Preprocessing: extra files in repository

[elimoss]

I've looked over the preprocessing repository, and there appears to be quite a bit of extraneous files and directories in the repository. Also, I'm not too sure which preprocessing*.nf file is the current workflow. To address this, please do the following and let me know so I can check it over again:

• use git rm to remove files which are not code that you have written or other materials needed to run the pipeline. In particular, the .nextflow folder and .nextflow.log.* files should be removed.
• use git mv to move the file containing the current workflow to h3ameta/preprocessing/preprocessing.nf, and remove the other similar files. That way it will be clear which file we should look at.

Please let me know if you have any questions about this : )

[elimoss]

whoop, side issue, adeyemi and abdul don't have github accounts, so i can't assign you to this issue! I'll follow up on Slack and get you on board.

[Rahmmy]

Hello Eli,
Thanks for your support yesterday. All redundant files have been removed and working files moved to the requested location. The h3ameta/preprocessing/preprocessing.nf is our working nextflow script sheet.

[Rahmmy]

so my issue is that there is a # in my trimmomatic script (preprocessing.nf) which nextflow rather identity's as an error.... Any suggestions please?

[Rahmmy]

The processes I'm running is

_process runTrimmomatic{

   input: file in_file 
    output:
    file("results") into step3_ch
     publishDir "results/TrimmedData"

    script:
    """
     #!/bin/bash

     input="/home/abdulrahman/h3ameta/preprocessing/quality_control"
     for i in $input/*_1.fq.gz;
     do
     withpath="${i}"
     filename=${withpath**#**#/}
     base="${filename%*_*.fq.gz}"
     sample_name=`echo "${base}" | awk -F ".fastq.gz" '{print $1}'`
     java -jar /home/abdulrahman/h3ameta/preprocessing/Trimmomatic-0.38/trimmomatic-0.38.jar PE -threads 6 -trimlog $output/"${base}".log $input/"${base}"_1.fq.gz  $input/"${base}"_2.fq.gz $output/"${base}"_R1.trimmed_PE.fastq $output/"${base}"_R1.trimmed_SE.fastq $output/"${base}"_2.trimmed_PE.fastq $output/"${base}"_2.trimmed_SE.fastq LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:20

     done
    """
    }_

Nextflow fails to recognize the highlighted # in the line starting with filename

The specific error is:
_ERROR ~ unexpected char: '#' @ line 56, column 29.
filename=${withpath##/}
^

1 error
_

[elimoss]

What's the intended behavior? I'm not too sure what the # is supposed to do--is this a string operator I'm not familiar with?