Merge pull request #449 from nf-core/dev

Dev -> Master 2.7.1
nf-core · Oct 27, 2024 · d16f8f8 · d16f8f8
2 parents aac172d + 07ec67a
commit d16f8f8
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Showing 34 changed files with 143 additions and 138 deletions.
diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
@@ -11,7 +11,7 @@ on:
 
 env:
   NXF_ANSI_LOG: false
-  NFT_VER: "0.9.0"
+  NFT_VER: "0.9.1"
   NFT_WORKDIR: "~"
   NFT_DIFF: "pdiff"
   NFT_DIFF_ARGS: "--line-numbers --width 120 --expand-tabs=2"

diff --git a/.nf-core.yml b/.nf-core.yml
@@ -1,12 +1,11 @@
-bump_version: null
 lint:
   actions_ci: false
   files_exist:
     - lib/nfcore_external_java_deps.jar
     - conf/modules.config
   modules_config: false
 nf_core_version: 3.0.2
-org_path: null
+org_path:
 repository_type: pipeline
 template:
   author: Phil Ewels, Sateesh Peri
@@ -17,6 +16,6 @@ template:
   name: methylseq
   org: nf-core
   outdir: .
-  skip_features: null
-  version: 2.7.0
-update: null
+  skip_features:
+  version: 2.7.1
+update:
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -1,5 +1,13 @@
 # nf-core/methylseq
 
+## [v2.7.1](https://github.com/nf-core/methylseq/releases/tag/2.7.1) - [2024-10-27]
+
+### Bug fixes & refactoring
+
+- 🐛 fix fasta symlink in bismark & bwameth align modules [#448](https://github.com/nf-core/methylseq/pull/448)
+
+### Pipeline Updates
+
 ## [v2.7.0](https://github.com/nf-core/methylseq/releases/tag/2.7.0) - [2024-10-25]
 
 ### Bug fixes & refactoring

diff --git a/assets/multiqc_config.yml b/assets/multiqc_config.yml
@@ -1,7 +1,8 @@
 report_comment: >
-  This report has been generated by the <a href="https://github.com/nf-core/methylseq/releases/tag/2.7.0" target="_blank">nf-core/methylseq</a>
-  analysis pipeline. For information about how to interpret these results, please see the
-  <a href="https://nf-co.re/methylseq/2.7.0/docs/output" target="_blank">documentation</a>.
+  This report has been generated by the <a href="https://github.com/nf-core/methylseq/releases/tag/2.7.1"
+  target="_blank">nf-core/methylseq</a> analysis pipeline. For information about how
+  to interpret these results, please see the <a href="https://nf-co.re/methylseq/2.7.1/docs/output"
+  target="_blank">documentation</a>.
 report_section_order:
   "nf-core-methylseq-methods-description":
     order: -1000

diff --git a/modules.json b/modules.json
@@ -7,7 +7,7 @@
                 "nf-core": {
                     "bismark/align": {
                         "branch": "master",
-                        "git_sha": "9c4438173b1fcbf3f9004080e3af74af19d5f56e",
+                        "git_sha": "dfd89399e3c6e2422c4cdcf0aaa8cf2393dc51c9",
                         "installed_by": ["modules"]
                     },
                     "bismark/coverage2cytosine": {
@@ -37,12 +37,12 @@
                     },
                     "bismark/summary": {
                         "branch": "master",
-                        "git_sha": "0755c617637d21b2c290b26d225debe3070aa109",
+                        "git_sha": "dfd89399e3c6e2422c4cdcf0aaa8cf2393dc51c9",
                         "installed_by": ["modules"]
                     },
                     "bwameth/align": {
                         "branch": "master",
-                        "git_sha": "9c4438173b1fcbf3f9004080e3af74af19d5f56e",
+                        "git_sha": "dfd89399e3c6e2422c4cdcf0aaa8cf2393dc51c9",
                         "installed_by": ["modules"]
                     },
                     "bwameth/index": {
@@ -127,7 +127,7 @@
                     },
                     "trimgalore": {
                         "branch": "master",
-                        "git_sha": "49f4e50534fe4b64101e62ea41d5dc43b1324358",
+                        "git_sha": "8c5eeedd45e295fc9a4f164631da6a8b37e6b9c6",
                         "installed_by": ["modules"]
                     },
                     "untar": {

diff --git a/modules/nf-core/bismark/align/main.nf b/modules/nf-core/bismark/align/main.nf
diff --git a/modules/nf-core/bismark/align/tests/main.nf.test b/modules/nf-core/bismark/align/tests/main.nf.test
diff --git a/...smark/align/tests/nextflow_bowtie2.config → ...-core/bismark/align/tests/nextflow.config b/...smark/align/tests/nextflow_bowtie2.config → ...-core/bismark/align/tests/nextflow.config
diff --git a/modules/nf-core/bismark/align/tests/nextflow_hisat2.config b/modules/nf-core/bismark/align/tests/nextflow_hisat2.config
diff --git a/modules/nf-core/bismark/align/tests/nextflow_minimap2.config b/modules/nf-core/bismark/align/tests/nextflow_minimap2.config
diff --git a/modules/nf-core/bismark/coverage2cytosine/nextflow.config b/modules/nf-core/bismark/coverage2cytosine/nextflow.config
diff --git a/modules/nf-core/bismark/summary/main.nf b/modules/nf-core/bismark/summary/main.nf
diff --git a/modules/nf-core/bwameth/align/main.nf b/modules/nf-core/bwameth/align/main.nf
diff --git a/modules/nf-core/trimgalore/environment.yml b/modules/nf-core/trimgalore/environment.yml
diff --git a/modules/nf-core/trimgalore/main.nf b/modules/nf-core/trimgalore/main.nf
diff --git a/modules/nf-core/trimgalore/tests/main.nf.test.snap b/modules/nf-core/trimgalore/tests/main.nf.test.snap
diff --git a/nextflow.config b/nextflow.config
@@ -289,7 +289,7 @@ manifest {
     description     = """Methylation (Bisulfite-Sequencing) Best Practice analysis pipeline, part of the nf-core community."""
     mainScript      = 'main.nf'
     nextflowVersion = '!>=24.04.2'
-    version         = '2.7.0'
+    version         = '2.7.1'
     doi             = '10.5281/zenodo.1343417'
 }
 

diff --git a/subworkflows/local/bwameth/main.nf b/subworkflows/local/bwameth/main.nf
@@ -80,7 +80,7 @@ workflow BWAMETH {
         PICARD_MARKDUPLICATES (
             SAMTOOLS_SORT.out.bam,
             fasta,
-            fasta_index.map{ fasta_index -> [[:], fasta_index]},
+            fasta_index.map{ index -> [[:], index]},
         )
         PICARD_MARKDUPLICATES.out.bam.dump(tag: 'BWAMETH/PICARD_MARKDUPLICATES: bam')
         /*