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Qualimap missing "-p" before $qualimap_direction #351

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zxl124 opened this issue Dec 4, 2019 · 1 comment

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zxl124 commented Dec 4, 2019

According to Qualimap documentation, the syntax for specifying read strandedness is "-p ". Current code is missing the "-p" part. Proposed change:

- qualimap --java-mem-size=${memory} rnaseq $qualimap_direction $paired -s -bam $bam -gtf $gtf -outdir ${bam.baseName}
+ qualimap --java-mem-size=${memory} rnaseq -p $qualimap_direction $paired -s -bam $bam -gtf $gtf -outdir ${bam.baseName}

FriederikeHanssen self-assigned this

FriederikeHanssen mentioned this issue

Add parameter -p to QualiMap #356

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ewels commented Dec 5, 2019

Fixed in #356

ewels closed this as completed

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