Fixed hisat2/align/main.nf: perl script manipulation via sed replacement in HISAT2_ALIGN/main.nf to set /tmp to ./tmp

[a1ultima]

Description of changes:

Configured perl wrappers that issue the Hisat2 program, via sed replacements in:

example-workflows/nf-core/workflows/rnaseq/modules/nf-core/hisat2/align/main.nf

From both instances of:

        """
        INDEX=`find -L ./ -name "*.1.ht2*" | sed 's/\\.1.ht2.*\$//'`
        hisat2 \\

To:

        """
        mkdir -p "./tmp"
        chmod 700 "./tmp"
        ls "./tmp"
        sed -i 's|temp_dir = "/tmp";|temp_dir = "./tmp";|g' /usr/local/bin/hisat2
        INDEX=`find -L ./ -name "*.1.ht2*" | sed 's/\\.1.ht2.*\$//'`
        hisat2 \\

Effect: Re-configuring default: From:

/tmp 

To:

./tmp.

Since, ./tmp has more disk capacity (aws omics run --storage-capacity <num>) than /tmp (~20-40 GiB) ⇒ run failure case space << before.

Kudos: @markjschreiber

[a1ultima]

I must correct my description of the patch:

We dont change the ~/tmp, but the /tmp --> ./tmp