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nf-core / oncoanalyser

A comprehensive cancer DNA/RNA analysis and reporting pipeline
https://nf-co.re/oncoanalyser
MIT License
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invalid file type: 'fastq' #89

Closed jkneppers closed 3 weeks ago

jkneppers commented 3 weeks ago

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'. image

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: 0881ae9936 [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: nf-amazon@1.7.2,nf-azure@0.13.2,nf-console@1.0.3,nf-ga4gh@1.0.3,nf-google@1.1.4,nf-sqldb@0.4.0,nf-tower@1.4.0 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 -

------------------------------------------------------ ,--./,-.  _ _ /,-..--~'  |\ | | / ` / \ |) | } {  | | | _, __/ | \ |__ `-.,--, .,.,'  nf-core/oncoanalyser v0.3.1 ------------------------------------------------------ Core Nextflow options revision : v0.3.1 runName : spontaneous_wilson containerEngine : docker launchDir : /path/N2N_mock workDir : /path/N2N_mock/work projectDir : /home/crunchshell/.nextflow/assets/nf-core/oncoanalyser userName : crunchshell profile : docker configFiles : /home/crunchshell/.nextflow/assets/nf-core/oncoanalyser/nextflow.config

Input/output options input : /path/N2N_mock/wgs/samplesheet.csv outdir : /path/N2N_mock/wgs/result_calls/

Other options mode : wgts isofox_read_length : 151

Reference data options genome : GRCh37_hmf ref_data_hmf_data_path : https://pub-29f2e5b2b7384811bdbbcba44f8b5083.r2.dev/hmf_reference_data/hmftools/5.34_37--0.tar.gz ref_data_virusbreakenddb_path : https://pub-29f2e5b2b7384811bdbbcba44f8b5083.r2.dev/virusbreakend/virusbreakenddb_20210401.tar.gz ref_data_genome_fasta : https://pub-29f2e5b2b7384811bdbbcba44f8b5083.r2.dev/genomes/GRCh37_hmf/Homo_sapiens.GRCh37.GATK.illumina.fasta ref_data_genome_fai : https://pub-29f2e5b2b7384811bdbbcba44f8b5083.r2.dev/genomes/GRCh37_hmf/samtools_index/1.16/Homo_sapiens.GRCh37.GATK.illumina.fasta.fai ref_data_genome_dict : https://pub-29f2e5b2b7384811bdbbcba44f8b5083.r2.dev/genomes/GRCh37_hmf/samtools_index/1.16/Homo_sapiens.GRCh37.GATK.illumina.fasta.dict ref_data_genome_bwa_index : https://pub-29f2e5b2b7384811bdbbcba44f8b5083.r2.dev/genomes/GRCh37_hmf/bwa_index/0.7.17-r1188.tar.gz ref_data_genome_bwa_index_image: https://pub-29f2e5b2b7384811bdbbcba44f8b5083.r2.dev/genomes/GRCh37_hmf/bwa_index_image/0.7.17-r1188/Homo_sapiens.GRCh37.GATK.illumina.fasta.img ref_data_genome_gridss_index : https://pub-29f2e5b2b7384811bdbbcba44f8b5083.r2.dev/genomes/GRCh37_hmf/gridss_index/2.13.2/Homo_sapiens.GRCh37.GATK.illumina.fasta.gridsscache

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

System information

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

scwatts commented 3 weeks ago

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!