invalid file type: 'fastq'

[jkneppers]

Description of the bug

Hi,

I'm trying to run oncoanalyser for the first time. I am using the test samplesheet.csv, which specifies dummy fastq.gz files for normal and tumor DNA, and RNA. These are categorized as 'fastq' in the filetype column.

However, after running the command below, I'm getting the output invalid file type: 'fastq'.

I am currently bound to nextflow version v22.04.3, this could be an issue as it is incompatible with the dev version, but I am getting nextflow outputs for -r v0.3.1. Am I missing something else?

Thanks,
J

Command used and terminal output

nextflow run nf-core/oncoanalyser \
  -profile docker \
  -revision v0.3.1 \
  --mode wgts \
  --genome GRCh37_hmf \
  --input /path/wgs/samplesheet.csv \
  --outdir /path/wgs/result_calls/

Relevant files

Aug-20 13:41:48.355 [main] DEBUG nextflow.cli.Launcher - $> nextflow run nf-core/oncoanalyser -profile docker -revision v0.3.1 --mode wgts --genome GRCh37_hmf --input /path/N2N_mock/wgs/samplesheet.csv --outdir /path/N2N_mock/wgs/result_calls/ -resume
Aug-20 13:41:48.460 [main] INFO nextflow.cli.CmdRun - N E X T F L O W ~ version 22.04.3
Aug-20 13:41:49.892 [main] DEBUG nextflow.scm.AssetManager - Git config: /home/crunchshell/.nextflow/assets/nf-core/oncoanalyser/.git/config; branch: master; remote: origin; url: https://github.com/nf-core/oncoanalyser.git
Aug-20 13:41:49.906 [main] DEBUG nextflow.scm.AssetManager - Git config: /home/crunchshell/.nextflow/assets/nf-core/oncoanalyser/.git/config; branch: master; remote: origin; url: https://github.com/nf-core/oncoanalyser.git
Aug-20 13:41:50.652 [main] DEBUG nextflow.config.ConfigBuilder - Found config base: /home/crunchshell/.nextflow/assets/nf-core/oncoanalyser/nextflow.config
Aug-20 13:41:50.653 [main] DEBUG nextflow.config.ConfigBuilder - Parsing config file: /home/crunchshell/.nextflow/assets/nf-core/oncoanalyser/nextflow.config
Aug-20 13:41:50.664 [main] DEBUG nextflow.config.ConfigBuilder - Applying config profile: docker
Aug-20 13:41:50.983 [main] DEBUG nextflow.plugin.PluginsFacade - Using Default plugins manager
Aug-20 13:41:51.000 [main] INFO org.pf4j.DefaultPluginStatusProvider - Enabled plugins: []
Aug-20 13:41:51.001 [main] INFO org.pf4j.DefaultPluginStatusProvider - Disabled plugins: []
Aug-20 13:41:51.005 [main] INFO org.pf4j.DefaultPluginManager - PF4J version 3.4.1 in 'deployment' mode
Aug-20 13:41:51.010 [main] DEBUG nextflow.plugin.PluginsFacade - Using Default plugins manager
Aug-20 13:41:51.860 [main] DEBUG nextflow.config.ConfigBuilder - Available config profiles: [bih, cfc_dev, uzl_omics, ifb_core, embl_hd, denbi_qbic, alice, mjolnir_globe, uppmax, incliva, ilifu, uge, rosalind_uge, lugh, mccleary, unibe_ibu, vai, czbiohub_aws, jax, ccga_med, scw, unc_longleaf, tigem, tubingen_apg, google, apollo, ipop_up, vsc_calcua, pdc_kth, googlels, daisybio, eddie, medair, biowulf, bi, bigpurple, adcra, cedars, pawsey_setonix, vsc_kul_uhasselt, pawsey_nimbus, ucl_myriad, utd_ganymede, charliecloud, icr_davros, ceres, munin, rosalind, hasta, cfc, uzh, ebi_codon_slurm, ebc, ccga_dx, crick, ku_sund_danhead, marvin, biohpc_gen, shifter, mana, mamba, york_viking, unc_lccc, wehi, awsbatch, wustl_htcf, arcc, imperial, maestro, software_license, genotoul, nci_gadi, abims, janelia, nu_genomics, googlebatch, oist, sahmri, mpcdf, leicester, vsc_ugent, create, sage, cambridge, jex, podman, ebi_codon, cheaha, xanadu, nyu_hpc, test, marjorie, computerome, ucd_sonic, seg_globe, sanger, dkfz, pasteur, einstein, ethz_euler, m3c, test_full, imb, ucl_cscluster, tuos_stanage, azurebatch, hki, crukmi, csiro_petrichor, qmul_apocrita, docker, engaging, gis, hypatia, psmn, eva, nygc, fgcz, conda, crg, singularity, mpcdf_viper, self_hosted_runner, tufts, uw_hyak_pedslabs, debug, genouest, cbe, phoenix, gitpod, seawulf, uod_hpc, fub_curta, uct_hpc, aws_tower, binac]
Aug-20 13:41:52.099 [main] DEBUG nextflow.cli.CmdRun - Applied DSL=2 from script declararion
Aug-20 13:41:52.100 [main] INFO nextflow.cli.CmdRun - Launching https://github.com/nf-core/oncoanalyser [spontaneous_wilson] DSL2 - revision: 0881ae9 [v0.3.1]
Aug-20 13:41:52.111 [main] DEBUG nextflow.plugin.PluginsFacade - Setting up plugin manager > mode=prod; plugins-dir=/home/crunchshell/.nextflow/plugins; core-plugins: [email protected],[email protected],[email protected],[email protected],[email protected],[email protected],[email protected]
Aug-20 13:41:52.114 [main] DEBUG nextflow.plugin.PluginsFacade - Plugins default=[]
Aug-20 13:41:52.121 [main] INFO org.pf4j.DefaultPluginStatusProvider - Enabled plugins: []
Aug-20 13:41:52.121 [main] INFO org.pf4j.DefaultPluginStatusProvider - Disabled plugins: []
Aug-20 13:41:52.123 [main] INFO org.pf4j.DefaultPluginManager - PF4J version 3.4.1 in 'deployment' mode
Aug-20 13:41:52.134 [main] INFO org.pf4j.AbstractPluginManager - No plugins
Aug-20 13:41:52.195 [main] DEBUG nextflow.Session - Session uuid: 68398e2b-afb4-49ab-ad82-94da889cc812
Aug-20 13:41:52.195 [main] DEBUG nextflow.Session - Run name: spontaneous_wilson
Aug-20 13:41:52.196 [main] DEBUG nextflow.Session - Executor pool size: 188
Aug-20 13:41:52.231 [main] DEBUG nextflow.cli.CmdRun -
Version: 22.04.3 build 5703
Created: 18-05-2022 19:22 UTC (21:22 CEST)
System: Linux 6.5.0-44-generic
Runtime: Groovy 3.0.10 on OpenJDK 64-Bit Server VM 11.0.24+8-post-Ubuntu-1ubuntu322.04
Encoding: UTF-8 (UTF-8)
Process: 3751968@rembrandt [127.0.1.1]
CPUs: 188 - Mem: 661.3 GB (16.8 GB) - Swap: 2 GB (1.8 GB)
Aug-20 13:41:52.268 [main] DEBUG nextflow.Session - Work-dir: /path/N2N_mock/work [nfs]
Aug-20 13:41:52.268 [main] DEBUG nextflow.Session - Script base path does not exist or is not a directory: /home/crunchshell/.nextflow/assets/nf-core/oncoanalyser/bin
Aug-20 13:41:52.281 [main] DEBUG nextflow.executor.ExecutorFactory - Extension executors providers=[]
Aug-20 13:41:52.299 [main] DEBUG nextflow.Session - Observer factory: DefaultObserverFactory
Aug-20 13:41:52.390 [main] DEBUG nextflow.cache.CacheFactory - Using Nextflow cache factory: nextflow.cache.DefaultCacheFactory
Aug-20 13:41:52.402 [main] DEBUG nextflow.util.CustomThreadPool - Creating default thread pool > poolSize: 189; maxThreads: 1000
Aug-20 13:41:52.495 [main] DEBUG nextflow.Session - Session start invoked
Aug-20 13:41:52.506 [main] DEBUG nextflow.trace.TraceFileObserver - Flow starting -- trace file: /path/N2N_mock/wgs/result_calls/pipeline_info/execution_trace_2024-08-20_13-41-51.txt
Aug-20 13:41:52.521 [main] DEBUG nextflow.Session - Using default localLib path: /home/crunchshell/.nextflow/assets/nf-core/oncoanalyser/lib
Aug-20 13:41:52.526 [main] DEBUG nextflow.Session - Adding to the classpath library: /home/crunchshell/.nextflow/assets/nf-core/oncoanalyser/lib
Aug-20 13:41:52.527 [main] DEBUG nextflow.Session - Adding to the classpath library: /home/crunchshell/.nextflow/assets/nf-core/oncoanalyser/lib/nfcore_external_java_deps.jar
Aug-20 13:41:54.616 [main] DEBUG nextflow.script.ScriptRunner - > Launching execution
Aug-20 13:41:54.908 [main] INFO nextflow.Nextflow -

