Merge pull request #496 from sateeshperi/dev

sateeshperi · web-flow · commit b212815663f9 · 2024-12-16T17:58:54.000+05:30
bump ver to 3.0.0 semver
diff --git a/.nf-core.yml b/.nf-core.yml
@@ -16,4 +16,4 @@ template:
   name: methylseq
   org: nf-core
   outdir: .
-  version: 2.8.0
+  version: 3.0.0
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -3,15 +3,18 @@
 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).
 
-## [v2.8.0](https://github.com/nf-core/methylseq/releases/tag/2.8.0) - [2024-12-15]
+## [v3.0.0](https://github.com/nf-core/methylseq/releases/tag/3.0.0) - [2024-12-16]
 
 ### Bug fixes & refactoring
 
 - 🐛 fix fasta gunzip output [#462](https://github.com/nf-core/methylseq/pull/457)
-- 🐛 fix bismark/align not resuming from cache [#461](https://github.com/nf-core/methylseq/pull/457)
-- 🐛 disable gunzip publish by default (https://github.com/nf-core/methylseq/pull/474)
+- 🐛 fix `bismark/align` not resuming from cache [#461](https://github.com/nf-core/methylseq/pull/457)
+- 🐛 uncompressed files won't be saved (https://github.com/nf-core/methylseq/pull/474)
+- Updated `conf/modules/samtools_index.config` publishDir configuration to dynamically enable `.bai` file publishing based on whether deduplication is skipped (`--skip_dedup` parameter). This publishing of index files now happens by default as compared to previous, when with `--save_align_intermeds` param.
 - 🔄 Updated template to nf-core/tools v3.1.0 [#490](https://github.com/nf-core/methylseq/pull/490)
 
+> Note: `bwameth/align` module still needs fixing for not resuming from cache. So, its cache has been made **`lenient`** (Minimal input file metadata (name and size only) are included in the cache keys) in its [config](./conf/modules/bwameth_align.config). This strategy provides a workaround for caching invalidation by current `bwameth/align` module requirement to touch the index files before alignment. An issue we hope to have fixed in a release soon.
+
 ### Pipeline Updates
 
 - 🔧 Install `fastq_align_dedup_bismark` subworkflow from nf-core/subworkflows [#453](https://github.com/nf-core/methylseq/pull/457)
diff --git a/README.md b/README.md
@@ -21,7 +21,7 @@
 
 **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.
 
-![nf-core/methylseq metro map](docs/images/metromap.png)
+![nf-core/methylseq metro map](docs/images/3.0.0_metromap.png)
 
 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 uses Docker / Singularity containers making installation trivial and results highly reproducible.
 
diff --git a/assets/multiqc_config.yml b/assets/multiqc_config.yml
@@ -1,7 +1,7 @@
 report_comment: >
-  This report has been generated by the <a href="https://github.com/nf-core/methylseq/releases/tag/2.8.0"
+  This report has been generated by the <a href="https://github.com/nf-core/methylseq/releases/tag/3.0.0"
   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/2.8.0/docs/output"
+  to interpret these results, please see the <a href="https://nf-co.re/methylseq/3.0.0/docs/output"
   target="_blank">documentation</a>.
 report_section_order:
   "nf-core-methylseq-methods-description":
diff --git a/docs/images/3.0.0_dag_fasta_index_bismark_bwameth.png b/docs/images/3.0.0_dag_fasta_index_bismark_bwameth.png
diff --git a/docs/images/3.0.0_dag_fastq_align_dedup_bismark.png b/docs/images/3.0.0_dag_fastq_align_dedup_bismark.png
diff --git a/docs/images/3.0.0_dag_fastq_align_dedup_bwameth.png b/docs/images/3.0.0_dag_fastq_align_dedup_bwameth.png
diff --git a/docs/images/3.0.0_dag_methylseq.png b/docs/images/3.0.0_dag_methylseq.png
diff --git a/docs/images/3.0.0_metromap.png b/docs/images/3.0.0_metromap.png
diff --git a/docs/images/3.0.0_metromap.svg b/docs/images/3.0.0_metromap.svg
diff --git a/docs/usage.md b/docs/usage.md
@@ -92,19 +92,19 @@ An [example samplesheet](../assets/samplesheet.csv) has been provided with the p
 
