Fix auto pairing for compressed file handling.

      forward: input_R1.fastq

      reverse: input_R2.fastq

- doc: Compressed _R1 _R2 fastqs split.

  inputs:

  - input_R1.fastq.gz

  - input_R2.fastq.gz

  paired:

    input:

      forward: input_R1.fastq.gz

      reverse: input_R2.fastq.gz

- doc: Joining common prefixes on _R1 _R2.

  inputs:

  - input541_R1.fastq

      forward: input.1.fastq

      reverse: input.2.fastq

- doc: Simple .1.fastq.gz/.2.fastq.gz split.

  inputs:

  - input.1.fastq.gz

  - input.2.fastq.gz

  paired:

    input:

      forward: input.1.fastq.gz

      reverse: input.2.fastq.gz

- doc: Simple _1/_2 split.

  inputs:

  - input_1.fastq

    input:

      forward: input_1.fastq

      reverse: input_2.fastq

- doc: Simple _1/_2 split on compressed files (.gz)

  inputs:

  - input_1.fastq.gz

  - input_2.fastq.gz

  paired:

    input:

      forward: input_1.fastq.gz

      reverse: input_2.fastq.gz

- doc: Simple _1/_2 split on compressed files (.bz2)

  inputs:

  - input_1.fastq.bz2

  - input_2.fastq.bz2

  paired:

    input:

      forward: input_1.fastq.bz2

      reverse: input_2.fastq.bz2

    if (willRemoveExtensions) {

        const lastDotIndex = lcs.lastIndexOf(".");

        if (lastDotIndex > 0) {

            const extension = lcs.slice(lastDotIndex, lcs.length);

            let extension = lcs.slice(lastDotIndex, lcs.length);

            if ([".gz", ".bz", ".bzip", ".bz2"].indexOf(extension) !== -1) {

                const secondLastDotIndex = lcs.lastIndexOf(".", lastDotIndex - 1);

                if (secondLastDotIndex > 0) {

                    extension = lcs.slice(secondLastDotIndex, lcs.length);

                }

            }

            lcs = lcs.replace(extension, "");

            fwdName = fwdName.replace(extension, "");

            revName = revName.replace(extension, "");