Preserve attributes of published files

[jjfarrell]

When PublishDir copies pairs of files such as (cram and cram.crai) and (vcf.gz and vcf.gz.tbi). the atributes of the files are not copied which includes the file creation time. Downstream software expects the index files (crai and tbi) to have a later time than the corresponding cram and vcf.gz files). To preserve the creation time of the files, the PublishDir code was modified to copy the files attributes which preserves the original file creation time. #1489 described the issue.

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[jjfarrell]

To test the changes, I modified tests/publish-dir.nf to add a sleep 1m between the creation of the bam and bai.

#!/usr/bin/env nextflow

process align {
    publishDir 'data', mode: 'copy'

    input:
    val(x)

    output:
    path("*.bam")
    path("${x}.bai")

    """
    echo ${x} > ${x}.bam
    sleep 1m
    echo ${x} | rev > ${x}.bai
    """
}

When running the test script without the PR, the published bam and bai files did not have the original file attributes and reflected the date of the asynchronous copy file creation. There is no 1m file difference between the bam and bai files. ls -lth data/

-rw-r--r-- 1 farrell cadre    6 Nov 19 10:20 delta.bam
-rw-r--r-- 1 farrell cadre    6 Nov 19 10:20 delta.bai
-rw-r--r-- 1 farrell cadre    6 Nov 19 10:20 alpha.bam
-rw-r--r-- 1 farrell cadre    6 Nov 19 10:20 alpha.bai
-rw-r--r-- 1 farrell cadre    5 Nov 19 10:20 beta.bai
-rw-r--r-- 1 farrell cadre    5 Nov 19 10:20 beta.bam

With the PR, the attributes were preserved with the 1m difference of the published bam and bai files. ls -lth data/

rw-r--r-- 1 farrell cadre    5 Nov 19 10:38 beta.bai
-rw-r--r-- 1 farrell cadre    6 Nov 19 10:38 delta.bai
-rw-r--r-- 1 farrell cadre    6 Nov 19 10:38 alpha.bai
-rw-r--r-- 1 farrell cadre    5 Nov 19 10:37 beta.bam
-rw-r--r-- 1 farrell cadre    6 Nov 19 10:37 delta.bam
-rw-r--r-- 1 farrell cadre    6 Nov 19 10:37 alpha.bam