always import base config

bactopia · Apr 3, 2024 · 823e1e2 · 823e1e2
1 parent 13cc192
commit 823e1e2
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Showing 4 changed files with 2 additions and 10 deletions.
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -13,6 +13,7 @@ description: A full list of Bactopia releases and a description of the changes.
 - full support of config files from nf-core/configs
     - no longer prints efficiency for `standard`, `docker`, and `singularity` profiles
     - now required non-integer values for `--max_time` (e.g. `4.h`) and `--max_memory` (e.g. `8.GB`)
+    - always import `base.config`
 
 ### `Fixed`
 

diff --git a/conf/profiles.config b/conf/profiles.config
@@ -5,27 +5,23 @@ profiles {
         conda.useMamba = params.use_mamba
         conda.cacheDir = "${params.condadir}"
         params.enable_conda = true
-        includeConfig "base.config"
     }
 
     aws {
         docker.enabled = true
         docker.runOptions = '-u $(id -u):$(id -g)'
         process.container = "quay.io/bactopia/bactopia:${manifest.version}"
-        includeConfig "base.config"
         includeConfig "profiles/aws.config"
     }
 
     docker {
         docker.enabled = true
         docker.runOptions = '-u $(id -u):$(id -g) -v ${HOME}/.cache:/.cache -v ${HOME}/.config:/.config -v ${PWD}:/.medaka'
-        includeConfig "base.config"
     }
 
     arm {
         docker.enabled = true
         docker.runOptions = '-u $(id -u):$(id -g) --platform=linux/amd64 -v ${HOME}/.cache:/.cache -v ${HOME}/.config:/.config'
-        includeConfig "base.config"
     }
 
     gcp {
@@ -36,7 +32,6 @@ profiles {
         singularity.enabled = true
         singularity.autoMounts = true
         singularity.cacheDir = "${singularity_cache}"
-        includeConfig "base.config"
         includeConfig "profiles/sge.config"
     }
 
@@ -45,22 +40,19 @@ profiles {
         apptainer.autoMounts = true
         apptainer.cacheDir = "${singularity_cache}"
         apptainer.runOptions = "${params.container_opts}"
-        includeConfig "base.config"
     }
 
     singularity {
         singularity.enabled = true
         singularity.autoMounts = true
         singularity.cacheDir = "${singularity_cache}"
         singularity.runOptions = "${params.container_opts}"
-        includeConfig "base.config"
     }
 
     slurm {
         singularity.enabled = true
         singularity.autoMounts = true
         singularity.cacheDir = "${singularity_cache}"
-        includeConfig "base.config"
         includeConfig "profiles/slurm.config"
     }
 
@@ -72,7 +64,6 @@ profiles {
     Custom User Configs.
     */
     arcc_hawk {
-        includeConfig "base.config"
         includeConfig "profiles/arcc_hawk.config"
     }
 }
diff --git a/modules/nf-core/csvtk/concat/main.nf b/modules/nf-core/csvtk/concat/main.nf
@@ -43,7 +43,6 @@ process CSVTK_CONCAT {
         ${out_delimiter} \\
         --out-file ${prefix}.${out_extension} \\
         --infile-list fofn.txt
-        $csv
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":

diff --git a/nextflow.config b/nextflow.config
@@ -13,6 +13,7 @@ manifest {
 bactopia_cache = System.getenv("BACTOPIA_CACHEDIR") ? "${BACTOPIA_CACHEDIR}" : "${HOME}/.bactopia"
 includeConfig "conf/params.config"
 includeConfig "conf/workflows.config"
+includeConfig "conf/base.config"
 if (params.workflows.containsKey(params.wf)) {
     if (params.workflows[params.wf].containsKey("is_workflow")) {
         // Running as main workflow (e.g. bactopia/staphopia)