 ## Parameters
 
-Check out the full list of parameters required, available for multiple aligners on [nf-core/methylseq pipeline parameters page](https://nf-co.re/methylseq/2.8.0/parameters/).
-
-- [Input/output options](https://nf-co.re/methylseq/2.8.0/parameters/#input-output-options)
-- [Save intermediate files](https://nf-co.re/methylseq/2.8.0/parameters/#save-intermediate-files)
-- [Reference genome options](https://nf-co.re/methylseq/2.8.0/parameters/#reference-genome-options)
-- [Alignment options](https://nf-co.re/methylseq/2.8.0/parameters/#alignment-options)
-- [Special library types](https://nf-co.re/methylseq/2.8.0/parameters/#special-library-types)
-- [Adapter Trimming](https://nf-co.re/methylseq/2.8.0/parameters/#adapter-trimming)
-- [Bismark options](https://nf-co.re/methylseq/2.8.0/parameters/#bismark-options)
-- [bwa-meth options](https://nf-co.re/methylseq/2.8.0/parameters/#bwa-meth-options)
-- [Qualimap Options](https://nf-co.re/methylseq/2.8.0/parameters/#bwa-meth-options)
-- [Skip pipeline steps](https://nf-co.re/methylseq/2.8.0/parameters/#skip-pipeline-steps)
-- [Run pipeline steps](https://nf-co.re/methylseq/2.8.0/parameters/#Run-pipeline-steps)
+Check out the full list of parameters required, available for multiple aligners on [nf-core/methylseq pipeline parameters page](https://nf-co.re/methylseq/3.0.0/parameters/).
+
+- [Input/output options](https://nf-co.re/methylseq/3.0.0/parameters/#input-output-options)
+- [Save intermediate files](https://nf-co.re/methylseq/3.0.0/parameters/#save-intermediate-files)
+- [Reference genome options](https://nf-co.re/methylseq/3.0.0/parameters/#reference-genome-options)
+- [Alignment options](https://nf-co.re/methylseq/3.0.0/parameters/#alignment-options)
+- [Special library types](https://nf-co.re/methylseq/3.0.0/parameters/#special-library-types)
+- [Adapter Trimming](https://nf-co.re/methylseq/3.0.0/parameters/#adapter-trimming)
+- [Bismark options](https://nf-co.re/methylseq/3.0.0/parameters/#bismark-options)
+- [bwa-meth options](https://nf-co.re/methylseq/3.0.0/parameters/#bwa-meth-options)
+- [Qualimap Options](https://nf-co.re/methylseq/3.0.0/parameters/#bwa-meth-options)
+- [Skip pipeline steps](https://nf-co.re/methylseq/3.0.0/parameters/#skip-pipeline-steps)
+- [Run pipeline steps](https://nf-co.re/methylseq/3.0.0/parameters/#Run-pipeline-steps)
 
 > It is mandatory to provide `--fasta` along with `--bismark_index`/`--bwameth_index` parameters
 
diff --git a/nextflow.config b/nextflow.config
@@ -361,7 +361,7 @@ manifest {
     mainScript      = 'main.nf'
     defaultBranch   = 'master'
     nextflowVersion = '!>=24.10.2'
-    version         = '2.8.0'
+    version         = '3.0.0'
     doi             = '10.5281/zenodo.1343417'
 }
 
