[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.

changed milestone to %V3.2.8

added Bug Dysfunction labels

Concerned script: /ui/nG6/lib/class.tx_nG6_utils.php Function : purge_directory()

Files to explude from the purge:

• *.log
• *.log.gz
• *.pdf
• 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

Also this filename to exclude: PCT0078

mentioned in commit dafd0076

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

mentioned in merge request !108 (closed)

mentioned in commit 884b21b3

mentioned in merge request !109 (merged)

changed milestone to %V3.2.7.5

mentioned in merge request !110 (merged)

mentioned in commit a2966774

Resolved with the following tag: https://forgemia.inra.fr/genotoul-bioinfo/ng6/-/tags/V3.2.7.3

closed