Merge pull request #70 from nf-core/initial-release-review-changes

Apply the sixth set of reviewer recommendations

docs/output.md

@@ -5,7 +5,7 @@
 This document describes the output produced by the pipeline. The directories listed below will be created in the results
 directory after the pipeline has finished. All paths are relative to the top-level results directory.
 
-```text
+```tree
 output/
 │  
 ├── subject_1/

docs/usage.md

@@ -316,7 +316,7 @@ See the below sections for further details on customising reference data.
 To override hmftools resource files, first [stage the bundle](#staging-reference-data) locally then copy in your
 custom file under the bundle directory and create a new config with relevant file paths:
 
-```text title="hmf_data.custom.config"
+```groovy title="hmf_data.custom.config"
 params {
     hmf_data_paths {
         '38' {
@@ -368,7 +368,7 @@ recommended to remove the Nextflow work directory after staging data to free dis
 
 For `oncoanalyser` to use locally staged reference data a custom config can be used:
 
-```text title="refdata.local.config"
+```groovy title="refdata.local.config"
 params {
 
     genomes {
@@ -431,7 +431,7 @@ It is strongly recommended to use a Hartwig-distributed reference genome for ali
 (`GRCh37_hmf` or `GRCh38_hmf`). Where it is not feasible to do so, a custom genome can instead be used by providing the
 relevant FASTA file in a configuration file:
 
-```text title='genome.custom.config'
+```groovy title='genome.custom.config'
 params {
     genomes {
         CustomGenome {

modules/local/amber/environment.yml

@@ -4,4 +4,4 @@ channels:
   - bioconda
   - defaults
 dependencies:
-  - bioconda::hmftools-amber=4.0
+  - bioconda::hmftools-amber=4.0.1

modules/local/custom/extract_tarball/main.nf

@@ -1,7 +1,7 @@
 process CUSTOM_EXTRACTTARBALL {
     label 'process_single'
 
-    conda "conda-forge::tar"
+    conda "conda-forge::tar=1.34"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/ubuntu:20.04' :
         'quay.io/nf-core/ubuntu:20.04' }"