Merge pull request #16 from drpatelh/release

Address review comments for v1.1 release
nf-core · Jun 22, 2021 · 098b8b1 · 098b8b1
2 parents 3e06f50 + 8f03fa7
commit 098b8b1
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diff --git a/README.md b/README.md
@@ -41,7 +41,7 @@ The columns in the auto-created samplesheet can be tailored to be accepted out-o
 
 3. Download the pipeline and test it on a minimal dataset with a single command:
 
-    ```console
+    ```bash
     nextflow run nf-core/fetchngs -profile test,<docker/singularity/podman/shifter/charliecloud/conda/institute>
     ```
 
@@ -51,7 +51,7 @@ The columns in the auto-created samplesheet can be tailored to be accepted out-o
 
 4. Start running your own analysis!
 
-    ```console
+    ```bash
     nextflow run nf-core/fetchngs --input ids.txt -profile <docker/singularity/podman/shifter/charliecloud/conda/institute>
     ```
 

diff --git a/docs/usage.md b/docs/usage.md
@@ -38,7 +38,7 @@ This downloads a text file called `SRR_Acc_List.txt` which can be directly provi
 
 The typical command for running the pipeline is as follows:
 
-```console
+```bash
 nextflow run nf-core/fetchngs --input ids.txt -profile docker
 ```
 
@@ -57,7 +57,7 @@ results         # Finished results (configurable, see below)
 
 When you run the above command, Nextflow automatically pulls the pipeline code from GitHub and stores it as a cached version. When running the pipeline after this, it will always use the cached version if available - even if the pipeline has been updated since. To make sure that you're running the latest version of the pipeline, make sure that you regularly update the cached version of the pipeline:
 
-```console
+```bash
 nextflow pull nf-core/fetchngs
 ```
 
@@ -221,6 +221,6 @@ Some HPC setups also allow you to run nextflow within a cluster job submitted yo
 In some cases, the Nextflow Java virtual machines can start to request a large amount of memory.
 We recommend adding the following line to your environment to limit this (typically in `~/.bashrc` or `~./bash_profile`):
 
-```console
+```bash
 NXF_OPTS='-Xms1g -Xmx4g'
 ```
diff --git a/nextflow_schema.json b/nextflow_schema.json
@@ -32,7 +32,7 @@
                 "sample_mapping_fields": {
                     "type": "string",
                     "fa_icon": "fas fa-globe-americas",
-                    "description": "Comma-separated list of ENA metadata fields used to create mappings file for sample id mapping or renaming.",
+                    "description": "Comma-separated list of ENA metadata fields used to create a separate 'id_mappings.csv' and 'multiqc_config.yml' with selected fields that can be used to rename samples in general and in MultiQC.",
                     "default": "run_accession,sample_accession,experiment_alias,run_alias,sample_alias,experiment_title,sample_title,sample_description,description"
                 },
                 "nf_core_pipeline": {