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nf-core · Oct 14, 2024 · 7b224c6 · 7b224c6
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Showing 3 changed files with 3 additions and 3 deletions.
diff --git a/docs/usage.md b/docs/usage.md
@@ -123,7 +123,7 @@ nextflow run nf-core/fetchngs -profile docker -params-file params.yaml
 with:
 
 ```yaml title="params.yaml"
-input: './samplesheet.csv'
+input: './ids.csv'
 outdir: './results/'
 <...>
 ```

diff --git a/nf-test.config b/nf-test.config
@@ -3,7 +3,7 @@ config {
     testsDir "."
 
     // nf-test directory including temporary files for each test
-    workDir ".nf-test"
+    workDir System.getenv("NFT_WORKDIR") ?: ".nf-test"
 
     // Run all test with defined profile(s) from the main nextflow.config
     profile "test"

diff --git a/subworkflows/local/utils_nfcore_fetchngs_pipeline/main.nf b/subworkflows/local/utils_nfcore_fetchngs_pipeline/main.nf
@@ -32,7 +32,7 @@ workflow PIPELINE_INITIALISATION {
     nextflow_cli_args   //   array: List of positional nextflow CLI args
     outdir              //  string: The output directory where the results will be saved
     input               //  string: File containing SRA/ENA/GEO/DDBJ identifiers one per line to download their associated metadata and FastQ files
-    ena_metadata_fields // string: Comma-separated list of ENA metadata fields to fetch before downloading data
+    ena_metadata_fields //  string: Comma-separated list of ENA metadata fields to fetch before downloading data
 
     main: