From 826e6651618c578031f960d326588a2202792251 Mon Sep 17 00:00:00 2001 From: Nick Waters Date: Tue, 14 Apr 2026 16:45:26 -0400 Subject: [PATCH 1/4] add test samplesheet with minigut --- samplesheets/test.csv | 4 ++++ 1 file changed, 4 insertions(+) create mode 100644 samplesheets/test.csv diff --git a/samplesheets/test.csv b/samplesheets/test.csv new file mode 100644 index 000000000..544d864ca --- /dev/null +++ b/samplesheets/test.csv @@ -0,0 +1,4 @@ +sample,run_accession,instrument_platform,fastq_1,fastq_2,fasta +2612,ERR5766176,ILLUMINA,https://raw.githubusercontent.com/nf-core/test-datasets/taxprofiler/data/fastq/ERX5474932_ERR5766176_1.fastq.gz,https://raw.githubusercontent.com/nf-core/test-datasets/taxprofiler/data/fastq/ERX5474932_ERR5766176_2.fastq.gz, +2612,ERR5766176_B,ILLUMINA,https://raw.githubusercontent.com/nf-core/test-datasets/taxprofiler/data/fastq/ERX5474932_ERR5766176_B_1.fastq.gz,https://raw.githubusercontent.com/nf-core/test-datasets/taxprofiler/data/fastq/ERX5474932_ERR5766176_B_2.fastq.gz, +minigut,1,ILLUMINA,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, \ No newline at end of file From b171cee986c3c9168bd652484ca00343cd5d3b26 Mon Sep 17 00:00:00 2001 From: Nick Waters Date: Fri, 17 Apr 2026 13:21:32 -0400 Subject: [PATCH 2/4] tests refactored, using small files exclusively now --- samplesheets/test.csv | 8 +++++--- 1 file changed, 5 insertions(+), 3 deletions(-) diff --git a/samplesheets/test.csv b/samplesheets/test.csv index 544d864ca..66f8715f0 100644 --- a/samplesheets/test.csv +++ b/samplesheets/test.csv @@ -1,4 +1,6 @@ sample,run_accession,instrument_platform,fastq_1,fastq_2,fasta -2612,ERR5766176,ILLUMINA,https://raw.githubusercontent.com/nf-core/test-datasets/taxprofiler/data/fastq/ERX5474932_ERR5766176_1.fastq.gz,https://raw.githubusercontent.com/nf-core/test-datasets/taxprofiler/data/fastq/ERX5474932_ERR5766176_2.fastq.gz, -2612,ERR5766176_B,ILLUMINA,https://raw.githubusercontent.com/nf-core/test-datasets/taxprofiler/data/fastq/ERX5474932_ERR5766176_B_1.fastq.gz,https://raw.githubusercontent.com/nf-core/test-datasets/taxprofiler/data/fastq/ERX5474932_ERR5766176_B_2.fastq.gz, -minigut,1,ILLUMINA,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, \ No newline at end of file +ERR5766176,ERR5766176,ILLUMINA,https://raw.githubusercontent.com/nf-core/test-datasets/taxprofiler/data/fastq/ERX5474937_ERR5766181_1.fastq.gz,https://raw.githubusercontent.com/nf-core/test-datasets/taxprofiler/data/fastq/ERX5474937_ERR5766181_2.fastq.gz, +minigut,1,ILLUMINA,https://raw.githubusercontent.com/nf-core/test-datasets/mag/test_data/test_minigut_R1.fastq.gz,https://raw.githubusercontent.com/nf-core/test-datasets/mag/test_data/test_minigut_R2.fastq.gz, +ERR5766176,ERR5766176,ILLUMINA,https://raw.githubusercontent.com/nf-core/test-datasets/taxprofiler/data/fastq/ERX5474937_ERR5766181_1.fastq.gz,https://raw.githubusercontent.com/nf-core/test-datasets/taxprofiler/data/fastq/ERX5474937_ERR5766181_2.fastq.gz, +multilib,1,ILLUMINA,https://raw.githubusercontent.com/nf-core/test-datasets/taxprofiler/data/fastq/ERX5474932_ERR5766176_1.fastq.gz,https://raw.githubusercontent.com/nf-core/test-datasets/taxprofiler/data/fastq/ERX5474932_ERR5766176_2.fastq.gz, +multilib,2,ILLUMINA,https://raw.githubusercontent.com/nf-core/test-datasets/mag/test_data/test_minigut_R1.fastq.gz,https://raw.githubusercontent.com/nf-core/test-datasets/mag/test_data/test_minigut_R2.fastq.gz, \ No newline at end of file From edb8b6517972475a015008335dc99c89a92df5f7 Mon Sep 17 00:00:00 2001 From: Nick Waters Date: Fri, 17 Apr 2026 13:31:28 -0400 Subject: [PATCH 3/4] nvm --- samplesheets/test.csv | 2 -- 1 file changed, 2 deletions(-) diff --git a/samplesheets/test.csv b/samplesheets/test.csv index 66f8715f0..c93beb863 100644 --- a/samplesheets/test.csv +++ b/samplesheets/test.csv @@ -2,5 +2,3 @@ sample,run_accession,instrument_platform,fastq_1,fastq_2,fasta ERR5766176,ERR5766176,ILLUMINA,https://raw.githubusercontent.com/nf-core/test-datasets/taxprofiler/data/fastq/ERX5474937_ERR5766181_1.fastq.gz,https://raw.githubusercontent.com/nf-core/test-datasets/taxprofiler/data/fastq/ERX5474937_ERR5766181_2.fastq.gz, minigut,1,ILLUMINA,https://raw.githubusercontent.com/nf-core/test-datasets/mag/test_data/test_minigut_R1.fastq.gz,https://raw.githubusercontent.com/nf-core/test-datasets/mag/test_data/test_minigut_R2.fastq.gz, ERR5766176,ERR5766176,ILLUMINA,https://raw.githubusercontent.com/nf-core/test-datasets/taxprofiler/data/fastq/ERX5474937_ERR5766181_1.fastq.gz,https://raw.githubusercontent.com/nf-core/test-datasets/taxprofiler/data/fastq/ERX5474937_ERR5766181_2.fastq.gz, -multilib,1,ILLUMINA,https://raw.githubusercontent.com/nf-core/test-datasets/taxprofiler/data/fastq/ERX5474932_ERR5766176_1.fastq.gz,https://raw.githubusercontent.com/nf-core/test-datasets/taxprofiler/data/fastq/ERX5474932_ERR5766176_2.fastq.gz, -multilib,2,ILLUMINA,https://raw.githubusercontent.com/nf-core/test-datasets/mag/test_data/test_minigut_R1.fastq.gz,https://raw.githubusercontent.com/nf-core/test-datasets/mag/test_data/test_minigut_R2.fastq.gz, \ No newline at end of file From dc82102d0b3c70398bd16f09a100b31e01c840c4 Mon Sep 17 00:00:00 2001 From: Nick Waters Date: Fri, 17 Apr 2026 13:33:25 -0400 Subject: [PATCH 4/4] fix name --- samplesheets/test.csv | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/samplesheets/test.csv b/samplesheets/test.csv index c93beb863..037457380 100644 --- a/samplesheets/test.csv +++ b/samplesheets/test.csv @@ -1,4 +1,3 @@ sample,run_accession,instrument_platform,fastq_1,fastq_2,fasta -ERR5766176,ERR5766176,ILLUMINA,https://raw.githubusercontent.com/nf-core/test-datasets/taxprofiler/data/fastq/ERX5474937_ERR5766181_1.fastq.gz,https://raw.githubusercontent.com/nf-core/test-datasets/taxprofiler/data/fastq/ERX5474937_ERR5766181_2.fastq.gz, +ERR5766181,ERR5766181,ILLUMINA,https://raw.githubusercontent.com/nf-core/test-datasets/taxprofiler/data/fastq/ERX5474937_ERR5766181_1.fastq.gz,https://raw.githubusercontent.com/nf-core/test-datasets/taxprofiler/data/fastq/ERX5474937_ERR5766181_2.fastq.gz, minigut,1,ILLUMINA,https://raw.githubusercontent.com/nf-core/test-datasets/mag/test_data/test_minigut_R1.fastq.gz,https://raw.githubusercontent.com/nf-core/test-datasets/mag/test_data/test_minigut_R2.fastq.gz, -ERR5766176,ERR5766176,ILLUMINA,https://raw.githubusercontent.com/nf-core/test-datasets/taxprofiler/data/fastq/ERX5474937_ERR5766181_1.fastq.gz,https://raw.githubusercontent.com/nf-core/test-datasets/taxprofiler/data/fastq/ERX5474937_ERR5766181_2.fastq.gz,