diff --git a/workflow/rules/star_mapping_pass1.rules b/workflow/rules/star_mapping_pass1.rules index 516ead4a87e0e51dca4486843ee7fce663f0de4a..3929b94624a1859e2acda2b8287cdbd935a5182d 100755 --- a/workflow/rules/star_mapping_pass1.rules +++ b/workflow/rules/star_mapping_pass1.rules @@ -45,7 +45,10 @@ rule star_mapping_pass1: star_mapping_pass1_logs shell: """ - if [[ {input.fastq} == "*.gz" ]] + tmp="{input}" + infiles=($tmp) + + if [[ ${{infiles[0]}} == "*.gz" ]] then STAR --genomeDir {params.index} \ --readFilesIn {input.fastq} \ diff --git a/workflow/rules/star_mapping_pass2.rules b/workflow/rules/star_mapping_pass2.rules index daae75f7d4cb39c0561106d910b22202c1b2f240..86bf57f7f4709408f133a61083a738a8d30c94ac 100755 --- a/workflow/rules/star_mapping_pass2.rules +++ b/workflow/rules/star_mapping_pass2.rules @@ -46,7 +46,10 @@ rule star_mapping_pass2: star_mapping_pass2_logs shell: """ - if [[ {input.fastq} == "*.gz" ]] + tmp="{input}" + infiles=($tmp) + + if [[ ${{infiles[0]}} == "*.gz" ]] then STAR --genomeDir {params.index} \ --readFilesIn {input.fastq} \