From 7b224c6aef8cf20c747dda63392b59d411eac3c9 Mon Sep 17 00:00:00 2001 From: Maxime U Garcia Date: Mon, 14 Oct 2024 13:05:05 +0200 Subject: [PATCH] Apply suggestions from code review --- docs/usage.md | 2 +- nf-test.config | 2 +- subworkflows/local/utils_nfcore_fetchngs_pipeline/main.nf | 2 +- 3 files changed, 3 insertions(+), 3 deletions(-) diff --git a/docs/usage.md b/docs/usage.md index b0e06bb9..214d3653 100644 --- 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 index dbda5a1d..df649f14 100644 --- 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 index 306b3932..4a5f5f40 100644 --- 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: