Merge pull request #211 from ewels/fix-bismark-align-command

Fix bismark align command

Author: phue

.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'
@@ -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}}

CHANGELOG.md

@@ -2,7 +2,18 @@
 
 ## v1.7dev
 
-_..nothing yet.._
+### 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
 

conf/test_paired.config

@@ -0,0 +1,34 @@
+/*
+ * -------------------------------------------------
+ *  Nextflow config file for running tests
+ * -------------------------------------------------
+ * Defines bundled input files and everything required
+ * to run a fast and simple test. Use as follows:
+ *   nextflow run nf-core/methylseq -profile test_paired,<conda/docker/singularity>
+ */
+
+params {
+  config_profile_name = 'Test profile'
+  config_profile_description = 'Minimal test dataset to check pipeline function'
+  // Limit resources so that this can run on GitHub Actions
+  max_cpus = 2
+  max_memory = 6.GB
+  max_time = 48.h
+
+  // Input data
+  single_end = false
+  input_paths = [
+    [
+      'Ecoli_10K_methylated',
+      [
+        'https://github.com/nf-core/test-datasets/raw/methylseq/testdata/Ecoli_10K_methylated_R1.fastq.gz',
+        'https://github.com/nf-core/test-datasets/raw/methylseq/testdata/Ecoli_10K_methylated_R2.fastq.gz'
+      ]
+    ]
+  ]
+  // Genome references
+  fasta = 'https://github.com/nf-core/test-datasets/raw/methylseq/reference/genome.fa'
+  fasta_index = 'https://github.com/nf-core/test-datasets/raw/methylseq/reference/genome.fa.fai'
+  // Ignore `--input` as otherwise the parameter validation will throw an error
+  schema_ignore_params = 'genomes,input_paths,input'
+}

environment.yml

@@ -21,8 +21,8 @@ dependencies:
   - bioconda::bismark=0.23.0
   - bioconda::qualimap=2.2.2d
   - bioconda::preseq=2.0.3
-  - bioconda::multiqc=1.10
+  - bioconda::multiqc=1.10.1
   # bwa-meth pipeline
-  - bioconda::picard=2.25.1
+  - bioconda::picard=2.25.4
   - bioconda::bwameth=0.2.2
   - bioconda::methyldackel=0.5.2

main.nf

@@ -546,7 +546,6 @@ if( params.aligner =~ /bismark/ ){
             $aligner \\
             --bam $pbat $non_directional $unmapped $mismatches $multicore $minins $maxins \\
             --genome $index \\
-            $reads \\
             $soft_clipping \\
             $splicesites
         """

nextflow.config

@@ -150,6 +150,7 @@ profiles {
     charliecloud.enabled = true
   }
   test { includeConfig 'conf/test.config' }
+  test_paired { includeConfig 'conf/test_paired.config' }
   test_full { includeConfig 'conf/test_full.config' }
 }