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Feature/samtools sort after STAR

Merged Feature/samtools sort after STAR
feature/samtools-sort into dev
1 unresolved thread
Merged BIOPZ-Gypas Foivos requested to merge feature/samtools-sort into dev
1 unresolved thread

Sort alignment files with SAMtools instead of STAR. Fixes #182 (closed)

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  • BIOPZ-Gypas Foivos
    BIOPZ-Gypas Foivos @gypas ·
    Author Maintainer

    @katsanto @herrmchr @bakma Do you think these changes are enough?

  • BIOPZ-Bak Maciej
  • BIOPZ-Bak Maciej
  • BIOPZ-Gypas Foivos added 1 commit

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  • BIOPZ-Katsantoni Maria
    BIOPZ-Katsantoni Maria @katsanto started a thread on an old version of the diff
    • workflow/Snakefile
    651 "samples",
    652 "{sample}",
    653 "map_genome",
    654 "{sample}.{seqmode}.Aligned.out.bam"),
    655
    656 output:
    657 bam = os.path.join(
    658 config["output_dir"],
    659 "samples",
    660 "{sample}",
    661 "map_genome",
    662 "{sample}.{seqmode}.Aligned.sortedByCoord.out.bam"),
    663
    664 params:
    665 cluster_log_path = config["cluster_log_dir"],
    666 prefix_temp = os.path.join(
  • BIOPZ-Bak Maciej
  • BIOPZ-Gypas Foivos added 1 commit

    added 1 commit

    • 2201efc0 - Update pipeline documentation. Add temp directory for samtools sort

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  • BIOPZ-Gypas Foivos added 1 commit

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  • BIOPZ-Gypas Foivos added 1 commit

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  • BIOPZ-Gypas Foivos added 1 commit

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  • BIOPZ-Gypas Foivos added 4 commits

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  • BIOPZ-Gypas Foivos
    BIOPZ-Gypas Foivos @gypas ·
    Author Maintainer

    @katsanto @bakma I think it's finally ready. Can you please check once more?

  • BIOPZ-Bak Maciej approved this merge request

    approved this merge request

  • BIOPZ-Gypas Foivos mentioned in commit 78ad9aaf

    mentioned in commit 78ad9aaf

  • BIOPZ-Gypas Foivos merged

    merged

  • BIOPZ-Bak Maciej mentioned in issue #182 (closed)

    mentioned in issue #182 (closed)

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