bt2n parameter for Bowtie2 not working when provided in params.json file

[IdoBar]

Check Documentation

I have checked the following places for your error:

• nf-core website: troubleshooting
• nf-core/eager pipeline documentation
  - nf-core/eager FAQ/troubleshooting can be found here

Description of the bug

Using "bt2n": "1" in the .json file doesn't work properly and produces an error message that the parameter is invalid.

Steps to reproduce

Steps to reproduce the behaviour:

1. Command line: nextflow run nf-core/eager -r 2.2.2 -params-file run.json -c awoonga.config
run.json includes the following:

...
"mapper": "bowtie2",
"bt2n": "1",
...

2. See error: error: invalid bowtie2 --bt2n (-N) parameter. Options: 0, 1. Found parameter: --bt2n 1.

Expected behaviour

The workflow should run and supply the -N 1 parameter to bowtie2 (it works as intended when provided in the CLI with --bt2n 1)

Log files

Have you provided the following extra information/files:

• The command used to run the pipeline
• The .nextflow.log file (see at bottom)
• The exact error: error: invalid bowtie2 --bt2n (-N) parameter. Options: 0, 1. Found parameter: --bt2n 1.

System

• Hardware: HPC
• Executor: PBSPro
• OS: RHEL
• Version Linux 3.10.0-693.5.2.el7.x86_64
• Runtime: Groovy 3.0.5 on OpenJDK 64-Bit Server VM 11.0.1+13-LTS

Nextflow Installation

• Version: 20.10.0 build 5430

Container engine

• Engine: Singularity
• version: 3.6.3
• Image tag: nfcore/eager:2.2.2

Additional context

.nextflow.log:

