nf-core · ramprasadn · Jun 24, 2024 · Jun 18, 2024 · Jun 18, 2024 · Jun 18, 2024
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -3,16 +3,28 @@
 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).
 
-## 2.2.0 - Dogmatix [XXXX-XX-XX]
+## 2.2.0dev - Dogmatix [XXXX-XX-XX]
 
 ### `Added`
 
+- Two new parameters `mbuffer_mem` and `samtools_sort_threads` to control resources given to mbuffer and samtools sort in the bwameme module [#570](https://github.com/nf-core/raredisease/pull/570)
+
 ### `Changed`
 
+- `readcount_intervals` parameter is now mandatory for running germlinecnvcaller. [#570](https://github.com/nf-core/raredisease/pull/570)
+
 ### `Fixed`
 
+- Docker manifest error from gnu-wget container [#570](https://github.com/nf-core/raredisease/pull/570)
 - Citations for bwameme [#563](https://github.com/nf-core/raredisease/pull/563)
 
+### Parameters
+
+| Old parameter | New parameter         |
+| ------------- | --------------------- |
+|               | mbuffer_mem           |
+|               | samtools_sort_threads |
+
 ## 2.1.0 - Obelix [2024-05-29]
 
 ### `Added`

diff --git a/conf/modules/prepare_references.config b/conf/modules/prepare_references.config
@@ -124,19 +124,4 @@ process {
         ext.when = { (params.vep_cache && params.vep_cache.endsWith("tar.gz")) }
     }
 
-    withName: '.*PREPARE_REFERENCES:GATK_PREPROCESS_WGS' {
-        ext.args =  { [
-            '--padding 0',
-            '--interval-merging-rule OVERLAPPING_ONLY',
-            "--exclude-intervals ${params.mito_name}",
-            "--tmp-dir ./"
-            ].join(' ') }
-        ext.when = { params.analysis_type.equals("wgs") && !params.readcount_intervals }
-    }
-
-    withName: '.*PREPARE_REFERENCES:GATK_PREPROCESS_WES' {
-        ext.args   = { "--bin-length 0 --interval-merging-rule OVERLAPPING_ONLY --exclude-intervals ${params.mito_name}" }
-        ext.when = { params.analysis_type.equals("wes") && !params.readcount_intervals }
-    }
-
 }
diff --git a/docs/usage.md b/docs/usage.md
@@ -215,14 +215,16 @@ The mandatory and optional parameters for each category are tabulated below.
 
 ##### 6. Copy number variant calling
 
-| Mandatory                      | Optional                        |
-| ------------------------------ | ------------------------------- |
-| ploidy_model<sup>1</sup>       | readcount_intervals<sup>3</sup> |
-| gcnvcaller_model<sup>1,2</sup> |                                 |
+| Mandatory                         | Optional |
+| --------------------------------- | -------- |
+| ploidy_model<sup>1,4</sup>        |          |
+| gcnvcaller_model<sup>1,2,4</sup>  |          |
+| readcount_intervals<sup>3,4</sup> |          |
 
 <sup>1</sup> Output from steps 3 & 4 of GATK's CNV calling pipeline run in cohort mode as described [here](https://gatk.broadinstitute.org/hc/en-us/articles/360035531152--How-to-Call-common-and-rare-germline-copy-number-variants).<br />
 <sup>2</sup> Sample file can be found [here](https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/gcnvmodels.tsv) (Note the header 'models' in the sample file).<br />
 <sup>3</sup> Output from step 1 of GATK's CNV calling pipeline as described [here](https://gatk.broadinstitute.org/hc/en-us/articles/360035531152--How-to-Call-common-and-rare-germline-copy-number-variants).<br />
+<sup>4</sup> All these files can be generated using the germlinecnvcaller tool option in nf-core/createpanelrefs.<br />
 
 ##### 7. SNV annotation & Ranking
 

diff --git a/modules.json b/modules.json
@@ -82,7 +82,7 @@
                     },
                     "bwameme/mem": {
                         "branch": "master",
-                        "git_sha": "79480293280ff4f10f30bdea1ddd903f223f8489",
+                        "git_sha": "0aa157a00b54bcbe2c50be375cafd68d928e7f4d",
                         "installed_by": ["modules"]
                     },
                     "cadd": {
@@ -206,11 +206,6 @@
                         "git_sha": "cf607b7749da0a8f5ca2a1e31233e13e3159e2fe",
                         "installed_by": ["modules"]
                     },
-                    "gatk4/preprocessintervals": {
-                        "branch": "master",
-                        "git_sha": "d742e3143f2ccb8853c29b35cfcf50b5e5026980",
-                        "installed_by": ["modules"]
-                    },
                     "gatk4/printreads": {
                         "branch": "master",
                         "git_sha": "d742e3143f2ccb8853c29b35cfcf50b5e5026980",

diff --git a/modules/local/get_chrom_sizes.nf b/modules/local/get_chrom_sizes.nf
@@ -4,8 +4,8 @@ process GET_CHROM_SIZES {
 
     conda "conda-forge::coreutils=8.31"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/gnu-wget:1.18--0' :
-        'biocontainers/gnu-wget:1.18--0' }"
+        'https://depot.galaxyproject.org/singularity/gnu-wget:1.18--h36e9172_9' :
+        'biocontainers/gnu-wget:1.18--h36e9172_9' }"
 
     input:
     tuple val(meta), path(fai)

diff --git a/modules/local/rename_align_files.nf b/modules/local/rename_align_files.nf
@@ -4,8 +4,8 @@ process RENAME_ALIGN_FILES {
 
     conda "conda-forge::coreutils=8.31"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/gnu-wget:1.18--0' :
-        'biocontainers/gnu-wget:1.18--0' }"
+        'https://depot.galaxyproject.org/singularity/gnu-wget:1.18--h36e9172_9' :
+        'biocontainers/gnu-wget:1.18--h36e9172_9' }"
 
     input:
     tuple val(meta), path(input)

diff --git a/modules/nf-core/bwameme/mem/main.nf b/modules/nf-core/bwameme/mem/main.nf
diff --git a/modules/nf-core/bwameme/mem/meta.yml b/modules/nf-core/bwameme/mem/meta.yml
diff --git a/modules/nf-core/bwameme/mem/tests/main.nf.test b/modules/nf-core/bwameme/mem/tests/main.nf.test