in Bismark alignment command that had no effect on the output ([#210](https://github.com/nf-core/methylseq/issues/210))
+
+### Software updates
+
+* Picard `2.25.1` > `2.25.4`
+* MultiQC `1.10` > `1.10.1`
+
 ## [v1.6](https://github.com/nf-core/methylseq/releases/tag/1.6) - 2021-03-26
 
 **:warning: Breaking change!**

Dockerfile

@@ -13,7 +13,7 @@ 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-methylseq-1.6/bin:$PATH
+ENV PATH /opt/conda/envs/nf-core-methylseq-1.6.1/bin:$PATH
 
 # Dump the details of the installed packages to a file for posterity
-RUN conda env export --name nf-core-methylseq-1.6 > nf-core-methylseq-1.6.yml
+RUN conda env export --name nf-core-methylseq-1.6.1 > nf-core-methylseq-1.6.1.yml

README.md

@@ -9,6 +9,8 @@
 [![Docker](https://img.shields.io/docker/automated/nfcore/methylseq.svg)](https://hub.docker.com/r/nfcore/methylseq)
 [![Get help on Slack](http://img.shields.io/badge/slack-nf--core%20%23methylseq-4A154B?logo=slack)](https://nfcore.slack.com/channels/methylseq)
 
+## Introduction
+
 **nf-core/methylseq** is a bioinformatics analysis pipeline used for Methylation (Bisulfite) sequencing data. It pre-processes raw data from FastQ inputs, aligns the reads and performs extensive quality-control on the results.
 
 The pipeline is built using [Nextflow](https://www.nextflow.io), a workflow tool to run tasks across multiple compute infrastructures in a very portable manner. It comes with docker containers making installation trivial and results highly reproducible.