Add task for bowtie aligner

Created by: johnmous

bowtie.wdl

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

[Ruben Vorderman]

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

[Ruben Vorderman]

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.

[Ruben Vorderman]

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).

[Ruben Vorderman]

Created by: DavyCats

No directory name is given here

[Ruben Vorderman]

Which dir are you creating here? I always use mkdir -p $(dirname ${sam}) to make sure any file creation attempts with the > sign work.

[Ruben Vorderman]

you forgot a \ here. Also otherOptions should preferably be removed

[Ruben Vorderman]

Created by: DavyCats

Isn't it possible to make a generic bowtie task for both paired and single end?

[Ruben Vorderman]

Bowtie_pe -> pe

[Ruben Vorderman]

Created by: johnmous

I could give it a try

[Ruben Vorderman]

See comments above

[Ruben Vorderman]

see comments above

[Ruben Vorderman]

| -> \