WIP: Fix warning nf corelint

.nf-core.yml

@@ -2,10 +2,8 @@ lint:
   files_exist:
     - .github/workflows/awsfulltest.yml
     - .github/workflows/awstest.yml
-    - .github/workflows/ci.yml
     - conf/modules.config
   files_unchanged:
-    - .gitignore
     - assets/nf-core-sarek_logo_light.png
     - docs/images/nf-core-sarek_logo_dark.png
     - docs/images/nf-core-sarek_logo_light.png

CHANGELOG.md

@@ -47,11 +47,15 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 | -------------------------------------- | ----------- | ----------- |
 | `ASCAT`                                | 3.1.1       | 3.2.0       |
 | `bcftools`                             | 1.20        | 1.21        |
+| `cnvkit`                               | 0.9.10      | 0.9.12      |
+| `deepvariant`                          | 1.8.0       | 1.9.0       |
 | `ensemblvep`                           | 113.0       | 113.4       |
 | `fastp`                                | 0.23.4      | 0.24.0      |
-| `fgbio`                                | 2.2.1       | 2.4.0       |
+| `fgbio`                                | 2.2.1       | 2.5.21      |
+| `freebayes`                            | 1.3.6       | 1.3.10      |
 | `gatk4`                                | 4.5.0.0     | 4.6.1.0     |
 | `mosdepth`                             | 0.3.8       | 0.3.10      |
+| `msisensor-pro`                        | 1.2.0       | 1.3.0       |
 | `MuSE`                                 |             | 2.1.2       |
 | `MultiQC`                              | 1.25.1      | 1.30        |
 | `samtools` (in `BWAMEM1_MEM`)          | 1.2         | 1.21        |
@@ -117,6 +121,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - [1932](https://github.com/nf-core/sarek/pull/1932) - Refactor and simplify pipeline test suite
 - [1936](https://github.com/nf-core/sarek/pull/1936) - Template update for nf-core/tools v3.3.2
 - [1954](https://github.com/nf-core/sarek/pull/1954) - Refactor bcftools annotation subworkflows so that no diff is necessary from nf-core/modules
+- [1955](https://github.com/nf-core/sarek/pull/1955) - Update all modules and subworkflows
 
 #### Fixed
 
@@ -135,6 +140,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - [1932](https://github.com/nf-core/sarek/pull/1932) - Fix typo for in UMI warning message
 - [1933](https://github.com/nf-core/sarek/pull/1933) - Correct link in README
 - [1935](https://github.com/nf-core/sarek/pull/1935) - Fix bug in samplesheet_to_channel workflow due to bad integer handling with lane
+- [1955](https://github.com/nf-core/sarek/pull/1955) - Fix nf-core/tools lint Pipeline Test Warnings
+- [1955](https://github.com/nf-core/sarek/pull/1955) - Fix nf-core/tools lint Subworkflow Test Warnings
 
 #### Removed
 

conf/base.config

@@ -9,8 +9,6 @@
 */
 
 process {
-
-    // TODO nf-core: Check the defaults for all processes
     cpus   = { 1      * task.attempt }
     memory = { 6.GB   * task.attempt }
     time   = { 8.h    * task.attempt }

conf/modules/recalibrate.config

@@ -19,7 +19,11 @@ process {
         if (params.use_gatk_spark) {
             containerOptions = ''
         }
-        ext.prefix       = { meta.num_intervals <= 1 ? "${meta.id}.recal" : "${meta.id}_${intervals.baseName}.recal" }
+        ext.prefix       = {
+            meta.num_intervals <= 1 ?
+                "${meta.id}.recal." + (params.save_output_as_bam ? 'bam' : 'cram') :
+                "${meta.id}_${intervals.baseName}.recal." + (params.save_output_as_bam ? 'bam' : 'cram')
+        }
         publishDir       = [
             mode: params.publish_dir_mode,
             path: { "${params.outdir}/preprocessing/" },