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Methods repository not accepting new Mutect2 WDL as a subworkflow

davidbendavidben BostonMember, Broadie, Dev ✭✭✭

I have a pipeline that runs Mutect2 as a subworkflow. The first line in the WDL imports the WDL used in the featured workspace:

import "https://raw.githubusercontent.com/gatk-workflows/gatk4-somatic-snvs-indels/2.6.0/mutect2.wdl" as m2

(Previously this was the 2.4.0/mutect2_nio.wdl version, which worked).

When I switched to this import (with no other change to the WDL) the methods repository gives the following error:

Error: Invalid WDL: Unrecognized token on line 445, column 42: samtools view -h -T ~{ref_fasta} ~{cram} | ^

Line 445, column 42 of the imported WDL is the tilde in ~{cram} inside a command block. The previous WDL in the featured workspace used a $ instead of a ~ here.

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