From ee642c73a195ff0d9a8c570ee924232ee6d0bc0f Mon Sep 17 00:00:00 2001 From: Yuuki Galaxy Date: Wed, 10 Jan 2024 15:45:32 +0800 Subject: [PATCH] modified: makefile --- python/salus/cmplatform/makefile | 8 +++++--- 1 file changed, 5 insertions(+), 3 deletions(-) diff --git a/python/salus/cmplatform/makefile b/python/salus/cmplatform/makefile index 2a2daa6c0..5ef7aa0b6 100644 --- a/python/salus/cmplatform/makefile +++ b/python/salus/cmplatform/makefile @@ -28,8 +28,8 @@ raw_Illumina/$1_S1_L001: touch $$@ sub_Salus/$1_S1_L001: $$(filter fastp_Salus/$1_S1_L001,$$(FASTP_TAGS)) mkdir -p $$(dir $$@) - micromamba run -n salus seqkit --compress-level 4 -o $@_R1_001.fastq.gz -w 200 -j 1 sample -p 0.666 -s 123456 $^_R1_001.fastq.gz - micromamba run -n salus seqkit --compress-level 4 -o $@_R2_001.fastq.gz -w 200 -j 1 sample -p 0.666 -s 123456 $^_R2_001.fastq.gz + micromamba run -n salus seqkit --compress-level 4 -o $@_R1_001.fastq.gz -w 200 -j 1 sample -p 0.666 -s 123456 $$^_R1_001.cut.gz + micromamba run -n salus seqkit --compress-level 4 -o $@_R2_001.fastq.gz -w 200 -j 1 sample -p 0.666 -s 123456 $$^_R2_001.cut.gz touch $$@ sub_Illumina/$1_S1_L001: $$(filter fastp_Illumina/$1_S1_L001,$$(FASTP_TAGS)) mkdir -p $$(dir $$@) @@ -43,7 +43,9 @@ define pf_smp_rule fastp_$1/$2_S1_L001: $$(filter raw_$1/$2_S1_L001,$$(MERGE_Salus) $$(MERGE_Illumina)) mkdir -p $$(dir $$@) micromamba run -n salus fastp --thread 4 -z 4 -A --max_len1 28 --max_len2 0 --dont_eval_duplication -q 20 -u 82 -n 4 --average_qual 20 --length_required 28 -y -Y 30 -g -x \ - -i $$<_R1_001.fastq.gz -I $$<_R2_001.fastq.gz -o $$@_R1_001.fastq.gz -O $$@_R2_001.fastq.gz -j $$@.json -h $$@.html 2>$$@.log + -i $$<_R1_001.fastq.gz -I $$<_R2_001.fastq.gz -o $$@_R1_001.fastp.gz -O $$@_R2_001.fastp.gz -j $$@.fastp.json -h $$@.fastp.html 2>$$@.fastp.log + micromamba run -n salus cutadapt -Z -j8 --pair-filter=any --minimum-length 28:50 --length 100 --times 0 --report full --json=$$@.cut.json \ + -o $$@_R1_001.cut.gz -p $$@_R2_001.cut.gz $$@_R1_001.fastp.gz $$@_R2_001.fastp.gz >$$@.cut.log touch $$@ endef $(foreach pf, $(PLATFORMS), $(foreach sample, $(SAMPLEID), $(eval $(call pf_smp_rule,$(pf),$(sample)))) ) -- 2.11.4.GIT