diff --git a/.gitignore b/.gitignore index 23a558a..22ce0e1 100644 --- a/.gitignore +++ b/.gitignore @@ -7,4 +7,8 @@ build/ .devenv result target/ + +# justfile testing *.fastq.gz +*.fa +dragmap/ diff --git a/justfile b/justfile index 2b43353..eb4257f 100644 --- a/justfile +++ b/justfile @@ -1,8 +1,16 @@ dragen := "./result/bin/dragen-os" -test_segfault: test_data - {{dragen}} -r narfmap --RGSM null --num-threads 2 -1 SRX882903_T2.fastq.gz +test_segfault: # test_data build_reference + {{dragen}} -r dragmap --RGSM test --num-threads 2 -1 SRX882903_T2.fastq.gz > output.log + +build_reference: test_data + # mkdir dragmap + {{dragen}} \ + --build-hash-table true \ + --ht-reference GRCh38_chr21.fa \ + --output-directory dragmap \ + --ht-num-threads 2 test_data: wget https://raw.githubusercontent.com/nf-core/test-datasets/nascent/testdata/SRX882903_T2.fastq.gz - + wget https://raw.githubusercontent.com/nf-core/test-datasets/nascent/reference/GRCh38_chr21.fa