[Purge] not include md5sum.txt file in purge process
The purge process deleted all the files in the raw data directory. Or we want to keep the md5sum.txt file which is a metadata file.
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- Claire Kuchly changed milestone to %V3.2.8
changed milestone to %V3.2.8
- Claire Kuchly added Bug Dysfunction labels
added Bug Dysfunction labels
- Developer
Concerned script: /ui/nG6/lib/class.tx_nG6_utils.php Function : purge_directory()
Files to explude from the purge:
- *.log
- *.log.gz
- GXB02039 (Nanopore machine name, appears in the name of the generated files.)
- md5sum.txt
Related Mantis : https://genomique.genotoul.fr/Mantis/view.php?id=4934#c16546
Edited by Romain Therville - Developer
Also this filename to exclude: PCT0078
- Romain Therville mentioned in commit dafd0076
mentioned in commit dafd0076
- Developer
The commit has been tested on ng6-test with the following inserts:
python3.4 /save/ng6-test/src/ng6-git-rtherville/bin/ng6_cli.py addrun --project-name test_project --name "test_run" --description "test_description" --date "10/09/2019" --data-nature DNA --admin-login CTD --sequencer "unknown" --species "unknown" --type "unknown" --sample sample-name=test type=pe insert-size=350 sample-id="id" sample-description="description" read1=/usr/local/bioinfo/src/NextflowWorkflows/example_on_cluster/data/MT_rep1_1_Ch6.fastq.gz read2=/usr/local/bioinfo/src/NextflowWorkflows/example_on_cluster/data/MT_rep1_2_Ch6.fastq.gz species="humain"
#Adds an analysis to the run (step 1) python3.4 /save/ng6-test/src/ng6-git-rtherville/bin/ng6_cli.py addanalysis --run-id 15282 --data-file /work/ng6-test/jflow_rtherville/test.log --analysis-name "Run analysis 1" --analysis-description "68 + 20 Manech" --analysis-software "GATK..." --analysis-software-options "-" --analysis-software-version "GATK:3.7 - Picard:2.1.1 - Bwa:0.7.15 - Samtools:1.3.1 - FastQC:v0.11.2 - Bcftools:1.3.1" --admin-login CTD
#Adds an analysis to the run (step 2) python3.4 /save/ng6-test/src/ng6-git-rtherville/bin/ng6_cli.py addanalysis --run-id 15282 --data-file /work/ng6-test/jflow_rtherville/test.pdf --analysis-name "Run analysis 2" --analysis-description "68 + 20 Manech" --analysis-software "GATK..." --analysis-software-options "-" --analysis-software-version "GATK:3.7 - Picard:2.1.1 - Bwa:0.7.15 - Samtools:1.3.1 - FastQC:v0.11.2 - Bcftools:1.3.1" --admin-login CTD
#Adds an analysis to the run (step 3) python3.4 /save/ng6-test/src/ng6-git-rtherville/bin/ng6_cli.py addanalysis --run-id 15282 --data-file /work/ng6-test/jflow_rtherville/xxx_GXB02039_1234.log --analysis-name "Run analysis 3" --analysis-description "68 + 20 Manech" --analysis-software "GATK..." --analysis-software-options "-" --analysis-software-version "GATK:3.7 - Picard:2.1.1 - Bwa:0.7.15 - Samtools:1.3.1 - FastQC:v0.11.2 - Bcftools:1.3.1" --admin-login CTD
#Adds an analysis to the run (step 4) python3.4 /save/ng6-test/src/ng6-git-rtherville/bin/ng6_cli.py addanalysis --run-id 15282 --data-file /work/ng6-test/jflow_rtherville/md5sum.txt --analysis-name "Run analysis 4" --analysis-description "68 + 20 Manech" --analysis-software "GATK..." --analysis-software-options "-" --analysis-software-version "GATK:3.7 - Picard:2.1.1 - Bwa:0.7.15 - Samtools:1.3.1 - FastQC:v0.11.2 - Bcftools:1.3.1" --admin-login CTD
#Adds an analysis to the run (step 5) python3.4 /save/ng6-test/src/ng6-git-rtherville/bin/ng6_cli.py addanalysis --run-id 15282 --data-file /work/ng6-test/jflow_rtherville/xxx_PCT0078_1234.log --analysis-name "Run analysis 5" --analysis-description "68 + 20 Manech" --analysis-software "GATK..." --analysis-software-options "-" --analysis-software-version "GATK:3.7 - Picard:2.1.1 - Bwa:0.7.15 - Samtools:1.3.1 - FastQC:v0.11.2 - Bcftools:1.3.1" --admin-login CTD
- Romain Therville mentioned in merge request !108 (closed)
mentioned in merge request !108 (closed)
- Romain Therville mentioned in commit 884b21b3
mentioned in commit 884b21b3
- Romain Therville mentioned in merge request !109 (merged)
mentioned in merge request !109 (merged)
- Romain Therville changed milestone to %V3.2.7.5
changed milestone to %V3.2.7.5
- Romain Therville mentioned in merge request !110 (merged)
mentioned in merge request !110 (merged)
- Celine Noirot mentioned in commit a2966774
mentioned in commit a2966774
- Developer
Resolved with the following tag: https://forgemia.inra.fr/genotoul-bioinfo/ng6/-/tags/V3.2.7.3
- Romain Therville closed
closed