diff --git a/test_src/fastp/R1.fq b/test_src/fastp/R1.fq new file mode 100644 index 0000000..f71f97c --- /dev/null +++ b/test_src/fastp/R1.fq @@ -0,0 +1,4 @@ +@NS500713:64:HFKJJBGXY:1:11101:1675:1101 1:N:0:TATAGCCT+GACCCCCA +AAAAAAAAGCTACTTGGAGTACCAATAATAAAGTGAGCCCACCTTCCTGGTACCCAGACATTTCAGGAGGTCGGGAAA ++ +6AAAAAEEEEE/E/EA/E/AEA6EE//AEE66/AAE//EEE/E//E/AA/EEE/A/AEE/EEA//EEEEEEEE6EEAA diff --git a/test_src/fastp/UMI_test.sh b/test_src/fastp/UMI_test.sh new file mode 100755 index 0000000..c8af127 --- /dev/null +++ b/test_src/fastp/UMI_test.sh @@ -0,0 +1,11 @@ +#!/bin/bash +fastp -i R1.fq -o out.R1.fq -U --umi_loc=read1 --umi_len=8 +echo +diff out.R1.fq out.R1.fq_expected +if [ "$?" = "0" ] +then + echo "Success" +else + echo "Fail!!!" + exit 1 +fi diff --git a/test_src/fastp/out.R1.fq_expected b/test_src/fastp/out.R1.fq_expected new file mode 100644 index 0000000..381dda7 --- /dev/null +++ b/test_src/fastp/out.R1.fq_expected @@ -0,0 +1,4 @@ +@NS500713:64:HFKJJBGXY:1:11101:1675:1101:AAAAAAAA 1:N:0:TATAGCCT+GACCCCCA +GCTACTTGGAGTACCAATAATAAAGTGAGCCCACCTTCCTGGTACCCAGACATTTCAGGAGGTCGGGAAA ++ +EEE/E/EA/E/AEA6EE//AEE66/AAE//EEE/E//E/AA/EEE/A/AEE/EEA//EEEEEEEE6EEAA diff --git a/tests/app.yaml b/tests/app.yaml index 9cce4e4..a6ebbd9 100644 --- a/tests/app.yaml +++ b/tests/app.yaml @@ -353,6 +353,22 @@ cp2k: action: store_true #------------------------------------------------------------------- +# fastp Test +#------------------------------------------------------------------- +fastp: + summary: fastp UNI test + build: + source_path: fastp + copy_files: + - ./** + schedule: + nodes: 1 + slurm: + run: + modules: ['gcc', 'fastp'] + cmds: + - '{{sched.test_cmd}} ./UMI_test.sh' + # Trycycler Test #------------------------------------------------------------------- trycycler: