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samtools sort overwrites #328

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bounlu opened this issue Jun 21, 2023 · 1 comment · Fixed by #414
Closed

samtools sort overwrites #328

bounlu opened this issue Jun 21, 2023 · 1 comment · Fixed by #414
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@bounlu
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bounlu commented Jun 21, 2023

I want to extract deduplicated and sorted bam file from the pipeline by using the Bismark aligner.

When I use --save_align_intermeds flag, SAMTOOLS_SORT module writes the sorted bam file to the output directory as per this config:

    withName: SAMTOOLS_SORT {
        ext.prefix = { "${meta.id}.sorted" }
        publishDir = [
            [
                path: { "${params.outdir}/${params.aligner}/deduplicated/" },
                mode: params.publish_dir_mode,
                pattern: "*markdup*.bam",
                enabled: params.save_align_intermeds
            ],
            [
                path: { "${params.outdir}/${params.aligner}/alignments/" },
                mode: params.publish_dir_mode,
                pattern: "*.bam",
                enabled: params.save_align_intermeds
            ]
        ]
    }

However, SAMTOOLS_SORT is used twice with alias in the BISMARK workflow, one is before and one is after deduplication. The sorted file before deduplication is saved, then the sorted file after deduplication is overwritten. This is because both files use identical filename after sorting due to the same prefix. This redundancy should be avoided by adding .deduplicated.sorted. for the latter.

Moreover, the overwritten file is written to the wrong folder /alignments/ instead of /deduplicated/.

@bounlu bounlu added the bug Something isn't working label Jun 21, 2023
@sateeshperi sateeshperi self-assigned this Sep 21, 2024
@sateeshperi sateeshperi added this to the 2.7.0 milestone Sep 21, 2024
@sateeshperi sateeshperi linked a pull request Sep 21, 2024 that will close this issue
@sateeshperi
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hey @bounlu Thanks for reporting this. I just put in some fixes based on your suggestion to the linked branch

If you could give it a look and lmk if the samtools sort is as expected now 🙏

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