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Add task for bowtie aligner

Closed Ruben Vorderman requested to merge Bowtie into master
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bowtie.wdl 0 → 100644
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task Bowtie_se {
    • bowtie.wdl will be imported as bowtie by default. Which means these tasks are called as bowtie.Bowtie_se. I propose that you change this to just task se { the task can then be called as bowtie.se

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File reference
File read1
String sam
String? precommand
Int? threads
    • You added threads here, but did not include a runtime section that uses the threads.

      runtime {
        cpu: ${default=1 threads}
      }

      You can also set the default here

        Int? threads = 1

      Which looks cleaner. And then use:

      runtime {
        cpu: select_first([threads])
      }

      But I have had issues with overriding this default from the config file. I should file a bug for that.

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String? otherOptions
    • I disagree with other options. If other options are required, another pull request should be made. Or alternatively, the entire command should be written out (which will take a lot of time, so may not be the best option for now).

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command {
## https://vaneyckt.io/posts/safer_bash_scripts_with_set_euxo_pipefail/
set -eo pipefail
mkdir -p
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${precommand}
bowtie \
${otherOptions}
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${"--threads" + threads} \
${reference} \
${read1} > \
${sam}
}
}
task Bowtie_pe {
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File reference
File read1
File read2
String sam
String? precommand
Int? threads
String? otherOptions
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command {
set -eo pipefail
mkdir -p
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${precommand}
bowtie \
${"--threads" + threads} \
${reference} \
-1 ${read1} |
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-2 ${read2}> \
${sam}
}
}
\ No newline at end of file
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