diff --git a/libworkflows/libworkflows.py b/libworkflows/libworkflows.py index 004293915f77b09efd0a634574d9481d7c37cb85..ba3e470c646267833daf870bb3b811cdb723b1b7 100644 --- a/libworkflows/libworkflows.py +++ b/libworkflows/libworkflows.py @@ -54,12 +54,14 @@ count_fastq_reads() sort_by_seq() {{ - niceload --mem 10000M fastq-sort -s || error_exit "fastq-sort failed" + # niceload --mem 10000M fastq-sort -s || error_exit "fastq-sort failed" + fastq-sort -s || error_exit "fastq-sort failed" }} dedup() {{ - sort_by_seq | niceload --mem 10000M remove-duplicates-from-sorted-fastq \\ + # sort_by_seq | niceload --mem 10000M remove-duplicates-from-sorted-fastq \\ + sort_by_seq | remove-duplicates-from-sorted-fastq \\ || error_exit "remove_duplicates_from_sorted_fastq failed" }} @@ -67,7 +69,8 @@ trim_random_nt() {{ # $1: nb of bases to trim at 5' end # $2: nb of bases to trim at 3' end - niceload --noswap -q cutadapt -u ${{1}} -u -${{2}} - 2> /dev/null \\ + # niceload --noswap -q cutadapt -u ${{1}} -u -${{2}} - 2> /dev/null \\ + cutadapt -u ${{1}} -u -${{2}} - 2> /dev/null \\ || error_exit "trim_random_nt failed" }}