fix: remove TODO placeholders and update zenodo reference

Author: rolivella

README.md

@@ -7,7 +7,7 @@
 
 [![Open in GitHub Codespaces](https://github.com/codespaces/badge.svg)](https://github.com/codespaces/new/nf-core/ribomsqc)
 [![GitHub Actions CI Status](https://github.com/nf-core/ribomsqc/actions/workflows/nf-test.yml/badge.svg)](https://github.com/nf-core/ribomsqc/actions/workflows/nf-test.yml)
-[![GitHub Actions Linting Status](https://github.com/nf-core/ribomsqc/actions/workflows/linting.yml/badge.svg)](https://github.com/nf-core/ribomsqc/actions/workflows/linting.yml)[![AWS CI](https://img.shields.io/badge/CI%20tests-full%20size-FF9900?labelColor=000000&logo=Amazon%20AWS)](https://nf-co.re/ribomsqc/results)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.XXXXXXX-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.XXXXXXX)
+[![GitHub Actions Linting Status](https://github.com/nf-core/ribomsqc/actions/workflows/linting.yml/badge.svg)](https://github.com/nf-core/ribomsqc/actions/workflows/linting.yml)[![AWS CI](https://img.shields.io/badge/CI%20tests-full%20size-FF9900?labelColor=000000&logo=Amazon%20AWS)](https://nf-co.re/ribomsqc/results)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.PENDING-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.PENDING)
 [![nf-test](https://img.shields.io/badge/unit_tests-nf--test-337ab7.svg)](https://www.nf-test.com)
 
 [![Nextflow](https://img.shields.io/badge/version-%E2%89%A525.04.0-green?style=flat&logo=nextflow&logoColor=white&color=%230DC09D&link=https%3A%2F%2Fnextflow.io)](https://www.nextflow.io/)

conf/base.config

@@ -10,7 +10,6 @@
 
 process {
 
-    // TODO nf-core: Check the defaults for all processes
     cpus   = { 1      * task.attempt }
     memory = { 6.GB   * task.attempt }
     time   = { 4.h    * task.attempt }
@@ -24,7 +23,6 @@ process {
     //        These labels are used and recognised by default in DSL2 files hosted on nf-core/modules.
     //        If possible, it would be nice to keep the same label naming convention when
     //        adding in your local modules too.
-    // TODO nf-core: Customise requirements for specific processes.
     // See https://www.nextflow.io/docs/latest/config.html#config-process-selectors
     withLabel:process_single {
         cpus   = { 1                   }

nextflow.config

@@ -12,7 +12,6 @@ nextflow.enable.moduleBinaries = true
 // Global default params, used in configs
 params {
 
-    // TODO nf-core: Specify your pipeline's command line flags
     // Input options
     input                        = null
 
@@ -198,7 +197,6 @@ includeConfig params.custom_config_base && (!System.getenv('NXF_OFFLINE') || !pa
 
 
 // Load nf-core/ribomsqc 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 params.custom_config_base && (!System.getenv('NXF_OFFLINE') || !params.custom_config_base.startsWith('http')) ? "${params.custom_config_base}/pipeline/ribomsqc.config" : "/dev/null"
 
 // Set default registry for Apptainer, Docker, Podman, Charliecloud and Singularity independent of -profile