diff --git a/CHANGELOG.md b/CHANGELOG.md index a85a844ae1fbdc299eb175ab14449bf9e20d40e0..04aeb94818b792677615d2e4bd6baf132fcd6b90 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -1,3 +1,9 @@ +# v.2.x.x (indev) +**User Facing** + +**Background** +* Corrected file search parameters due to name inconsistency (#129) + # v2.0.0 **User Facing** * Endness metadata "Single Read" changed to "Single End" in data-hub, pipeline updated to handle (#110) ("Single Read" still acceptable for backwards compatibility) diff --git a/rna-seq.nf b/rna-seq.nf index 0adcc63f7b7a1a540b2be56a2e94b86376e617bf..159805d91f41c6451eec27db96ef199265f3b07a 100644 --- a/rna-seq.nf +++ b/rna-seq.nf @@ -634,7 +634,7 @@ process fastqc { # run fastqc echo -e "LOG: running fastq on raw fastqs" >> ${repRID}.fastqc.log fastqc *.fastq.gz -o . &> fastqc.out || true - fastqcErrorOut=\$(cat fastqc.out | grep -c 'Failed to process file') || fastqcErrorOut=0 + fastqcErrorOut=\$(cat fastqc.out | grep -c 'Failed to process') || fastqcErrorOut=0 fastqFileError=false fastqFileError_details="" if [ "\${fastqcErrorOut}" -ne "0" ]