diff --git a/.nf-core.yml b/.nf-core.yml
index 0a79964c..1d1684b9 100644
--- a/.nf-core.yml
+++ b/.nf-core.yml
@@ -10,9 +10,12 @@ lint:
- conf/modules.config
files_unchanged:
- .github/PULL_REQUEST_TEMPLATE.md
+ - assets/nf-core-fetchngs_logo_light.png
- assets/sendmail_template.txt
- modules_config: False
- multiqc_config: False
+ - docs/images/nf-core-fetchngs_logo_dark.png
+ - docs/images/nf-core-fetchngs_logo_light.png
+ modules_config: false
+ multiqc_config: false
nf_core_version: 3.0.2
org_path: null
repository_type: pipeline
diff --git a/CHANGELOG.md b/CHANGELOG.md
index 8283f2ed..50d26b5c 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -15,6 +15,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
- [PR #320](https://github.com/nf-core/fetchngs/pull/320) - Update module multiqc_mappings_config and sratools/prefetch for TES compliance
- [PR #320](https://github.com/nf-core/fetchngs/pull/320) - Refactor workflow tests
- [PR #323](https://github.com/nf-core/fetchngs/pull/323) - Template update for nf-core/tools v3.0.2
+- [PR #333](https://github.com/nf-core/fetchngs/pull/333) - Add logo
### Software dependencies
diff --git a/assets/nf-core-fetchngs_logo_light.png b/assets/nf-core-fetchngs_logo_light.png
index 919b9063..603f43e2 100644
Binary files a/assets/nf-core-fetchngs_logo_light.png and b/assets/nf-core-fetchngs_logo_light.png differ
diff --git a/conf/base.config b/conf/base.config
index 13b3c3e7..b7341737 100644
--- a/conf/base.config
+++ b/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 = { 4.h * task.attempt }
diff --git a/docs/images/nf-core-fetchngs_logo_dark.png b/docs/images/nf-core-fetchngs_logo_dark.png
index 63ff1472..e598c68a 100644
Binary files a/docs/images/nf-core-fetchngs_logo_dark.png and b/docs/images/nf-core-fetchngs_logo_dark.png differ
diff --git a/docs/images/nf-core-fetchngs_logo_dark.svg b/docs/images/nf-core-fetchngs_logo_dark.svg
new file mode 100644
index 00000000..a6489cc5
--- /dev/null
+++ b/docs/images/nf-core-fetchngs_logo_dark.svg
@@ -0,0 +1,11422 @@
+
+
+
+
diff --git a/docs/images/nf-core-fetchngs_logo_light.png b/docs/images/nf-core-fetchngs_logo_light.png
index ffc6d41a..6496a024 100644
Binary files a/docs/images/nf-core-fetchngs_logo_light.png and b/docs/images/nf-core-fetchngs_logo_light.png differ
diff --git a/docs/images/nf-core-fetchngs_logo_light.svg b/docs/images/nf-core-fetchngs_logo_light.svg
new file mode 100644
index 00000000..46b7e22b
--- /dev/null
+++ b/docs/images/nf-core-fetchngs_logo_light.svg
@@ -0,0 +1,11423 @@
+
+
+
+
diff --git a/docs/images/nf-core-fetchngs_metro_map_grey.png b/docs/images/nf-core-fetchngs_metro_map_grey.png
index eb4b49bc..c43caf35 100644
Binary files a/docs/images/nf-core-fetchngs_metro_map_grey.png and b/docs/images/nf-core-fetchngs_metro_map_grey.png differ
diff --git a/docs/images/nf-core-fetchngs_metro_map_grey.svg b/docs/images/nf-core-fetchngs_metro_map_grey.svg
index 9857bc12..f7806c6f 100644
--- a/docs/images/nf-core-fetchngs_metro_map_grey.svg
+++ b/docs/images/nf-core-fetchngs_metro_map_grey.svg
@@ -7,7 +7,7 @@
viewBox="0 0 520.81024 211.71736"
version="1.1"
id="svg1"
- inkscape:version="1.3.2 (1:1.3.2+202311252150+091e20ef0f)"
+ inkscape:version="1.4 (1:1.4+202410161351+e7c3feb100)"
sodipodi:docname="nf-core-fetchngs_metro_map_grey.svg"
inkscape:export-filename="nf-core-fetchngs_metro_map_grey.png"
inkscape:export-xdpi="96"
@@ -27,9 +27,9 @@
inkscape:pagecheckerboard="0"
inkscape:deskcolor="#d1d1d1"
inkscape:document-units="mm"
- inkscape:zoom="0.35355339"
- inkscape:cx="722.66313"
- inkscape:cy="352.13918"
+ inkscape:zoom="0.5"
+ inkscape:cx="693"
+ inkscape:cy="456"
inkscape:window-width="1920"
inkscape:window-height="1128"
inkscape:window-x="0"
@@ -4401,13 +4401,7 @@
id="clipPath413">3nf-core/fetchngsENAENASRASRADDBJDDBJGEOGEODATABASE IDsDATABASE IDsSTAGESTAGE2. Download FASTQ files2. Download FASTQ files1. Download metadata1. Download metadata3. Downstream pipelines3. Downstream pipelines GermlineSarek SomaticSarek Sarek Exome GermlineSarek SomaticSarek Sarek Exome GermlineSarek SomaticSarek Sarek Exome GermlineSarek SomaticSarek Sarek Exome GermlineSarek SomaticSarek Sarek Exome GermlineSarek SomaticSarek Sarek Exome GermlineSarek SomaticSarek Sarek Exome GermlineSarek SomaticSarek Sarek Exome GermlineSarek SomaticSarek Sarek Exome GermlineSarek SomaticSarek Sarek Exome GermlineSarek SomaticSarek Sarek Exome GermlineSarek SomaticSarek Sarek Exome GermlineSarek SomaticSarek Sarek Exome GermlineSarek SomaticSarek Sarek Exome GermlineSarek SomaticSarek Sarek Exome GermlineSarek SomaticSarek Sarek Exomenf-core/fetchngs
diff --git a/nextflow.config b/nextflow.config
index b69fc9b5..a047ab96 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -161,8 +161,7 @@ profiles {
includeConfig !System.getenv('NXF_OFFLINE') && params.custom_config_base ? "${params.custom_config_base}/nfcore_custom.config" : "/dev/null"
// Load nf-core/fetchngs custom profiles from different institutions.
-// TODO nf-core: Optionally, you can add a pipeline-specific nf-core config at https://github.com/nf-core/configs
-// includeConfig !System.getenv('NXF_OFFLINE') && params.custom_config_base ? "${params.custom_config_base}/pipeline/fetchngs.config" : "/dev/null"
+includeConfig !System.getenv('NXF_OFFLINE') && params.custom_config_base ? "${params.custom_config_base}/pipeline/fetchngs.config" : "/dev/null"
// Set default registry for Apptainer, Docker, Podman, Charliecloud and Singularity independent of -profile
// Will not be used unless Apptainer / Docker / Podman / Charliecloud / Singularity are enabled