diff --git a/CHANGELOG.md b/CHANGELOG.md index 1feda591e54e241a26f75ad56dfa8d1195dd183b..a85a844ae1fbdc299eb175ab14449bf9e20d40e0 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -38,6 +38,7 @@ * Add test for DNAnexus env * Add test for AWS env * Fix fetch fastq count +* Fix failPreExecutionRun error collection *Known Bugs* * Override params (inputBag, fastq, species) aren't checked for integrity diff --git a/rna-seq.nf b/rna-seq.nf index a1dcd029e428d15ed8fed56acee5df8d728d0bd0..e1a0777b8a8815f7dceaf0a89a10b4d6752d460f 100644 --- a/rna-seq.nf +++ b/rna-seq.nf @@ -2715,19 +2715,19 @@ process failPreExecutionRun { errorDetails="" if [ ${fastqCountError} == true ] then - errorDetails=\$(echo ${fastqCountError_details}"\\n") + errorDetails=\$(echo "${fastqCountError_details}"\\n") elif [ ${fastqReadError} == true ] then - errorDetails=\$(echo \$(errorDetails)${fastqReadError_details}"\\n") + errorDetails=\$(echo "\${errorDetails}${fastqReadError_details}\\n") elif [ ${fastqFileError} == true ] then - errorDetails=\$(echo \$(errorDetails)${fastqFileError_details}"\\n") + errorDetails=\$(echo "\${errorDetails}${fastqFileError_details}\\n") elif [ ${seqtypeError} == true ] then - errorDetails=\$(echo \$(errorDetails)${seqtypeError_details}"\\n") + errorDetails=\$(echo "\${errorDetails}${seqtypeError_details}\\n") elif [ ${speciesError} == true ] then - errorDetails=\$(echo \$(errorDetails)${speciesError_details}"\\n") + errorDetails=\$(echo "\${errorDetails}${speciesError_details}\\n") fi echo LOG: searching for workflow RID - BICF mRNA ${workflow.manifest.version} >> ${repRID}.failPreExecutionRun.log