I recently updated my wf-artic version from v0.3.21 to the newest v.0.3.32, however when i ran my samples I didnt have the nextclade.tsv output. Otherwise the workflow ran as usual. In the .html report the lineages are speciafied, the analysis ran correctly. What could be causing this issue?
Relevant log output
N E X T F L O W ~ version 23.04.2
Launching `https://github.com/epi2me-labs/wf-artic` [clever_keller] DSL2 - revision: 443c9f0e1b [master]
|||||||||| _____ ____ ___ ____ __ __ _____ _ _
|||||||||| | ____| _ \_ _|___ \| \/ | ____| | | __ _| |__ ___
||||| | _| | |_) | | __) | |\/| | _| _____| |/ _` | '_ \/ __|
||||| | |___| __/| | / __/| | | | |__|_____| | (_| | |_) \__ \
|||||||||| |_____|_| |___|_____|_| |_|_____| |_|\__,_|_.__/|___/
|||||||||| wf-artic v0.3.32-g443c9f0
--------------------------------------------------------------------------------
Core Nextflow options
revision : master
runName : clever_keller
containerEngine: docker
launchDir : /data2/Storage/ANALYSIS/SARS-CoV-2/test
workDir : /data2/Storage/ANALYSIS/SARS-CoV-2/test/work
projectDir : /home/user/.nextflow/assets/epi2me-labs/wf-artic
userName : user
profile : standard
configFiles : /home/user/.nextflow/assets/epi2me-labs/wf-artic/nextflow.config
Input Options
fastq : ./fastq_pass
Primer Scheme Selection
scheme_version : Midnight-ONT/V1
Sample Options
sample_sheet : samplesheet.csv
Advanced Options
min_len : 200
max_len : 1300
!! Only displaying parameters that differ from the pipeline defaults !!
--------------------------------------------------------------------------------
If you use epi2me-labs/wf-artic for your analysis please cite:
* The nf-core framework
https://doi.org/10.1038/s41587-020-0439-x
--------------------------------------------------------------------------------
This is epi2me-labs/wf-artic v0.3.32-g443c9f0.
--------------------------------------------------------------------------------
------------------------------------
Available Primer Schemes:
------------------------------------
Name Version
SARS-CoV-2 NEB-VarSkip/v1a
SARS-CoV-2 NEB-VarSkip/v2b
SARS-CoV-2 NEB-VarSkip/v1a-long
SARS-CoV-2 NEB-VarSkip/v2
SARS-CoV-2 ARTIC/V2
SARS-CoV-2 ARTIC/V5.3.2
SARS-CoV-2 ARTIC/V4.1
SARS-CoV-2 ARTIC/V1
SARS-CoV-2 ARTIC/V3
SARS-CoV-2 ARTIC/V4
SARS-CoV-2 Midnight-ONT/V2
SARS-CoV-2 Midnight-ONT/V1
SARS-CoV-2 Midnight-ONT/V3
SARS-CoV-2 Midnight-IDT/V2
SARS-CoV-2 Midnight-IDT/V1
------------------------------------
Searching input for [.fastq, .fastq.gz, .fq, .fq.gz] files.
executor > local (32)
[31/84610b] process > validate_sample_sheet [100%] 1 of 1 ✔
[c3/8abf5a] process > fastcat (2) [100%] 2 of 2 ✔
[0a/d2e1f2] process > pipeline:getVersions [100%] 1 of 1 ✔
[b4/6bc622] process > pipeline:getParams [100%] 1 of 1 ✔
[01/b4827a] process > pipeline:lookup_medaka_variant_model (1) [100%] 1 of 1 ✔
[a9/7a027c] process > pipeline:runArtic (2) [100%] 2 of 2 ✔
[85/8931f9] process > pipeline:combineDepth [100%] 1 of 1 ✔
[2e/92a3bb] process > pipeline:allConsensus [100%] 1 of 1 ✔
[be/1081f4] process > pipeline:allVariants [100%] 1 of 1 ✔
[55/c7a176] process > pipeline:prep_nextclade [100%] 1 of 1 ✔
[ab/6fa433] process > pipeline:nextclade [100%] 1 of 1 ✔
[7f/e7a73b] process > pipeline:pangolin [100%] 1 of 1 ✔
[52/05e589] process > pipeline:report [100%] 1 of 1 ✔
[2c/615c15] process > output (15) [100%] 17 of 17 ✔
Completed at: 17-Nov-2023 14:25:34
Duration : 1m 29s
CPU hours : 0.1
Succeeded : 32
Operating System
Ubuntu 22.04
Other Linux
No response
Workflow Version
v.0.3.32
Workflow Execution
Command line
EPI2ME Version
No response
CLI command run
nextflow run epi2me-labs/wf-artic --update_data --fastq ./fastq_pass --sample_sheet samplesheet.csv --scheme_version Midnight-ONT/V1 --min_len 200 --max_len 1300Workflow Execution - CLI Execution Profile
None
What happened?
I recently updated my wf-artic version from v0.3.21 to the newest v.0.3.32, however when i ran my samples I didnt have the nextclade.tsv output. Otherwise the workflow ran as usual. In the .html report the lineages are speciafied, the analysis ran correctly. What could be causing this issue?
Relevant log output
Application activity log entry
No response