From be69d1716daca7108e4cc27c0659a15320513bd2 Mon Sep 17 00:00:00 2001 From: LaurenceKuhl Date: Fri, 9 Jun 2023 15:13:07 +0200 Subject: [PATCH 1/3] fix the commas.. --- testdata/full_test/samplesheet_full.csv | 12 ++++++------ 1 file changed, 6 insertions(+), 6 deletions(-) diff --git a/testdata/full_test/samplesheet_full.csv b/testdata/full_test/samplesheet_full.csv index af0fbf66b..b7a5410b6 100644 --- a/testdata/full_test/samplesheet_full.csv +++ b/testdata/full_test/samplesheet_full.csv @@ -1,6 +1,6 @@ -sample;fastq_1;fastq_2;condition -SRR8983579;s3://ngi-igenomes/test-data/crisprseq/SRR8983579.fastq.gz;;control_A -SRR8983580;s3://ngi-igenomes/test-data/crisprseq/SRR8983580.fastq.gz;;control_B -SRR8983581;s3://ngi-igenomes/test-data/crisprseq/SRR8983581.fastq.gz;;drugA -SRR8983582;s3://ngi-igenomes/test-data/crisprseq/SRR8983582.fastq.gz;;drugB -SRR8983583;s3://ngi-igenomes/test-data/crisprseq/SRR8983583.fastq.gz;;drugC \ No newline at end of file +sample,fastq_1,fastq_2,condition +SRR8983579,s3://ngi-igenomes/test-data/crisprseq/SRR8983579.fastq.gz,,control_A +SRR8983580,s3://ngi-igenomes/test-data/crisprseq/SRR8983580.fastq.gz,,control_B +SRR8983581,s3://ngi-igenomes/test-data/crisprseq/SRR8983581.fastq.gz,,drugA +SRR8983582,s3://ngi-igenomes/test-data/crisprseq/SRR8983582.fastq.gz,,drugB +SRR8983583,s3://ngi-igenomes/test-data/crisprseq/SRR8983583.fastq.gz,,drugC \ No newline at end of file From 543021ae81d5c4e0e4077aed2a69dea5a933ce60 Mon Sep 17 00:00:00 2001 From: LaurenceKuhl Date: Tue, 24 Oct 2023 15:34:24 +0200 Subject: [PATCH 2/3] Add contrasts for mageck rra --- testdata/rra_contrasts.txt | 2 ++ 1 file changed, 2 insertions(+) create mode 100644 testdata/rra_contrasts.txt diff --git a/testdata/rra_contrasts.txt b/testdata/rra_contrasts.txt new file mode 100644 index 000000000..3f1643103 --- /dev/null +++ b/testdata/rra_contrasts.txt @@ -0,0 +1,2 @@ +treatment;reference +SRR8983579;SRR8983580 From 0585d00ca6465f0e582efc7680ea88dc5bf2bd41 Mon Sep 17 00:00:00 2001 From: LaurenceKuhl Date: Thu, 2 Nov 2023 10:59:41 +0100 Subject: [PATCH 3/3] Add commas --- testdata/full_test/samplesheet_full.csv | 9 +++++---- testdata/samplesheet_test.csv | 6 +++--- 2 files changed, 8 insertions(+), 7 deletions(-) diff --git a/testdata/full_test/samplesheet_full.csv b/testdata/full_test/samplesheet_full.csv index 165b633f2..5d45527ac 100644 --- a/testdata/full_test/samplesheet_full.csv +++ b/testdata/full_test/samplesheet_full.csv @@ -1,5 +1,6 @@ sample,fastq_1,fastq_2 -SRR8983579,s3://ngi-igenomes/test-data/crisprseq/SRR8983579.fastq.gz -SRR8983580,s3://ngi-igenomes/test-data/crisprseq/SRR8983580.fastq.gz -SRR8983581,s3://ngi-igenomes/test-data/crisprseq/SRR8983581.fastq.gz -SRR8983582,s3://ngi-igenomes/test-data/crisprseq/SRR8983582.fastq.gz +SRR8983579,s3://ngi-igenomes/test-data/crisprseq/SRR8983579.fastq.gz, +SRR8983580,s3://ngi-igenomes/test-data/crisprseq/SRR8983580.fastq.gz, +SRR8983581,s3://ngi-igenomes/test-data/crisprseq/SRR8983581.fastq.gz, +SRR8983582,s3://ngi-igenomes/test-data/crisprseq/SRR8983582.fastq.gz, +SRR8983583,s3://ngi-igenomes/test-data/crisprseq/SRR8983583.fastq.gz, diff --git a/testdata/samplesheet_test.csv b/testdata/samplesheet_test.csv index 2e33267cf..e75eb1ec4 100644 --- a/testdata/samplesheet_test.csv +++ b/testdata/samplesheet_test.csv @@ -1,3 +1,3 @@ -sample,fastq_1,fastq_2,condition -SRR8983579,https://raw.githubusercontent.com/nf-core/test-datasets/crisprseq/testdata/SRR8983579.small.fastq.gz,,control -SRR8983580,https://raw.githubusercontent.com/nf-core/test-datasets/crisprseq/testdata/SRR8983580.small.fastq.gz,,treatment +sample,fastq_1,fastq_2 +SRR8983579,https://raw.githubusercontent.com/nf-core/test-datasets/crisprseq/testdata/SRR8983579.small.fastq.gz, +SRR8983580,https://raw.githubusercontent.com/nf-core/test-datasets/crisprseq/testdata/SRR8983580.small.fastq.gz,