ERROR ~ Invalid process definition -- Unknown keyword stub @ line 34, column 5.

[ld9866]

Dear developer:

We want to use the egapx in a local machine with 128core and 2T memory, and I think the singularity model is easier.

The step:
Download the Singularity image:
Clone the repo
Download EGAPx related files from NCBI:
Download SRA reads:
all works well.

We cp the examples/input_D_farinae_small.yaml as example.yaml, and the example.yaml is:

genome: /home/lidong/data1/05.NCBI.annountation/02.docker/egapx/sradir/GCA_020809275.1_ASM2080927v1_genomic.fna.gz
taxid: 6954
reads:

• /home/lidong/data1/05.NCBI.annountation/02.docker/egapx/sradir/SRR8506572_1.fasta
• /home/lidong/data1/05.NCBI.annountation/02.docker/egapx/sradir/SRR8506572_2.fasta
• /home/lidong/data1/05.NCBI.annountation/02.docker/egapx/sradir/SRR9005248_1.fasta
• /home/lidong/data1/05.NCBI.annountation/02.docker/egapx/sradir/SRR9005248_2.fasta
  annotation_provider: GenBank submitter
  annotation_name_prefix: GCA_020809275.1
  locus_tag_prefix: egapxtmp

I think everything is ok.

When I want to prepare the file with code:

python3 ui/egapx.py examples/test.yaml -e singularity -w testwork -o testresult -lc ../local_cache

#The erro is:

!!WARNING!!
This is an alpha release with limited features and organism scope to collect initial feedback on execution. Outputs are not yet complete and not intended for production use.

N E X T F L O W ~ version 0.30.1
Launching /media/piglab/a004dcd3-2ca0-4929-aaec-239b6432c960/lidong/05.NCBI.annountation/02.docker/egapx/ui/../nf/ui.nf [thirsty_mayer] - revision: 283c15af5b
ERROR ~ Invalid process definition -- Unknown keyword stub @ line 34, column 5.
"""
^
1 error
-- Check '/media/piglab/a004dcd3-2ca0-4929-aaec-239b6432c960/lidong/05.NCBI.annountation/02.docker/egapx/testresult/nextflow.log' file for details
None

To resume execution, run: sh /media/piglab/a004dcd3-2ca0-4929-aaec-239b6432c960/lidong/05.NCBI.annountation/02.docker/egapx/testresult/resume.sh

I also prepared the log file ,can you help me?

Best day!
Dong

nextflow.log

resume.sh

#!/bin/bash
nextflow -C /media/piglab/a004dcd3-2ca0-4929-aaec-239b6432c960/lidong/05.NCBI.annountation/02.docker/egapx/egapx_config/singularity.config,/media/piglab/a004dcd3-2ca0-4929-aaec-239b6432c960/lidong/05.NCBI.annountation/02.docker/egapx/ui/assets/config/default.config,/media/piglab/a004dcd3-2ca0-4929-aaec-239b6432c960/lidong/05.NCBI.annountation/02.docker/egapx/ui/assets/config/docker_image.config,/media/piglab/a004dcd3-2ca0-4929-aaec-239b6432c960/lidong/05.NCBI.annountation/02.docker/egapx/ui/assets/config/process_resources.config -log /media/piglab/a004dcd3-2ca0-4929-aaec-239b6432c960/lidong/05.NCBI.annountation/02.docker/egapx/testresult/nextflow.log run /media/piglab/a004dcd3-2ca0-4929-aaec-239b6432c960/lidong/05.NCBI.annountation/02.docker/egapx/ui/../nf/ui.nf --output /media/piglab/a004dcd3-2ca0-4929-aaec-239b6432c960/lidong/05.NCBI.annountation/02.docker/egapx/testresult -with-report /media/piglab/a004dcd3-2ca0-4929-aaec-239b6432c960/lidong/05.NCBI.annountation/02.docker/egapx/testresult/run.report.html -with-timeline /media/piglab/a004dcd3-2ca0-4929-aaec-239b6432c960/lidong/05.NCBI.annountation/02.docker/egapx/testresult/run.timeline.html -with-dag dag.dot -with-trace /media/piglab/a004dcd3-2ca0-4929-aaec-239b6432c960/lidong/05.NCBI.annountation/02.docker/egapx/testresult/run.trace.txt -params-file /media/piglab/a004dcd3-2ca0-4929-aaec-239b6432c960/lidong/05.NCBI.annountation/02.docker/egapx/testresult/run_params.yaml -resume -work-dir testwork

[victzh]

Dear Dong,
you use a very antiquated version of Nextflow, we now use 24.10.2 and yours reported as 0.30.1. Since then Nextflow evolved a lot, introduced the keyword 'stub' in particular. Please update your version of Nextflow and try again.