Merge pull request #433 from sateeshperi/dev

update CI and Changelog
nf-core · Oct 22, 2024 · 25061bf · 25061bf
2 parents 0f930ac + ad2b289
commit 25061bf
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Showing 3 changed files with 31 additions and 17 deletions.
diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
@@ -14,7 +14,7 @@ env:
   NFT_VER: "0.9.0"
   NFT_WORKDIR: "~"
   NFT_DIFF: "pdiff"
-  NFT_DIFF_ARGS: "--line-numbers --expand-tabs=2"
+  NFT_DIFF_ARGS: "--line-numbers --width 120 --expand-tabs=2"
   NXF_SINGULARITY_CACHEDIR: ${{ github.workspace }}/.singularity
   NXF_SINGULARITY_LIBRARYDIR: ${{ github.workspace }}/.singularity
 
@@ -35,6 +35,7 @@ jobs:
           - "24.04.2"
           - "latest-everything"
         shard: [1, 2, 3, 4, 5]
+        filter: [pipeline, workflow]
         profile:
           - "conda"
           - "docker"
@@ -49,6 +50,12 @@ jobs:
             profile: "conda"
           - isMaster: false
             profile: "singularity"
+          - profile: "conda"
+            nf_test_files: "tests/bwameth_save_reference_save_align_intermeds.nf.test"
+          - profile: "conda"
+            nf_test_files: "tests/bwameth_skip_trimming.nf.test"
+          - profile: "conda"
+            nf_test_files: "tests/bwameth_skip_deduplication.nf.test"
     steps:
       - name: Check out pipeline code
         uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4
@@ -104,7 +111,13 @@ jobs:
               --shard ${{ matrix.shard }}/${{ strategy.job-total }} \
               --changed-since HEAD^ \
               --profile "+${{ matrix.profile }}" \
-              --filter pipeline,workflow
+              --filter ${{ matrix.filter }}
+
+      - name: Output log on failure
+        if: failure()
+        run: |
+          sudo apt install bat > /dev/null
+          batcat --decorations=always --color=always ${{ github.workspace }}/.nf-test/tests/*/meta/nextflow.log
 
       - name: Publish Test Report
         uses: mikepenz/action-junit-report@v3

diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -1,6 +1,6 @@
 # nf-core/methylseq
 
-## [v2.7.0](https://github.com/nf-core/methylseq/releases/tag/2.7.0) - [2024-10-18]
+## [v2.7.0](https://github.com/nf-core/methylseq/releases/tag/2.7.0) - [2024-10-22]
 
 ### Bug fixes & refactoring
 
@@ -16,6 +16,7 @@
 - 🐛 fix bwameth pipeline skipping all bwameth steps when --fasta, --fasta_index, and --bwa_meth_index are provided. (issue-#396) [#414](https://github.com/nf-core/methylseq/pull/414)
 - 🐛 fix typo in samplesheet in README and usage doc (issue-#391) [#414](https://github.com/nf-core/methylseq/pull/418)
 - 🐛 stage fasta separately from the index folders for bismark & bwameth. Fixes issue with using a local copy of fasta (issue-#305) [#428](https://github.com/nf-core/methylseq/pull/428)
+- 🐛 fix bismark, bwameth align modules + other module updates + update snaps [#432](https://github.com/nf-core/methylseq/pull/432)
 
 ### Pipeline Updates
 

diff --git a/README.md b/README.md
@@ -30,20 +30,20 @@ On release, automated continuous integration tests run the pipeline on a full-si
 The pipeline allows you to choose between running either [Bismark](https://github.com/FelixKrueger/Bismark) or [bwa-meth](https://github.com/brentp/bwa-meth) / [MethylDackel](https://github.com/dpryan79/methyldackel).
 Choose between workflows by using `--aligner bismark` (default, uses bowtie2 for alignment), `--aligner bismark_hisat` or `--aligner bwameth`.
 
-| Step                                         | Bismark workflow | bwa-meth workflow     |
-| -------------------------------------------- | ---------------- | --------------------- |
-| Generate Reference Genome Index _(optional)_ | Bismark          | bwa-meth              |
-| Merge re-sequenced FastQ files               | cat              | cat                   |
-| Raw data QC                                  | FastQC           | FastQC                |
-| Adapter sequence trimming                    | Trim Galore!     | Trim Galore!          |
-| Align Reads                                  | Bismark          | bwa-meth              |
-| Deduplicate Alignments                       | Bismark          | Picard MarkDuplicates |
-| Extract methylation calls                    | Bismark          | MethylDackel          |
-| Sample report                                | Bismark          | -                     |
-| Summary Report                               | Bismark          | -                     |
-| Alignment QC                                 | Qualimap         | Qualimap              |
-| Sample complexity                            | Preseq           | Preseq                |
-| Project Report                               | MultiQC          | MultiQC               |
+| Step                                         | Bismark workflow         | bwa-meth workflow     |
+| -------------------------------------------- | ------------------------ | --------------------- |
+| Generate Reference Genome Index _(optional)_ | Bismark                  | bwa-meth              |
+| Merge re-sequenced FastQ files               | cat                      | cat                   |
+| Raw data QC                                  | FastQC                   | FastQC                |
+| Adapter sequence trimming                    | Trim Galore!             | Trim Galore!          |
+| Align Reads                                  | Bismark (bowtie2/hisat2) | bwa-meth              |
+| Deduplicate Alignments                       | Bismark                  | Picard MarkDuplicates |
+| Extract methylation calls                    | Bismark                  | MethylDackel          |
+| Sample report                                | Bismark                  | -                     |
+| Summary Report                               | Bismark                  | -                     |
+| Alignment QC                                 | Qualimap                 | Qualimap              |
+| Sample complexity                            | Preseq                   | Preseq                |
+| Project Report                               | MultiQC                  | MultiQC               |
 
 ## Usage