docker image deprecation

Hi! By running the following command:

nextflow run mop_preprocess.nf -with-docker -bg --fast5 " " --fastq files "/home/MOP2/mop_preprocess/fastq/ " --reference "Homo_sapiens.GRCh37.cdna.fa" --annotation "/home/MOP2/mop_preprocess/Homo_sapiens.GRCh37.gtf" --pars_tools cdna_tool_opt.tsv --output "/home/MOP2/mop_preprocess/ " --ref_type transcriptome --GPU OFF --mapping minimap2 --counting nanocount --saveSpace YES

I got the following error. I guess docker image needs an update or am I doing something wrong?

----------------------CHECK TOOLS -----------------------------

basecalling will be skipped demultiplexing will be skipped mapping : minimap2 filtering : nanoq counting : nanocount discovery will be skipped

[3d/6d5338] Submitted process > preprocess_simple:MINIMAP2:map (files) [aa/50d158] Submitted process > preprocess_simple:checkRef (Checking Homo_sapiens.GRCh37.cdna.fa) [a6/915faa] Submitted process > preprocess_simple:FASTQC:fastQC (files) [c1/776d4d] Submitted process > preprocess_simple:SAMTOOLS_SORT:sortAln (files) ERROR ~ Error executing process > 'preprocess_simple:FASTQC:fastQC (files)'

Caused by: Process preprocess_simple:FASTQC:fastQC (files) terminated with an error exit status (125)

Command executed:

fastqc -t 8 files

Command exit status: 125

Command output: (empty)

Command error: Unable to find image 'quay.io/biocontainers/fastqc:0.11.9--0' locally 0.11.9--0: Pulling from biocontainers/fastqc docker: [DEPRECATION NOTICE] Docker Image Format v1 and Docker Image manifest version 2, schema 1 support is disabled by default and will be removed in an upcoming release. Suggest the author of quay.io/biocontainers/fastqc:0.11.9--0 to upgrade the image to the OCI Format or Docker Image manifest v2, schema 2. More information at https://docs.docker.com/go/deprecated-image-specs/. See 'docker run --help'.

Work dir: /home/tutku/MOP2/mop_preprocess/work/a6/915faa22a7b344759ae87b7147c860

Tip: when you have fixed the problem you can continue the execution adding the option -resume to the run command line

-- Check '.nextflow.log' file for details Pipeline BIOCORE@CRG Master of Pore - preprocess completed! Started at 2024-05-09T17:16:03.939914170+03:00 Finished at 2024-05-09T17:16:20.032480573+03:00 Time elapsed: 16.1s Execution status: failed WARN: Killing running tasks (1)

Thanks for any help in advance!

biocorecrg / MOP2

docker image deprecation #61

basecalling will be skipped demultiplexing will be skipped mapping : minimap2 filtering : nanoq counting : nanocount discovery will be skipped