From 4b3859c4c852c518b18d809954b60d8ce00c5d15 Mon Sep 17 00:00:00 2001
From: Blaise Li <blaise.li__git@nsup.org>
Date: Tue, 17 Dec 2019 19:20:04 +0100
Subject: [PATCH] Removing niceload.
---
libworkflows/libworkflows.py | 9 ++++++---
1 file changed, 6 insertions(+), 3 deletions(-)
diff --git a/libworkflows/libworkflows.py b/libworkflows/libworkflows.py
index 0042939..ba3e470 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"
}}
--
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