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fix log output
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@alienzj
alienzj committed Aug 22, 2023
1 parent c4be6ed commit 2f52530
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Showing 2 changed files with 18 additions and 26 deletions.
4 changes: 2 additions & 2 deletions metapi/rules/binning_multisplit.smk
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Original file line number Diff line number Diff line change
Expand Up @@ -214,7 +214,7 @@ rule binning_vamb_align_scaftigs:
-m 3G -@4 \
-T $OUTPE/temp \
-O BAM \
-o $OUTPE/sorted.bam 2>> {log}
-o $OUTPE/sorted.bam
fi
if [ "$RS" != "" ];
Expand All @@ -237,7 +237,7 @@ rule binning_vamb_align_scaftigs:
-m 3G -@4 \
-T $OUTSE/temp \
-O BAM \
-o $OUTSE/sorted.bam 2>> {log}
-o $OUTSE/sorted.bam
fi
if [ -s $OUTPE/sorted.bam ] && [ -s $OUTSE/sorted.bam ];
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40 changes: 16 additions & 24 deletions metapi/rules/rmhost.smk
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Original file line number Diff line number Diff line change
Expand Up @@ -101,7 +101,7 @@ if config["params"]["rmhost"]["bwa"]["do"]:
-k {params.minimum_seed_length} \
-t {threads} \
{params.index_prefix} \
$R1 $R2 | \
$R1 $R2 2> {log} | \
tee >(samtools flagstat \
-@4 - > $STATSPE) | \
tee >(samtools fastq \
Expand All @@ -114,23 +114,21 @@ if config["params"]["rmhost"]["bwa"]["do"]:
-m 3G \
-@4 \
-T {params.pe_bam_dir}/temp \
-O BAM -o $BAM - \
2> {log}
-O BAM -o $BAM -
else
{params.bwa} mem \
-k {params.minimum_seed_length} \
-t {threads} \
{params.index_prefix} \
$R1 $R2 | \
$R1 $R2 2> {log} | \
tee >(samtools flagstat \
-@4 - > $STATSPE) | \
samtools fastq \
-@4 \
-c {params.compression} \
-N -f 12 -F 256 \
-1 $FQ1 \
-2 $FQ2 - \
2> {log}
-2 $FQ2 -
fi
fi
Expand All @@ -151,7 +149,7 @@ if config["params"]["rmhost"]["bwa"]["do"]:
-k {params.minimum_seed_length} \
-t {threads} \
{params.index_prefix} \
$RS | \
$RS 2>> {log} | \
tee >(samtools flagstat \
-@4 - > $STATSSE) | \
tee >(samtools fastq \
Expand All @@ -164,23 +162,21 @@ if config["params"]["rmhost"]["bwa"]["do"]:
-m 3G \
-@4 \
-T {params.se_bam_dir}/temp \
-O BAM -o $BAM - \
2>> {log}
-O BAM -o $BAM -
else
{params.bwa} mem \
-k {params.minimum_seed_length} \
-t {threads} \
{params.index_prefix} \
$RS | \
$RS 2>> {log} | \
tee >(samtools flagstat \
-@4 - > $STATSSE) | \
samtools fastq \
-@4 \
-c {params.compression} \
-N -f 4 -F 256 - | \
pigz -cf -p {threads} \
> $FQS \
2>> {log}
> $FQS
fi
fi
Expand Down Expand Up @@ -490,7 +486,7 @@ if config["params"]["rmhost"]["minimap2"]["do"]:
-t {threads} \
-ax {params.preset} \
{input.index} \
$R1 $R2 | \
$R1 $R2 2> {log} | \
tee >(samtools flagstat \
-@4 - > $STATSPE) | \
tee >(samtools fastq \
Expand All @@ -503,23 +499,21 @@ if config["params"]["rmhost"]["minimap2"]["do"]:
-m 3G \
-@4 \
-T {params.pe_bam_dir}/temp \
-O BAM -o $BAM - \
2> {log}
-O BAM -o $BAM -
else
minimap2 \
-t {threads} \
-ax {params.preset} \
{input.index} \
$R1 $R2 | \
$R1 $R2 2> {log} | \
tee >(samtools flagstat \
-@4 - > $STATSPE) | \
samtools fastq \
-@4 \
-c {params.compression} \
-N -f 12 -F 256 \
-1 $FQ1 \
-2 $FQ2 - \
2> {log}
-2 $FQ2 -
fi
fi
Expand All @@ -539,7 +533,7 @@ if config["params"]["rmhost"]["minimap2"]["do"]:
minimap2 \
-t {threads} \
{input.index} \
$RS | \
$RS 2> {log} | \
tee >(samtools flagstat \
-@4 - > $STATSSE) | \
tee >(samtools fastq \
Expand All @@ -552,22 +546,20 @@ if config["params"]["rmhost"]["minimap2"]["do"]:
-m 3G \
-@4 \
-T {params.se_bam_dir}/temp \
-O BAM -o $BAM - \
2> {log}
-O BAM -o $BAM -
else
minimap2 \
-t {threads} \
{input.index} \
$RS | \
$RS 2> {log} | \
tee >(samtools flagstat \
-@4 - > $STATSSE) | \
samtools fastq \
-@4 \
-c {params.compression} \
-N -f 4 -F 256 - | \
pigz -cf -p {threads} \
> $FQS \
2> {log}
> $FQS
fi
fi
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