Imogen's Maths A Tutor Group

How to get the path for the folder containing a bash script within the bash script:

# Get the directory where the script resides
SCRIPT_DIR="$(cd "$(dirname "$0")" && pwd)"
echo $SCRIPTDIR

How to gather and group all tuple elements in a NextFlow channel by the first and second indexes of each tuple, perform a process on a file containing the first and second indices, and then reform the original channel by scattering:

hc_ch = Channel.of(
    ['abc', 1, file('file1.txt')],
    ['abc', 1, file('file2.txt')],
    ['abc', 1, file('file3.txt')],
    ['def', 2, file('file4.txt')]
)

combinedChannel = hc_ch.groupTuple(by: [0, 1])

• Expected structure of combinedChannel:

[ ['abc', 1, [file('file1.txt'), file('file2.txt'), file('file3.txt')]],
['def', 2, [file('file4.txt')]]
]

process delete_txt {

    input:
    tuple val(id), val(sub_id), val(files) from combinedChannel

    output:
    tuple val(id), val(sub_id), val(files) into processedChannel

    script:
    """
    rm ${id}_${sub_id}.txt
    """
}

• Expected structure of processedChannel:

[ ['abc', 1, [file('file1.txt'), file('file2.txt'), file('file3.txt')]],
['def', 2, [file('file4.txt')]]
]

flattenedChannel = processedChannel.flatMap { id, sub_id, files -> files.collect { [id, sub_id, it] } }

• Expected structure of flattenedChannel:
  [ ['abc', 1, file('file1.txt')],
  ['abc', 1, file('file2.txt')],
  ['abc', 1, file('file3.txt')],
  ['def', 2, file('file4.txt')]
  ]

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