Follow up fixes to #57

CHANGELOG.md

@@ -5,10 +5,17 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ## [[1.6](https://github.com/nf-core/fetchngs/releases/tag/1.6)] - 2022-05-17
 
+- [#57](https://github.com/nf-core/fetchngs/pull/57) - fetchngs fails if FTP is blocked
 - [#89](https://github.com/nf-core/fetchngs/pull/89) - Improve detection and usage of the NCBI user settings by using the standardized sra-tools modules from nf-core.
 - [[nf-core/rnaseq#764](https://github.com/nf-core/rnaseq/issues/764)] - Test fails when using GCP due to missing tools in the basic biocontainer
 - Updated pipeline template to [nf-core/tools 2.4.1](https://github.com/nf-core/tools/releases/tag/2.4.1)
 
+### Software dependencies
+
+| Dependency      | Old version | New version |
+| --------------- | ----------- | ----------- |
+| `synapseclient` | 2.4.0       | 2.6.0       |
+
 ## [[1.5](https://github.com/nf-core/fetchngs/releases/tag/1.5)] - 2021-12-01
 
 - Finish porting the pipeline to the updated Nextflow DSL2 syntax adopted on nf-core/modules

docs/usage.md

@@ -57,6 +57,10 @@ The final sample information for the FastQ files used for samplesheet generation
 
 As a bonus, the columns in the auto-created samplesheet can be tailored to be accepted out-of-the-box by selected nf-core pipelines, these currently include [nf-core/rnaseq](https://nf-co.re/rnaseq/usage#samplesheet-input) and the Illumina processing mode of [nf-core/viralrecon](https://nf-co.re/viralrecon/usage#illumina-samplesheet-format). You can use the `--nf_core_pipeline` parameter to customise this behaviour e.g. `--nf_core_pipeline rnaseq`. More pipelines will be supported in due course as we adopt and standardise samplesheet input across nf-core. It is highly recommended that you double-check that all of the identifiers you defined using `--input` are represented in the samplesheet. Also, public databases don't reliably hold information such as strandedness information so you may need to amend these entries too if for example your samplesheet was created by providing `--nf_core_pipeline rnaseq`.
 
+### Bypass `FTP` data download
+
+If FTP connections are blocked on your network use the [`--force_sratools_download`](https://nf-co.re/fetchngs/parameters#force_sratools_download) parameter to force the pipeline to download data using sra-tools instead of the ENA FTP.
+
 ## Running the pipeline
 
 The typical command for running the pipeline is as follows:
@@ -259,9 +263,3 @@ We recommend adding the following line to your environment to limit this (typica
 ```console
 NXF_OPTS='-Xms1g -Xmx4g'
 ```
-
-## Troubleshooting
-
-### `FTP` download is blocked at my workplace/institution, how can I still use _nf-core/fetchngs_ ?
-
-If downloading data with FTP is blocked on your network connection, you may want to use the [`--force_sratools_download`](https://nf-co.re/fetchngs/1.5/parameters#force_sratools_download) flag to force fetchngs download using [sra-tools](https://github.com/ncbi/sra-tools) instead of the ENA FTP.

nextflow_schema.json

@@ -49,7 +49,7 @@
                     "type": "boolean",
                     "fa_icon": "fas fa-tools",
                     "description": "Force download FASTQ files via sra-tools instead of via the ENA FTP.",
-                    "help_text": "If downloading data through FTP is blocked on your network connection, you may want to use this flag to force fetchngs to download using sra-tools instead of the ENA FTP.  "
+                    "help_text": "If FTP connections are blocked on your network use this flag to force the pipeline to download data using sra-tools instead of the ENA FTP."
                 },
                 "skip_fastq_download": {
                     "type": "boolean",