FIxedInputStream raises false error when reading only part of a file

[bentsherman]

FixedInputStream was added to detect truncated files:

nextflow/modules/nf-httpfs/src/main/nextflow/file/http/FixedInputStream.groovy

Lines 67 to 72 in 324de3d

	@Override
	void close() throws IOException {
	if( bytesRead != length )
	throw new IOException("Read data length does not match expected size - bytes read: ${bytesRead}; expected: ${length}")
	super.close()
	}

However this does not handle the case where only part of a file is read. Consider this example from sarek:

// Get first line of a FASTQ file
def readFirstLineOfFastq(path) {
    def line = null
    try {
        path.withInputStream {
            InputStream gzipStream = new java.util.zip.GZIPInputStream(it)
            Reader decoder = new InputStreamReader(gzipStream, 'ASCII')
            BufferedReader buffered = new BufferedReader(decoder)
            line = buffered.readLine()
            assert line.startsWith('@')
        }
    } catch (Exception e) {
        log.warn "FASTQ file(${path}): Error streaming"
        log.warn "${e.message}"
    }
    return line
}

It will log this error every time:

Read data length does not match expected size - bytes read: 2756; expected: 16013759

cc @maxulysse

[pditommaso]

Related to #5275 and #5214

[pditommaso]

Solved by #5405