tbprofiler v6.4.1

[sage-wright]

Update TBProfiler to v6.4.1

Pull Request (PR) checklist:

• Include a description of what is in this pull request in this message.
• The dockerfile successfully builds to a test target for the user creating the PR. (i.e. docker build --tag samtools:1.15test --target test docker-builds/samtools/1.15 )
• Directory structure as name of the tool in lower case with special characters removed with a subdirectory of the version number (i.e. spades/3.12.0/Dockerfile)
  • (optional) All test files are located in same directory as the Dockerfile (i.e. shigatyper/2.0.1/test.sh)
• Create a simple container-specific README.md in the same directory as the Dockerfile (i.e. spades/3.12.0/README.md)
  • If this README is longer than 30 lines, there is an explanation as to why more detail was needed
• Dockerfile includes the recommended LABELS
• Main README.md has been updated to include the tool and/or version of the dockerfile(s) in this PR
• Program_Licenses.md contains the tool(s) used in this PR and has been updated for any missing

[kapsakcj]

Simple change from previous dockerfile:

$ diff tbprofiler/6.4.0/Dockerfile tbprofiler/6.4.1/Dockerfile 
6c6
< ARG TBPROFILER_VER="6.4.0"
---
> ARG TBPROFILER_VER="6.4.1"

Looks like the test passed:

#12 [test 3/3] RUN wget -q ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR166/009/ERR1664619/ERR1664619_1.fastq.gz &&     wget -q ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR166/009/ERR1664619/ERR1664619_2.fastq.gz &&     tb-profiler profile -1 ERR1664619_1.fastq.gz -2 ERR1664619_2.fastq.gz -t 2 -p ERR1664619 --txt
#12 16.24 [19:00:09] INFO     Using ref file:                                    db.py:614
#12 16.24                     /opt/conda/share/tbprofiler//tbdb.fasta                     
#12 16.24            INFO     Using gff file:                                    db.py:614
#12 16.24                     /opt/conda/share/tbprofiler//tbdb.gff                       
#12 16.24            INFO     Using bed file:                                    db.py:614
#12 16.24                     /opt/conda/share/tbprofiler//tbdb.bed                       
#12 16.24            INFO     Using json_db file:                                db.py:614
#12 16.24                     /opt/conda/share/tbprofiler//tbdb.dr.json                   
#12 16.36            INFO     Using variables file:                              db.py:614
#12 16.36                     /opt/conda/share/tbprofiler//tbdb.variables.json            
#12 16.37            INFO     Using spoligotype_spacers file:                    db.py:614
#12 16.37                     /opt/conda/share/tbprofiler//tbdb.spoligotype_spac          
#12 16.37                     ers.txt                                                     
#12 16.37            INFO     Using spoligotype_annotations file:                db.py:614
#12 16.37                     /opt/conda/share/tbprofiler//tbdb.spoligotype_list          
#12 16.37                     .csv                                                        
#12 16.37            INFO     Using bedmask file:                                db.py:614
#12 16.37                     /opt/conda/share/tbprofiler//tbdb.mask.bed                  
#12 16.37            INFO     Using barcode file:                                db.py:614
#12 16.37                     /opt/conda/share/tbprofiler//tbdb.barcode.bed               
#12 16.37            INFO     Using rules file:                                  db.py:614
#12 16.37                     /opt/conda/share/tbprofiler//tbdb.rules.txt                 
#12 16.37            INFO     Trimming reads                                   fastq.py:39
#12 19.18 [19:00:12] INFO     Mapping to reference genome                      fastq.py:53
#12 65.12 
Calling variants:   0%|          | 0/73 [00:00<?, ?it/s]
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Calling variants:  14%|█▎        | 10/73 [00:01<00:04, 13.17it/s]
Calling variants:  16%|█▋        | 12/73 [00:01<00:04, 13.16it/s]
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Calling variants:  22%|██▏       | 16/73 [00:01<00:04, 13.98it/s]
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Calling variants:  44%|████▍     | 32/73 [00:02<00:02, 15.16it/s]
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Calling variants:  90%|█████████ | 66/73 [00:04<00:00, 14.32it/s]
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Calling variants: 100%|██████████| 73/73 [00:05<00:00, 14.02it/s]
#12 70.33 
Indexing variants:   0%|          | 0/73 [00:00<?, ?it/s]
Indexing variants:  18%|█▊        | 13/73 [00:00<00:00, 127.99it/s]
Indexing variants:  40%|███▉      | 29/73 [00:00<00:00, 137.72it/s]
Indexing variants:  89%|████████▉ | 65/73 [00:00<00:00, 234.26it/s]
Indexing variants: 100%|██████████| 73/73 [00:00<00:00, 205.53it/s]
#12 70.86 [19:01:04] INFO     Running delly                                      bam.py:84
#12 74.86 [19:01:08] INFO     Running snpEff                                    vcf.py:126
#12 76.94 [19:01:10] INFO     Loading snpEff annotations                        vcf.py:164
#12 77.74 [19:01:11] INFO     Getting genotypes for positions in bed file       bam.py:291
#12 80.00 [19:01:13] INFO     Calculating bamstats                              bam.py:351
#12 82.58 [19:01:16] INFO     Getting qc metrics for regions                    bam.py:388
#12 82.58            INFO     Calculating depth in regions                       bam.py:54
#12 85.77 [19:01:19] INFO     Calculating median depth using samtools           bam.py:221
#12 87.96 [19:01:21] INFO     Getting missing genomic positions                 bam.py:381
#12 88.58 [19:01:22] INFO     Writing outputs                                  output.py:8
#12 88.58            INFO     Writing json file:                              output.py:15
#12 88.58                     /tests/results/ERR1664619.results.json                      
#12 88.59            INFO     Writing text file:                              output.py:19
#12 88.59                     /tests/results/ERR1664619.results.txt                       
#12 88.67            INFO     Profiling finished sucessfully!              tb-profiler:221
#12 DONE 88.9s

[kapsakcj]

thank you for the PR! Deploy workflow here: https://github.com/StaPH-B/docker-builds/actions/runs/11955528637

The docker image should be up on dockerhub and quay shortly

[kapsakcj]

I re-launched the deploy workflow. I think it's failing in the test layer when downloading the test FASTQs. Likely just the download from ENA causing the error