Increased resources for the Trinity module as this step often times out. This addresses Issue #12.
Trinity documentation suggests that for 1 M pairs of Illumina reads, you would need 1GB of memory and 0.5-1hr of time.
For estimation purposes, based on samples on NCBI's SRA, I would say 1 sample=~30M paired reads. To make an assembly from 6 samples, 180GB memory and 90-180 hrs would seem like a reasonable amount of resources to try out.
PR checklist
[X] This comment contains a description of changes (with reason).
[N/A] If you've fixed a bug or added code that should be tested, add tests!
[N/A] If you've added a new tool - have you followed the pipeline conventions in the contribution docs
[X] If necessary, also make a PR on the nf-core/denovotranscript branch on the nf-core/test-datasets repository.
[X] Make sure your code lints (nf-core lint).
[X] Ensure the test suite passes (nextflow run . -profile test,docker --outdir <OUTDIR>).
[X] Check for unexpected warnings in debug mode (nextflow run . -profile debug,test,docker --outdir <OUTDIR>).
[N/A] Usage Documentation in docs/usage.md is updated.
[N/A] Output Documentation in docs/output.md is updated.
[N/A] CHANGELOG.md is updated.
[N/A] README.md is updated (including new tool citations and authors/contributors).
Increased resources for the Trinity module as this step often times out. This addresses Issue #12.
Trinity documentation suggests that for 1 M pairs of Illumina reads, you would need 1GB of memory and 0.5-1hr of time. For estimation purposes, based on samples on NCBI's SRA, I would say 1 sample=~30M paired reads. To make an assembly from 6 samples, 180GB memory and 90-180 hrs would seem like a reasonable amount of resources to try out.
PR checklist
nf-core lint).nextflow run . -profile test,docker --outdir <OUTDIR>).nextflow run . -profile debug,test,docker --outdir <OUTDIR>).docs/usage.mdis updated.docs/output.mdis updated.CHANGELOG.mdis updated.README.mdis updated (including new tool citations and authors/contributors).