Closed hariszaf closed 1 year ago
@hariszaf
The changes don't break the wf. It produces an output almost similar. I did notice some small differences in the output.
These files are absent in the output:
sequence-categorisation:
- alpha_tmrna.rf01849.fasta.gz
- metazoa_srp.rf00017.fasta.gz
- tmrna.rf00023.fasta.gz
diff of the parameters yml files:
7d6
< count_faa_from_previous_run: null
9a9
> diamond_maxTargetSeqs: 1
diamond_maxTargeSeqs was changed, so the differences are the expected. Do you think it's normal these files to be absent?
Additional to a better documentation it also solve examples of pseudo paths for partial runs. I think this PR is a good improvement.
Great, i will remove the unused variable and once i commit and yiu run a test again we can merge.
Question: how long does it take to run the pipeline with the small data you added ?!
I will check the output difs you mentioned asap.
Question: how long does it take to run the pipeline with the small data you added ?!
This one took around 4 hours.
I will check the output difs you mentioned asap.
I also left a few comments on the commit, just referring to check if you notice then, but they are just suggestions
@jprmachado could you run your test case and merge if everything's fine? Thanks
Results of test . ├── fastp.html ├── final.contigs.fa ├── functional-annotation │ ├── stats │ │ ├── go.stats │ │ ├── interproscan.stats │ │ ├── ko.stats │ │ ├── orf.stats │ │ └── pfam.stats │ ├── test.merged_CDS.I5.tsv.chunks │ ├── test.merged_CDS.I5.tsv.gz │ ├── test.merged.hmm.tsv.chunks │ ├── test.merged.hmm.tsv.gz │ ├── test.merged.summary.go │ ├── test.merged.summary.go_slim │ ├── test.merged.summary.ips │ ├── test.merged.summary.ko │ └── test.merged.summary.pfam ├── merged_qc │ ├── GC-distribution.out.full │ ├── GC-distribution.out.full_bin │ ├── GC-distribution.out.full_pcbin │ ├── nucleotide-distribution.out.full │ ├── seq-length.out.full │ ├── seq-length.out.full_bin │ ├── seq-length.out.full_pcbin │ └── summary.out ├── qc_summary ├── RNA-counts ├── sequence-categorisation │ ├── 5_8S.fa.gz │ ├── LSU.fasta.chunks │ ├── LSU.fasta.gz │ ├── LSU_rRNA_archaea.RF02540.fa.gz │ ├── LSU_rRNA_bacteria.RF02541.fa.gz │ ├── LSU_rRNA_eukarya.RF02543.fa.gz │ ├── SSU.fasta.chunks │ ├── SSU.fasta.gz │ ├── SSU_rRNA_bacteria.RF00177.fa.gz │ ├── SSU_rRNA_eukarya.RF01960.fa.gz │ └── tRNA.RF00005.fasta.gz ├── taxonomy-summary │ ├── LSU │ │ ├── krona.html │ │ ├── test.merged_LSU.fasta.mseq.gz │ │ ├── test.merged_LSU.fasta.mseq_hdf5.biom │ │ ├── test.merged_LSU.fasta.mseq_json.biom │ │ ├── test.merged_LSU.fasta.mseq.tsv │ │ └── test.merged_LSU.fasta.mseq.txt │ └── SSU │ ├── krona.html │ ├── test.merged_SSU.fasta.mseq.gz │ ├── test.merged_SSU.fasta.mseq_hdf5.biom │ ├── test.merged_SSU.fasta.mseq_json.biom │ ├── test.merged_SSU.fasta.mseq.tsv │ └── test.merged_SSU.fasta.mseq.txt ├── test_1_fwd_HWLTKDRXY_600000 │ ├── GC-distribution.out.full │ ├── GC-distribution.out.full_bin │ ├── GC-distribution.out.full_pcbin │ ├── nucleotide-distribution.out.full │ ├── seq-length.out.full │ ├── seq-length.out.full_bin │ ├── seq-length.out.full_pcbin │ └── summary.out ├── test_1_fwd_HWLTKDRXY_600000.fastq.gz.sha1 ├── test_1_fwd_HWLTKDRXY_600000.fastq.trimmed.fasta ├── test_2_rev_HWLTKDRXY_600000 │ ├── GC-distribution.out.full │ ├── GC-distribution.out.full_bin │ ├── GC-distribution.out.full_pcbin │ ├── nucleotide-distribution.out.full │ ├── seq-length.out.full │ ├── seq-length.out.full_bin │ ├── seq-length.out.full_pcbin │ └── summary.out ├── test_2_rev_HWLTKDRXY_600000.fastq.gz.sha1 ├── test_2_rev_HWLTKDRXY_600000.fastq.trimmed.fasta ├── test.merged_CDS.faa ├── test.merged_CDS.ffn ├── test.merged.cmsearch.all.tblout.deoverlapped ├── test.merged.fasta ├── test.merged.motus.tsv └── test.merged.unfiltered_fasta
9 directories, 75 files
Any change in the output related with sequence-characterization might be associated with the parameter diamond_maxTargetSeqs: 1
IMO we could merge this PR and that will close the #15 since that change is already done here
Looks like everything's up-to-date.. weird :grinning:
This PR aims to provide descriptions of the arguments provided by the user though the
config.yml
file.