Merge pull request #276 from nf-core/dev

Dev -> Master for v2.2.0 release

Author: ewels

CHANGELOG.md

@@ -1,5 +1,23 @@
 # nf-core/methylseq
 
+## [v2.2.0](https://github.com/nf-core/methylseq/releases/tag/2.2.0) - 2022-11-29
+
+### Pipeline Updates
+
+- ✨ Updated the `bismark2summary` step so that it no longer stages the aligned BAM files into the working directory. Should be much faster / cheaper for running on the cloud ([#268](https://github.com/nf-core/methylseq/pull/268))
+- ✨ Added ability to merge FastQ files based on shared IDs in sample sheet ([#272](https://github.com/nf-core/methylseq/pull/272))
+
+### Bug fixes & refactoring
+
+- 🐛 Fixed typo in parameter handling for input reference indices ([#263](https://github.com/nf-core/methylseq/issues/263))
+- 🧹 Removed orphaned `--bismark_align_cpu_per_multicore` and `--bismark_align_cpu_per_multicore` parameters.
+  - Multi-core usage for Bismark alignment is now automatically set. If you would like to overwrite this, you can do so by setting `ext.args` for the process in a custom config.
+- 🧹 Removed duplicate option `--coverage2cytosine` ([#273](https://github.com/nf-core/methylseq/issues/273))
+  - Use the existing option `--cytosine_report` to launch the new `COVERAGE2CYTOSINE` process.
+  - Removed option `--cytosine_report genome_index` from the Bismark methylation extractor.
+
+### Software Updates
+
 ## [v2.1.0](https://github.com/nf-core/methylseq/releases/tag/2.1.0) - 2022-11-10
 
 ### Pipeline Updates

README.md

@@ -28,6 +28,7 @@ Choose between workflows by using `--aligner bismark` (default, uses bowtie2 for
 | 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              |

bin/check_samplesheet.py

@@ -210,8 +210,8 @@ def check_samplesheet(file_in, file_out):
             except AssertionError as error:
                 logger.critical(f"{str(error)} On line {i + 2}.")
                 sys.exit(1)
-        # TODO: ADD THIS BACK WHEN WE HAVE LANE MERGING?
-        # checker.validate_unique_samples()
+        # Ties into FastQ merging process
+        checker.validate_unique_samples()
     header = list(reader.fieldnames)
     header.insert(1, "single_end")
     # See https://docs.python.org/3.9/library/csv.html#id3 to read up on `newline=""`.

conf/modules.config

@@ -207,7 +207,6 @@ process {
     withName: BISMARK_METHYLATIONEXTRACTOR {
         ext.args = { [
             params.comprehensive   ? ' --comprehensive --merge_non_CpG' : '',
-            params.cytosine_report ? ' --cytosine_report --genome_folder BismarkIndex' : '',
             params.meth_cutoff     ? " --cutoff ${params.meth_cutoff}" : '',
             params.nomeseq         ? '--CX' : '',
             meta.single_end ? '' : (params.no_overlap           ? ' --no_overlap'                         : '--include_overlap'),
@@ -278,6 +277,7 @@ process {
         ]
     }
 
+
     withName: BISMARK_SUMMARY {
         ext.args = ''
         publishDir = [

main.nf

@@ -20,8 +20,8 @@ nextflow.enable.dsl = 2
 
 params.fasta = WorkflowMain.getGenomeAttribute(params, 'fasta')
 params.fasta_index = WorkflowMain.getGenomeAttribute(params, 'fasta_index')
-params.bismark_index = WorkflowMain.getGenomeAttribute(params, 'fasta_index')
-params.bwa_meth_index = WorkflowMain.getGenomeAttribute(params, 'fasta_index')
+params.bismark_index = WorkflowMain.getGenomeAttribute(params, 'bismark')
+params.bwa_meth_index = WorkflowMain.getGenomeAttribute(params, 'bwa_meth')
 
 /*
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

modules.json

@@ -31,7 +31,7 @@
                     },
                     "bismark/summary": {
                         "branch": "master",
-                        "git_sha": "cdaaf00a580a2b3378926b08dd44db1de44ed7b5"
+                        "git_sha": "e84cc8f07607ad7970db9b6cf79b815b78d9cacd"
                     },
                     "bwameth/align": {
                         "branch": "master",
@@ -41,6 +41,10 @@
                         "branch": "master",
                         "git_sha": "cdaaf00a580a2b3378926b08dd44db1de44ed7b5"
                     },
+                    "cat/fastq": {
+                        "branch": "master",
+                        "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905"
+                    },
                     "custom/dumpsoftwareversions": {
                         "branch": "master",
                         "git_sha": "8022c68e7403eecbd8ba9c49496f69f8c49d50f0"