Switch to DSL 2

[skrakau]

No description provided.

[skrakau]

Remaining todos:

• Clean up usage of meta vs. other fields
• Fix problem that combination of meta and assembly seems to get mixed up in BOWTIE2_INDEX_ASSEMBLY ???
• Compare results to latest DSL1 version
• Make process names more consistent
• tool names used for collection of software version, when used in multiple process ?
• Update output.md and README etc.
• Update CHANGELOG
• Update nf-core/test-datasets
• Check recent structure of workflow directory that should be used
• Use new nf-core fastp module
• Run and check full-size test (different CAT DB, so slightly different results)
• Solve CAT db problem or check alternatives
• Check params printed to summary, inconsistently at the moment (printed if value from nextflow_schema.json does not match default given in nextflow.config, default type in schema does need to match type)
• Check caching
• Handle nextflow - S3 problem for full-size test: newer version need extra nf-amazon plugin loaded, various issues currently on CFC(will be addressed with next nextflow release)
• Generalize modules where possible and port to nf-core/modules (-> Generalize modules where possible and port to nf-core/modules #169)

[skrakau]

The current CAT BioContainer does not work with the latest CAT database, because of different Diamond versions (see #90). However, just creating a new BioContainer with the according Diamond version does not solve such issues for the future: see MGXlab/CAT_pack#54

Need to think about alternatives, if there will be no solution.

[skrakau]

Use of nf-amazon plugin for full-size test with recent nextflow edge versions: see nextflow-io/nextflow#1964

[skrakau]

CAT BioContainer is updated and works now for current CAT database (tbb.bio.uu.nl/bastiaan/CAT_prepare/CAT_prepare_20210107.tar.gz). Log term maintenance will be handled separately.

[skrakau]

Solved in #162 , #171

[gailrosen]

pipeline_report.txt
software_versions.csv

I don't know why, but I still get this error. [2021-05-07 14:21:46.114194] 47 bin(s) found!

Command error:
Error: Database was built with a different version of Diamond and is incompatib
le.
[2021-05-07 14:34:47.300571] ERROR: DIAMOND finished abnormally.

Work dir:
/ifs/groups/eces450650Grp/data/Assembly_Binning_old/work/81/95fee99d939f76a9ae3
1784c62007d

Tip: you can replicate the issue by changing to the process work dir and entering
the command bash .command.run

The workflow was completed at 2021-05-07T14:47:11.875034-
04:00 (duration: 1h 4m 7
s)

The command used to launch the workflow was as follows:

nextflow run nf-core/mag -resume -profile singularity --input 'CSJP002A_{R1,R2}
.fastq.gz' -c nextflow.config --max_memory 186.GB --max_cpus 20 --kraken2_db k2_p
luspf_20210127.tar.gz --cat_db CAT_prepare_20210107.tar.gz --outdir results_cat