Merge pull request #331 from nf-core/dev

Patch release 2.2.1

CHANGELOG.md

@@ -3,6 +3,19 @@
 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).
 
+## v2.2.1 - 2022/08/25
+
+### `Added`
+
+### `Changed`
+
+### `Fixed`
+
+- [#328](https://github.com/nf-core/mag/pull/328) - Fix too many symbolic links issue in local convert_depths module (reported by @ChristophKnapp and fixed by @apeltzer, @jfy133)
+- [#329](https://github.com/nf-core/mag/pull/329) - Each sample now gets it's own result directory for PyDamage analysis and filter (reported and fixed by @maxibor)
+
+### `Dependencies`
+
 ## v2.2.0 - 2022/06/14
 
 ### `Added`

conf/modules.config

@@ -368,15 +368,15 @@ process {
 
     withName: PYDAMAGE_ANALYZE {
         publishDir = [
-            path: {"${params.outdir}/Ancient_DNA/pydamage/analyze" },
+            path: {"${params.outdir}/Ancient_DNA/pydamage/analyze/${meta.id}" },
             mode: params.publish_dir_mode
         ]
     }
 
     withName: PYDAMAGE_FILTER {
         ext.args   = "-t ${params.pydamage_accuracy}"
         publishDir = [
-            path: {"${params.outdir}/Ancient_DNA/pydamage/filter" },
+            path: {"${params.outdir}/Ancient_DNA/pydamage/filter/${meta.id}" },
             mode: params.publish_dir_mode
         ]
     }

modules/local/convert_depths.nf

@@ -17,7 +17,7 @@ process CONVERT_DEPTHS {
     script:
     def prefix = task.ext.prefix ?: "${meta.id}"
     """
-    gunzip $depth
+    gunzip -f $depth
     bioawk -t '{ { if (NR > 1) { { print \$1, \$3 } } } }' ${depth.toString() - '.gz'} > ${prefix}_mb2_depth.txt
 
     cat <<-END_VERSIONS > versions.yml

nextflow.config

@@ -267,7 +267,7 @@ manifest {
     description     = 'Assembly, binning and annotation of metagenomes'
     mainScript      = 'main.nf'
     nextflowVersion = '!>=21.10.3'
-    version = '2.2.0'
+    version = '2.2.1'
 }
 
 // Load modules.config for DSL2 module specific options

nextflow_schema.json

@@ -14,6 +14,7 @@
             "properties": {
                 "input": {
                     "type": "string",
+                    "mimetype": "text/csv",
                     "format": "file-path",
                     "description": "Input FastQ files or CSV samplesheet file containing information about the samples in the experiment.",
                     "help_text": "Use this to specify the location of your input FastQ files. For example:\n\n```bash\n--input 'path/to/data/sample_*_{1,2}.fastq.gz'\n``` \n\nAlternatively, to assign different groups or to include long reads for hybrid assembly with metaSPAdes, you can specify a CSV samplesheet input file with 5 columns and the following header: sample,group,short_reads_1,short_reads_2,long_reads. See [usage docs](https://nf-co.re/mag/usage#input-specifications).",