Jan.-10 23:24:31.584 [main] DEBUG nextflow.cli.Launcher - $> nextflow run nf-core/eager -r 2.2.2 -params-file Dingo_aDNA_NF5.CanFam3.1.bt2-local-N1.freebayes.json -c /home/ibar/.nextflow/awoonga.config
Jan.-10 23:24:31.778 [main] INFO  nextflow.cli.CmdRun - N E X T F L O W  ~  version 20.10.0
Jan.-10 23:24:34.107 [main] DEBUG nextflow.scm.AssetManager - Git config: /home/ibar/.nextflow/assets/nf-core/eager/.git/config; branch: master; remote: origin; url: https://github.com/nf-core/eager.git
Jan.-10 23:24:34.129 [main] DEBUG nextflow.scm.AssetManager - Git config: /home/ibar/.nextflow/assets/nf-core/eager/.git/config; branch: master; remote: origin; url: https://github.com/nf-core/eager.git
Jan.-10 23:24:34.532 [main] INFO  nextflow.cli.CmdRun - Launching `nf-core/eager` [loving_mccarthy] - revision: 85e2e3288a [2.2.2]
Jan.-10 23:24:36.034 [main] DEBUG nextflow.config.ConfigBuilder - Found config base: /home/ibar/.nextflow/assets/nf-core/eager/nextflow.config
Jan.-10 23:24:36.039 [main] DEBUG nextflow.config.ConfigBuilder - User config file: /home/ibar/.nextflow/awoonga.config
Jan.-10 23:24:36.039 [main] DEBUG nextflow.config.ConfigBuilder - Parsing config file: /home/ibar/.nextflow/assets/nf-core/eager/nextflow.config
Jan.-10 23:24:36.039 [main] DEBUG nextflow.config.ConfigBuilder - Parsing config file: /home/ibar/.nextflow/awoonga.config
Jan.-10 23:24:36.048 [main] DEBUG nextflow.config.ConfigBuilder - Applying config profile: `standard`
Jan.-10 23:24:37.751 [main] DEBUG nextflow.config.ConfigBuilder - Applying config profile: `standard`
Jan.-10 23:24:38.042 [main] DEBUG nextflow.Session - Session uuid: b50d1460-6ca0-4cea-af2e-249f4e36e45d
Jan.-10 23:24:38.042 [main] DEBUG nextflow.Session - Run name: loving_mccarthy
Jan.-10 23:24:38.042 [main] DEBUG nextflow.Session - Executor pool size: 2
Jan.-10 23:24:38.086 [main] DEBUG nextflow.cli.CmdRun -
  Version: 20.10.0 build 5430
  Created: 01-11-2020 15:14 UTC (02-11-2020 01:14 AEDT)
  System: Linux 3.10.0-693.5.2.el7.x86_64
  Runtime: Groovy 3.0.5 on OpenJDK 64-Bit Server VM 11.0.1+13-LTS
  Encoding: UTF-8 (UTF-8)
  Process: 58746@awoonga1.local [10.120.50.11]
  CPUs: 2 - Mem: 251.6 GB (12 GB) - Swap: 1000 MB (992.8 MB)
Jan.-10 23:24:38.106 [main] DEBUG nextflow.Session - Work-dir: /gpfs1/scratch/30days/ibar/data/Dingo/Dingo_aDNA_NF5_process_10_01_2021/work [gpfs]
Jan.-10 23:24:38.153 [main] DEBUG nextflow.Session - Observer factory: TowerFactory
Jan.-10 23:24:38.187 [main] DEBUG nextflow.Session - Observer factory: DefaultObserverFactory
Jan.-10 23:24:38.523 [main] DEBUG nextflow.Session - Session start invoked
Jan.-10 23:24:38.536 [main] DEBUG io.seqera.tower.plugin.TowerClient - Creating Tower observer -- endpoint=https://api.tower.nf; requestInterval=1s; aliveInterval=1m; maxRetries=5; backOffBase=3; backOffDelay=250
Jan.-10 23:24:39.848 [main] DEBUG nextflow.trace.TraceFileObserver - Flow starting -- trace file: /gpfs1/scratch/30days/ibar/data/Dingo/Dingo_aDNA_NF5_process_10_01_2021/results/pipeline_info/execution_trace.txt
Jan.-10 23:24:47.921 [main] DEBUG nextflow.script.ScriptRunner - > Launching execution
Jan.-10 23:24:47.936 [main] DEBUG nextflow.Session - Workflow process names [dsl1]: library_merge, genotyping_hc, output_documentation, eigenstrat_snp_coverage, nuclear_contamination, makeFastaIndex, convertBam, multivcfanalyzer, mtnucratio, genotyping_freebayes, lanemerge_hostremoval_fastq, hostremoval_input_fastq, makeSeqDict, genotyping_ug, makeBT2Index, bowtie2, adapter_removal, maltextract, bwa, malt, genotyping_angsd, kraken, vcf2genome, samtools_flagstat, unzip_reference, sex_deterrmine, bedtools, damageprofiler, seqtype_merge, fastqc_after_clipping, circularmapper, preseq, genotyping_pileupcaller, kraken_parse, samtools_flagstat_after_filter, indexinputbam, bam_trim, samtools_filter, print_nuclear_contamination, get_software_versions, bwamem, additional_library_merge, circulargenerator, multiqc, fastp, endorSpy, qualimap, kraken_merge, decomp_kraken, lanemerge, dedup, pmdtools, fastqc, makeBWAIndex, markduplicates
Jan.-10 23:24:48.144 [main] ERROR nextflow.Nextflow - [nf-core/eager] error: invalid bowtie2 --bt2n (-N) parameter. Options: 0, 1. Found parameter: --bt2n 1.

[jfy133]

Thanks @IdoBar for the report! Following up with nf-core first (https://nfcore.slack.com/archives/CUC8PPDL2/p1610343655159600) but should be pretty straightforward fix if my suspicion is correct.

[jfy133]

Ok, indeed my suspicion was correct but goes deeper than I thought: nf-core/tools#823

I will need to manually go through and fix our parameter schema (not hard, but will take a bit of time). Will do this in the patch release with the readgroup issue in #655

[jfy133]

@IdoBar in the meantime I'm your Params.json you can just remove the quotes around the 1 and it should work.