diff --git a/ro-crate-metadata.json b/ro-crate-metadata.json
diff --git a/tests/bismark_cat_fastq_skip_trimming_skip_deduplication.nf.test.snap b/tests/bismark_cat_fastq_skip_trimming_skip_deduplication.nf.test.snap
@@ -19,7 +19,7 @@
                     "gunzip": 1.1
                 },
                 "Workflow": {
-                    "nf-core/methylseq": "v2.8.0"
+                    "nf-core/methylseq": "v3.0.0"
                 }
             },
             [
diff --git a/tests/bismark_cytosine_report.nf.test.snap b/tests/bismark_cytosine_report.nf.test.snap
@@ -21,7 +21,7 @@
                     "pigz": 2.8
                 },
                 "Workflow": {
-                    "nf-core/methylseq": "v2.8.0"
+                    "nf-core/methylseq": "v3.0.0"
                 }
             },
             [
@@ -383,4 +383,4 @@
         },
         "timestamp": "2024-12-14T09:55:56.701520376"
     }
-}
+}
diff --git a/tests/bismark_emseq_clip_r1.nf.test.snap b/tests/bismark_emseq_clip_r1.nf.test.snap
@@ -21,7 +21,7 @@
                     "pigz": 2.8
                 },
                 "Workflow": {
-                    "nf-core/methylseq": "v2.8.0"
+                    "nf-core/methylseq": "v3.0.0"
                 }
             },
             [
diff --git a/tests/bismark_hisat.nf.test.snap b/tests/bismark_hisat.nf.test.snap
@@ -31,7 +31,7 @@
                     "pigz": 2.8
                 },
                 "Workflow": {
-                    "nf-core/methylseq": "v2.8.0"
+                    "nf-core/methylseq": "v3.0.0"
                 }
             },
             [
diff --git a/tests/bismark_hisat_rrbs.nf.test.snap b/tests/bismark_hisat_rrbs.nf.test.snap
@@ -21,7 +21,7 @@
                     "pigz": 2.8
                 },
                 "Workflow": {
-                    "nf-core/methylseq": "v2.8.0"
+                    "nf-core/methylseq": "v3.0.0"
                 }
             },
             [
diff --git a/tests/bismark_hisat_save_reference_save_align_intermeds.nf.test.snap b/tests/bismark_hisat_save_reference_save_align_intermeds.nf.test.snap
@@ -21,7 +21,7 @@
                     "pigz": 2.8
                 },
                 "Workflow": {
-                    "nf-core/methylseq": "v2.8.0"
+                    "nf-core/methylseq": "v3.0.0"
                 }
             },
             [
diff --git a/tests/bismark_nomeseq.nf.test.snap b/tests/bismark_nomeseq.nf.test.snap
@@ -21,7 +21,7 @@
                     "pigz": 2.8
                 },
                 "Workflow": {
-                    "nf-core/methylseq": "v2.8.0"
+                    "nf-core/methylseq": "v3.0.0"
                 }
             },
             [
diff --git a/tests/bismark_rrbs.nf.test.snap b/tests/bismark_rrbs.nf.test.snap
@@ -21,7 +21,7 @@
                     "pigz": 2.8
                 },
                 "Workflow": {
-                    "nf-core/methylseq": "v2.8.0"
+                    "nf-core/methylseq": "v3.0.0"
                 }
             },
             [
diff --git a/tests/bismark_run_preseq.nf.test.snap b/tests/bismark_run_preseq.nf.test.snap
@@ -21,7 +21,7 @@
                     "pigz": 2.8
                 },
                 "Workflow": {
-                    "nf-core/methylseq": "v2.8.0"
+                    "nf-core/methylseq": "v3.0.0"
                 }
             },
             [
diff --git a/tests/bismark_run_qualimap.nf.test.snap b/tests/bismark_run_qualimap.nf.test.snap
@@ -24,7 +24,7 @@
                     "pigz": 2.8
                 },
                 "Workflow": {
-                    "nf-core/methylseq": "v2.8.0"
+                    "nf-core/methylseq": "v3.0.0"
                 }
             },
             [
diff --git a/tests/bismark_save_reference_save_align_intermeds.nf.test.snap b/tests/bismark_save_reference_save_align_intermeds.nf.test.snap
@@ -21,7 +21,7 @@
                     "pigz": 2.8
                 },
                 "Workflow": {
-                    "nf-core/methylseq": "v2.8.0"
+                    "nf-core/methylseq": "v3.0.0"
                 }
             },
             [
diff --git a/tests/bismark_skip_deduplication.nf.test.snap b/tests/bismark_skip_deduplication.nf.test.snap
