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OpenOmics / metamorph

Metagenomics and Metatranscriptomics pipeline
https://openomics.github.io/metamorph/
MIT License
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Metawrap workflow through genome assembly (per-sample) #5

Closed rroutsong closed 10 months ago

rroutsong commented 10 months ago

Piecewise PR containing the workflow (on a per-sample basis) up to genome assembly.

Dry run output:

localrule all:
    input: /data/NHLBI_IDSS/dev/metamorph/pipeline/metawrap_readqc/Control.dna101/Control.dna101.R1_bmtagger_report.html, /data/NHLBI_IDSS/dev/metamorph/pipeline/metawrap_readqc/Control.dna101/Control.dna101.R2_bmtagger_report.html, /data/NHLBI_IDSS/dev/metamorph/pipeline/Control.dna101.R1_readqc.fastq.gz, /data/NHLBI_IDSS/dev/metamorph/pipeline/Control.dna101.R2_readqc.fastq.gz, /data/NHLBI_IDSS/dev/metamorph/pipeline/metawrap_assembly/Control.dna101/final_assembly.fasta, /data/NHLBI_IDSS/dev/metamorph/pipeline/metawrap_assembly/Control.dna101/assembly_report.html
    jobid: 0
    reason: Input files updated by another job: /data/NHLBI_IDSS/dev/metamorph/pipeline/metawrap_assembly/Control.dna101/assembly_report.html, /data/NHLBI_IDSS/dev/metamorph/pipeline/metawrap_readqc/Control.dna101/Control.dna101.R2_bmtagger_report.html, /data/NHLBI_IDSS/dev/metamorph/pipeline/metawrap_assembly/Control.dna101/final_assembly.fasta, /data/NHLBI_IDSS/dev/metamorph/pipeline/Control.dna101.R1_readqc.fastq.gz, /data/NHLBI_IDSS/dev/metamorph/pipeline/Control.dna101.R2_readqc.fastq.gz, /data/NHLBI_IDSS/dev/metamorph/pipeline/metawrap_readqc/Control.dna101/Control.dna101.R1_bmtagger_report.html
    resources: tmpdir=/lscratch/7086074

Job stats:
job                         count    min threads    max threads
------------------------  -------  -------------  -------------
all                             1              1              1
metawrap_genome_assembly        1             24             24
metawrap_read_qc                1             24             24
total                           3              1             24

Reasons:
    (check individual jobs above for details)
    input files updated by another job:
        all, metawrap_genome_assembly
    missing output files:
        metawrap_genome_assembly, metawrap_read_qc

This was a dry-run (flag -n). The order of jobs does not reflect the order of execution.