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�[0;34mref_data_genome_gridss_index : �[0;32mhttps://pub-29f2e5b2b7384811bdbbcba44f8b5083.r2.dev/genomes/GRCh37_hmf/gridss_index/2.13.2/Homo_sapiens.GRCh37.GATK.illumina.fasta.gridsscache�[0m

!! Only displaying parameters that differ from the pipeline defaults !!
-�[2m----------------------------------------------------�[0m-
If you use nf-core/oncoanalyser for your analysis please cite:

• The nf-core framework
  https://doi.org/10.1038/s41587-020-0439-x

• Software dependencies
  https://github.com/nf-core/oncoanalyser/blob/master/CITATIONS.md
  -�[2m----------------------------------------------------�[0m-
  Aug-20 13:41:55.548 [main] ERROR nextflow.Nextflow - received invalid file type: 'fastq'. Valid options are:

  • bam
  • bai
  • amber_dir
  • bamtools
  • cobalt_dir
  • gridss_vcf
  • gridss_vcf_tbi
  • gripss_vcf
  • gripss_vcf_tbi
  • gripss_unfiltered_vcf
  • gripss_unfiltered_vcf_tbi
  • isofox_dir
  • lilac_dir
  • linx_anno_dir
  • pave_vcf
  • purple_dir
  • sage_vcf
  • sage_vcf_tbi
  • sage_append_vcf
  • virusinterpreter_dir
  • chord_dir
  • sigs_dir
  • cuppa_dir
  • flagstat
  • linx_plot_dir
  • sage_dir

System information

Nextflow v22.04.3
HPC
local
Docker
linux
-r v0.3.1

[scwatts]

Hi @jkneppers, FASTQ input is only supported from the 0.4.0 oncoanalyser release so the error message you're seeing with 0.3.1 is expected.

I would recommend using the dev branch since I'll be making the 1.0.0 release from this within the next week or so, and it contains several important fixes.

Please try with again using -revision dev and reopen the issue if that doesn't work!