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srst2v2.xml |
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| diff -r 6787d952242e -r 8bf4865cc3e3 srst2v2.xml --- a/srst2v2.xml Sun May 19 07:36:55 2019 -0400 +++ b/srst2v2.xml Sun May 19 10:07:05 2019 -0400 |
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| @@ -3,21 +3,44 @@ <requirement type="package" version="0.2.0">srst2</requirement> </requirements> <command detect_errors="exit_code"><![CDATA[ + #if $paired_conditional.sPaired == "paired" - ln -s $paired_conditional.fastq1 sample_1.fastq; - ln -s $paired_conditional.fastq2 sample_2.fastq; + #if $paired_conditional.fastq1.is_of_type("fastq.gz") + zcat $paired_conditional.fastq1 > sample_1.fastq; + zcat $paired_conditional.fastq2 > sample_2.fastq; + #else if $paired_conditional.fastq1.is_of_type("fastqsanger.gz") + zcat $paired_conditional.fastq1 > sample_1.fastq; + zcat $paired_conditional.fastq2 > sample_2.fastq; + #else + ln -s $paired_conditional.fastq1 sample_1.fastq; + ln -s $paired_conditional.fastq2 sample_2.fastq; + #end if #else if $paired_conditional.sPaired == "paired_coll" - ln -s $paired_conditional.coll.forward sample_1.fastq; - ln -s $paired_conditional.coll.reverse sample_2.fastq; + #if $paired_conditional.coll.forward.is_of_type("fastq.gz") + zcat $paired_conditional.coll.forward > sample_1.fastq; + zcat $paired_conditional.coll.reverse > sample_2.fastq; + #else if $paired_conditional.coll.forward.is_of_type("fastqsanger.gz") + zcat $paired_conditional.coll.forward > sample_1.fastq; + zcat $paired_conditional.coll.reverse > sample_2.fastq; + #else + ln -s $paired_conditional.coll.forward sample_1.fastq; + ln -s $paired_conditional.coll.reverse sample_2.fastq; + #end if + #else if $paired_conditional.sPaired == "single" + #if $paired_conditional.fastq1.is_of_type("fastq.gz") + zcat $paired_conditional.fastq1 > sample_1.fastq; + #else if $paired_conditional.fastq1.is_of_type("fastqsanger.gz") + zcat $paired_conditional.fastq1 > sample_1.fastq; + #else + ln -s $paired_conditional.fastq1 sample_1.fastq; + #end if #end if srst2 #if $paired_conditional.sPaired == "single" - --input_se $paired_conditional.fastq1 - #else if $paired_conditional.sPaired == "paired" - --input_pe sample_1.fastq sample_2.fastq - #else if $paired_conditional.sPaired == "paired_coll" + --input_se sample_1.fastq1 + #else --input_pe sample_1.fastq sample_2.fastq #end if |