@@ -21,7 +21,7 @@
                     "pigz": 2.8
                 },
                 "Workflow": {
-                    "nf-core/methylseq": "v2.8.0"
+                    "nf-core/methylseq": "v3.0.0"
                 }
             },
             [
diff --git a/tests/bismark_skip_multiqc.nf.test.snap b/tests/bismark_skip_multiqc.nf.test.snap
@@ -21,7 +21,7 @@
                     "pigz": 2.8
                 },
                 "Workflow": {
-                    "nf-core/methylseq": "v2.8.0"
+                    "nf-core/methylseq": "v3.0.0"
                 }
             },
             [
diff --git a/tests/bismark_skip_trimming.nf.test.snap b/tests/bismark_skip_trimming.nf.test.snap
@@ -16,7 +16,7 @@
                     "gunzip": 1.1
                 },
                 "Workflow": {
-                    "nf-core/methylseq": "v2.8.0"
+                    "nf-core/methylseq": "v3.0.0"
                 }
             },
             [
diff --git a/tests/bwameth.nf.test.snap b/tests/bwameth.nf.test.snap
@@ -21,7 +21,7 @@
                     "pigz": 2.8
                 },
                 "Workflow": {
-                    "nf-core/methylseq": "v2.8.0"
+                    "nf-core/methylseq": "v3.0.0"
                 }
             },
             [
diff --git a/tests/bwameth_cat_fastq_skip_trimming_skip_deduplication.nf.test.snap b/tests/bwameth_cat_fastq_skip_trimming_skip_deduplication.nf.test.snap
@@ -19,7 +19,7 @@
                     "gunzip": 1.1
                 },
                 "Workflow": {
-                    "nf-core/methylseq": "v2.8.0"
+                    "nf-core/methylseq": "v3.0.0"
                 }
             },
             [
diff --git a/tests/bwameth_rrbs.nf.test.snap b/tests/bwameth_rrbs.nf.test.snap
@@ -21,7 +21,7 @@
                     "pigz": 2.8
                 },
                 "Workflow": {
-                    "nf-core/methylseq": "v2.8.0"
+                    "nf-core/methylseq": "v3.0.0"
                 }
             },
             [
diff --git a/tests/bwameth_run_qualimap.nf.test.snap b/tests/bwameth_run_qualimap.nf.test.snap
@@ -24,7 +24,7 @@
                     "pigz": 2.8
                 },
                 "Workflow": {
-                    "nf-core/methylseq": "v2.8.0"
+                    "nf-core/methylseq": "v3.0.0"
                 }
             },
             [
diff --git a/tests/bwameth_save_reference_save_align_intermeds.nf.test.snap b/tests/bwameth_save_reference_save_align_intermeds.nf.test.snap
@@ -21,7 +21,7 @@
                     "pigz": 2.8
                 },
                 "Workflow": {
-                    "nf-core/methylseq": "v2.8.0"
+                    "nf-core/methylseq": "v3.0.0"
                 }
             },
             [
diff --git a/tests/bwameth_skip_deduplication.nf.test.snap b/tests/bwameth_skip_deduplication.nf.test.snap
@@ -21,7 +21,7 @@
                     "pigz": 2.8
                 },
                 "Workflow": {
-                    "nf-core/methylseq": "v2.8.0"
+                    "nf-core/methylseq": "v3.0.0"
                 }
             },
             [
diff --git a/tests/bwameth_skip_trimming.nf.test.snap b/tests/bwameth_skip_trimming.nf.test.snap
@@ -16,7 +16,7 @@
                     "gunzip": 1.1
                 },
                 "Workflow": {
-                    "nf-core/methylseq": "v2.8.0"
+                    "nf-core/methylseq": "v3.0.0"
                 }
             },
             [
diff --git a/tests/bwameth_use_gpu.nf.test.snap b/tests/bwameth_use_gpu.nf.test.snap
@@ -21,7 +21,7 @@
                     "pigz": 2.8
                 },
                 "Workflow": {
-                    "nf-core/methylseq": "v2.8.0"
+                    "nf-core/methylseq": "v3.0.0"
                 }
             },
             [
diff --git a/tests/default.nf.test.snap b/tests/default.nf.test.snap
@@ -31,7 +31,7 @@
                     "pigz": 2.8
                 },
                 "Workflow": {
-                    "nf-core/methylseq": "v2.8.0"
+                    "nf-core/methylseq": "v3.0.0"
                 }
             },
             [

