Merge pull request #133 from nf-core/prep_1.0.0

remove TODOs
nf-core · Jun 21, 2023 · 97ed667 · 97ed667
2 parents 224d2ab + d605eba
commit 97ed667
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diff --git a/.github/workflows/awsfulltest.yml b/.github/workflows/awsfulltest.yml
@@ -15,7 +15,6 @@ jobs:
     steps:
       - name: Launch workflow via tower
         uses: seqeralabs/action-tower-launch@v1
-        # TODO nf-core: You can customise AWS full pipeline tests as required
         # Add full size test data (but still relatively small datasets for few samples)
         # on the `test_full.config` test runs with only one set of parameters
         with:

diff --git a/README.md b/README.md
@@ -40,22 +40,6 @@ On release, automated continuous integration tests run the pipeline on a full-si
 > to set-up Nextflow. Make sure to [test your setup](https://nf-co.re/docs/usage/introduction#how-to-run-a-pipeline)
 > with `-profile test` before running the workflow on actual data.
 
-<!-- TODO nf-core: Describe the minimum required steps to execute the pipeline, e.g. how to prepare samplesheets.
-     Explain what rows and columns represent. For instance (please edit as appropriate):
-
-First, prepare a samplesheet with your input data that looks as follows:
-
-`samplesheet.csv`:
-
-```csv
-sample,fastq_1,fastq_2
-CONTROL_REP1,AEG588A1_S1_L002_R1_001.fastq.gz,AEG588A1_S1_L002_R2_001.fastq.gz
-```
-
-Each row represents a fastq file (single-end) or a pair of fastq files (paired end).
-
--->
-
 Now, you can run the pipeline using:
 
 ```bash

diff --git a/assets/methods_description_template.yml b/assets/methods_description_template.yml
@@ -3,7 +3,6 @@ description: "Suggested text and references to use when describing pipeline usag
 section_name: "nf-core/pangenome Methods Description"
 section_href: "https://github.com/nf-core/pangenome"
 plot_type: "html"
-## TODO nf-core: Update the HTML below to your prefered methods description, e.g. add publication citation for this pipeline
 ## You inject any metadata in the Nextflow '${workflow}' object
 data: |
   <h4>Methods</h4>

diff --git a/conf/base.config b/conf/base.config
@@ -10,7 +10,6 @@
 
 process {
 
-    // TODO nf-core: Check the defaults for all processes
     cpus   = { check_max( 1    * task.attempt, 'cpus'   ) }
     memory = { check_max( 6.GB * task.attempt, 'memory' ) }
     time   = { check_max( 4.h  * task.attempt, 'time'   ) }
@@ -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   = { check_max( 1                  , 'cpus'    ) }

diff --git a/conf/test.config b/conf/test.config
@@ -20,8 +20,6 @@ params {
     max_time   = '6.h'
 
     // Input data
-    // TODO nf-core: Specify the paths to your test data on nf-core/test-datasets
-    // TODO nf-core: Give any required params for the test so that command line flags are not needed
     input  = 'https://github.com/nf-core/test-datasets/raw/pangenome/data/DRB1-3123/DRB1-3123.fa.gz'
     n_haplotypes = 12
 }
diff --git a/docs/output.md b/docs/output.md
@@ -6,8 +6,6 @@ This document describes the output produced by the pipeline. Most of the plots a
 
 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.
 
-<!-- TODO nf-core: Write this documentation describing your workflow's output -->
-
 ## Pipeline overview
 
 The pipeline is built using [Nextflow](https://www.nextflow.io/) and processes data using the following steps:

diff --git a/docs/usage.md b/docs/usage.md
@@ -6,8 +6,6 @@
 
 ## Introduction
 
-<!-- TODO nf-core: Add documentation about anything specific to running your pipeline. For general topics, please point to (and add to) the main nf-core website. -->
-
 ### Pangenome sequence naming of FASTA input
 
 Reformat the sequence names in your FASTA input file according to the [PanSN-spec](https://github.com/pangenome/PanSN-spec) naming scheme to simplify the identification of samples and haplotypes in pangenomes.

diff --git a/nextflow.config b/nextflow.config
@@ -9,7 +9,6 @@
 // Global default params, used in configs
 params {
 
-    // TODO nf-core: Specify your pipeline's command line flags
     // Input options
     input                       = null
     n_haplotypes                = 0