Merge pull request #1032 from LaurenceKuhl/crisprseq

Crisprseq adding mageck rra contrasts
nf-core · Nov 3, 2023 · bcb7ff7 · bcb7ff7
2 parents c529ca8 + 0585d00
commit bcb7ff7
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Showing 3 changed files with 11 additions and 9 deletions.
diff --git 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
+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,
+SRR8983583,s3://ngi-igenomes/test-data/crisprseq/SRR8983583.fastq.gz,
diff --git a/testdata/rra_contrasts.txt b/testdata/rra_contrasts.txt
@@ -0,0 +1,2 @@
+treatment;reference
+SRR8983579;SRR8983580
diff --git 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,