missing output or inconsisted output when rersubmit jobs on SLURM

[henryone0910]

Bug report

I ran a nextflow pipeline with command:
nextflow main.nf -c main.config -entry Workflow -resume

And I configured the process in modules.conf in conf folder, here are some examples:

process {

    publishDir = [
        path: "${params.outdir}",
        mode: params.publish_dir_mode,
        saveAs: { filename -> savefile(filename) }
    ]

    withName:FASTQC {
        publishDir = [
            path: { "${params.outdir}/fastqc" },
            mode: params.publish_dir_mode,
            saveAs: { filename -> savefile(filename) }
        ]
    }

    withName: BBMAP_TRIM {
        publishDir = [
            path: { "${params.outdir}/trim" },
            mode: params.publish_dir_mode,
            saveAs: { filename -> savefile(filename) }
        ]
        ext.args = "minlen=30 trimq=20"
    }

    withName:BWA_ALIGN {
        publishDir = [
            path: { "${params.outdir}/map" },
            mode: params.publish_dir_mode,
            saveAs: { filename -> savefile(filename) }
        ]
    }
}

def savefile (filename) {

    c1 = filename.endsWith('versions.yml')
    c2 = filename.endsWith('mqc.yml')
    c3 = filename.endsWith('.bam')
    c4 = filename.endsWith('.bai')
    c5 = filename.endsWith('.fastq.gz')
    c6 = filename.endsWith('multiqc_citations.txt')
    c7 = filename.endsWith('multiqc_sources.txt')
    c8 = filename.endsWith('Rplots.pdf')
    res = c1 || c2 || c5 || c6 || c7 || c8 ? null : filename
    // res = c1 || c2 || c3 || c4 || c5 || c6 || c7 ? filename : null
    return res
}

def savenull (filename) {
    return null
}

with params.publish_dir_mode='copy' .

Expected behavior and actual behavior

The output should be in 3 folders: fastqc, trim and map.

• fastqc: zip and HTML files.
• trim: log files.
• map: bam files.

But the actual outputs I saw when I reran were irregular and did not follow any rules. E.g: bam files published into trim and log published into map,... or any other folders.

Steps to reproduce the problem

The pipeline was published normally into the output folder only if I run it first and no errors occurred. If not, when I reran it, the files did not publish into the right folders.

• Nextflow version: 23.04.10 and upper.
• Java version: unkown.
• Operating system: CentOS Stream 8
• • Bash version: GNU bash, version 4.4.20(1)-release (x86_64-redhat-linux-gnu)

Additional context

[bentsherman]

Hard to say without seeing your pipeline code. Can you provide a minimal reproducible example?