Original file line number	Diff line number	Diff line change
`@@ -361,7 +361,7 @@ manifest {`
`361`	`361`	`mainScript = 'main.nf'`
`362`	`362`	`defaultBranch = 'master'`
`363`	`363`	`nextflowVersion = '!>=24.10.2'`
`364`		`- version = '2.8.0'`
	`364`	`+ version = '3.0.0'`
`365`	`365`	`doi = '10.5281/zenodo.1343417'`
`366`	`366`	`}`
`367`	`367`
Original file line number	Diff line number	Diff line change
`@@ -19,7 +19,7 @@`
`19`	`19`	`"gunzip": 1.1`
`20`	`20`	`},`
`21`	`21`	`"Workflow": {`
`22`		`- "nf-core/methylseq": "v2.8.0"`
	`22`	`+ "nf-core/methylseq": "v3.0.0"`
`23`	`23`	`}`
`24`	`24`	`},`
`25`	`25`	`[`
Original file line number	Diff line number	Diff line change
`@@ -21,7 +21,7 @@`
`21`	`21`	`"pigz": 2.8`
`22`	`22`	`},`
`23`	`23`	`"Workflow": {`
`24`		`- "nf-core/methylseq": "v2.8.0"`
	`24`	`+ "nf-core/methylseq": "v3.0.0"`
`25`	`25`	`}`
`26`	`26`	`},`
`27`	`27`	`[`
`@@ -383,4 +383,4 @@`
`383`	`383`	`},`
`384`	`384`	`"timestamp": "2024-12-14T09:55:56.701520376"`
`385`	`385`	`}`
`386`		`-}`
	`386`	`+}`
Original file line number	Diff line number	Diff line change
`@@ -31,7 +31,7 @@`
`31`	`31`	`"pigz": 2.8`
`32`	`32`	`},`
`33`	`33`	`"Workflow": {`
`34`		`- "nf-core/methylseq": "v2.8.0"`
	`34`	`+ "nf-core/methylseq": "v3.0.0"`
`35`	`35`	`}`
`36`	`36`	`},`
`37`	`37`	`[`
Original file line number	Diff line number	Diff line change
`@@ -24,7 +24,7 @@`
`24`	`24`	`"pigz": 2.8`
`25`	`25`	`},`
`26`	`26`	`"Workflow": {`
`27`		`- "nf-core/methylseq": "v2.8.0"`
	`27`	`+ "nf-core/methylseq": "v3.0.0"`
`28`	`28`	`}`
`29`	`29`	`},`
`30`	`30`	`[`
Original file line number	Diff line number	Diff line change
`@@ -16,7 +16,7 @@`
`16`	`16`	`"gunzip": 1.1`
`17`	`17`	`},`
`18`	`18`	`"Workflow": {`
`19`		`- "nf-core/methylseq": "v2.8.0"`
	`19`	`+ "nf-core/methylseq": "v3.0.0"`
`20`	`20`	`}`
`21`	`21`	`},`
`22`	`22`	`[`