From f6e6b0f9fa964b49b810da3c34f3eef44c24c1a6 Mon Sep 17 00:00:00 2001 From: kylacochrane Date: Wed, 25 Sep 2024 17:24:26 -0400 Subject: [PATCH] Edits to README and usage docs --- README.md | 2 +- assets/samplesheet.csv | 8 ++++---- assets/samplesheet_minimal.csv | 4 ++++ docs/usage.md | 2 +- 4 files changed, 10 insertions(+), 6 deletions(-) create mode 100644 assets/samplesheet_minimal.csv diff --git a/README.md b/README.md index b780f93..07fb475 100644 --- a/README.md +++ b/README.md @@ -14,7 +14,7 @@ The input to the pipeline is a standard sample sheet (passed as `--input samples | ------- | --------------- | --------------- | | SampleA | file_1.fastq.gz | file_2.fastq.gz | -An [example samplesheet](../assets/samplesheet.csv) has been provided with the pipeline. +An [example samplesheet](../assets/samplesheet_minimal.csv) has been provided with the pipeline. The structure of this file is defined in [assets/schema_input.json](assets/schema_input.json). Validation of the sample sheet is performed by [nf-validation](https://nextflow-io.github.io/nf-validation/). diff --git a/assets/samplesheet.csv b/assets/samplesheet.csv index 9986717..46a711c 100644 --- a/assets/samplesheet.csv +++ b/assets/samplesheet.csv @@ -1,4 +1,4 @@ -sample,fastq_1,fastq_2 -SAMPLE1,https://github.com/nf-core/test-datasets/raw/mag/test_data/test_minigut_R1.fastq.gz,https://github.com/nf-core/test-datasets/raw/mag/test_data/test_minigut_R2.fastq.gz -SAMPLE2,https://github.com/nf-core/test-datasets/raw/mag/test_data/test_minigut_sample2_R1.fastq.gz,https://github.com/nf-core/test-datasets/raw/mag/test_data/test_minigut_sample2_R2.fastq.gz -SAMPLE3,https://github.com/nf-core/test-datasets/raw/mag/test_data/test_minigut_R1.fastq.gz, +sample,sample_name,fastq_1,fastq_2 +SAMPLE1,A1,https://github.com/nf-core/test-datasets/raw/mag/test_data/test_minigut_R1.fastq.gz,https://github.com/nf-core/test-datasets/raw/mag/test_data/test_minigut_R2.fastq.gz +SAMPLE2,B2,https://github.com/nf-core/test-datasets/raw/mag/test_data/test_minigut_sample2_R1.fastq.gz,https://github.com/nf-core/test-datasets/raw/mag/test_data/test_minigut_sample2_R2.fastq.gz +SAMPLE3,C3,https://github.com/nf-core/test-datasets/raw/mag/test_data/test_minigut_R1.fastq.gz, diff --git a/assets/samplesheet_minimal.csv b/assets/samplesheet_minimal.csv new file mode 100644 index 0000000..9986717 --- /dev/null +++ b/assets/samplesheet_minimal.csv @@ -0,0 +1,4 @@ +sample,fastq_1,fastq_2 +SAMPLE1,https://github.com/nf-core/test-datasets/raw/mag/test_data/test_minigut_R1.fastq.gz,https://github.com/nf-core/test-datasets/raw/mag/test_data/test_minigut_R2.fastq.gz +SAMPLE2,https://github.com/nf-core/test-datasets/raw/mag/test_data/test_minigut_sample2_R1.fastq.gz,https://github.com/nf-core/test-datasets/raw/mag/test_data/test_minigut_sample2_R2.fastq.gz +SAMPLE3,https://github.com/nf-core/test-datasets/raw/mag/test_data/test_minigut_R1.fastq.gz, diff --git a/docs/usage.md b/docs/usage.md index 8c4e97d..a728f3b 100644 --- a/docs/usage.md +++ b/docs/usage.md @@ -26,7 +26,7 @@ SAMPLE2,sample2_R1.fastq.gz,sample2_R2.fastq.gz SAMPLE3,sample3_R1.fastq.gz, ``` -A [example samplesheet](../assets/samplesheet.csv) has been provided with the pipeline. +A [example samplesheet](../assets/samplesheet_minimal.csv) has been provided with the pipeline. ### IRIDA-Next Optional Samplesheet Configuration