From 2e56022e31baa24ba2c581f92925e39ff4f5e845 Mon Sep 17 00:00:00 2001 From: Edmund Miller Date: Tue, 24 Nov 2020 14:16:20 -0600 Subject: [PATCH] test(fastqc): Remove input symlinks Co-authored-by: Harshil Patel --- tests/fastqc/input/test_R1.fastq.gz | 1 - tests/fastqc/input/test_R2.fastq.gz | 1 - tests/fastqc/input/test_single_end.fastq.gz | 1 - tests/fastqc/main.nf | 4 ++-- 4 files changed, 2 insertions(+), 5 deletions(-) delete mode 120000 tests/fastqc/input/test_R1.fastq.gz delete mode 120000 tests/fastqc/input/test_R2.fastq.gz delete mode 120000 tests/fastqc/input/test_single_end.fastq.gz diff --git a/tests/fastqc/input/test_R1.fastq.gz b/tests/fastqc/input/test_R1.fastq.gz deleted file mode 120000 index e7b4b614..00000000 --- a/tests/fastqc/input/test_R1.fastq.gz +++ /dev/null @@ -1 +0,0 @@ -../../../../tests/data/fastq/rna/test_R1.fastq.gz \ No newline at end of file diff --git a/tests/fastqc/input/test_R2.fastq.gz b/tests/fastqc/input/test_R2.fastq.gz deleted file mode 120000 index 5b7b57a3..00000000 --- a/tests/fastqc/input/test_R2.fastq.gz +++ /dev/null @@ -1 +0,0 @@ -../../../../tests/data/fastq/rna/test_R2.fastq.gz \ No newline at end of file diff --git a/tests/fastqc/input/test_single_end.fastq.gz b/tests/fastqc/input/test_single_end.fastq.gz deleted file mode 120000 index 7d0654e1..00000000 --- a/tests/fastqc/input/test_single_end.fastq.gz +++ /dev/null @@ -1 +0,0 @@ -../../data/fastq/rna/test_single_end.fastq.gz \ No newline at end of file diff --git a/tests/fastqc/main.nf b/tests/fastqc/main.nf index b6fd5dbc..6d25e53d 100644 --- a/tests/fastqc/main.nf +++ b/tests/fastqc/main.nf @@ -12,7 +12,7 @@ workflow test_single_end { def input = [] input = [ [ id:'test', single_end:true ], // meta map - [ file("${projectDir}/input/test_single_end.fastq.gz", checkIfExists: true) ] ] + [ file("${launchDir}/tests/data/fastq/rna/test_single_end.fastq.gz", checkIfExists: true) ] ] FASTQC_SE ( input ) } @@ -25,7 +25,7 @@ workflow test_paired_end { def input = [] input = [ [ id:'test', single_end:false ], // meta map [ file("${launchDir}/tests/data/fastq/rna/test_R1.fastq.gz", checkIfExists: true), - file("${projectDir}/../data/fastq/rna/test_R2.fastq.gz", checkIfExists: true) ] ] + file("${launchDir}/tests/data/fastq/rna/test_R2.fastq.gz", checkIfExists: true) ] ] FASTQC_PE ( input ) }