Commits on Source (45)
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Kenza Bazi-Kabbaj authored145669e5
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Kenza Bazi-Kabbaj authored97306e11
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Kenza Bazi-Kabbaj authored4c34da44
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Kenza Bazi-Kabbaj authoredcd7f25f6
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Kenza Bazi-Kabbaj authored85bf7e76
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Maria Bernard authored29d4b829
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Maria Bernard authoredf3153b10
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Maria Bernard authoreda808ff8b
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Maria Bernard authored7fbb9dc4
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Maria Bernard authored3edd5800
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Maria Bernard authored178c039a
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Maria Bernard authored8a51d8d2
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mariabernard authoreda1d4c2db
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mariabernard authored79c95e84
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mariabernard authored23548843
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mariabernard authoreddcfeab55
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Maria Bernard authored36e3dc9a
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mariabernard authored9ae7f1ff
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mariabernard authored093af7f4
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mariabernard authored30b71c61
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mariabernard authored33ef13bc
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mariabernard authored5e59c856
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mariabernard authored32023f08
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mariabernard authored547ed035
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mariabernard authored00b17e5c
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mariabernard authorede7677d9a
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Maria Bernard authored7ef3cf9d
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Maria Bernard authored4551ebe5
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Maria Bernard authoredf7e2c87b
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Maria Bernard authored72d966e3
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Maria Bernard authored03b2e61c
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mariabernard authored055a8c60
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Maria Bernard authoredeef374cd
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Maria Bernard authored02b30b7a
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Maria Bernard authored42f62285
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Sarah Maman-Haddad authored4bea8745
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Sarah Maman-Haddad authoredd029c21e
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Sarah Maman-Haddad authored
In sample.tsv header, replace "name" by "sample_name" (because table dataframe attribute is "sample_name" ligne 133 of Snakefile_calling file).
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Sarah Maman-Haddad authored
Replace count = get_RSEM_res (ligne 453) by because count is reserved for internal use and using count generate an AttributeError
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Sarah Maman-Haddad authored90a08e59
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Sarah Maman-Haddad authored
(minor) check make Results/Fai_Dict_Index/ directory. Error message 'Invalid argument 'R'.' if spaces before and after "R=". Idem for O option.
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Sarah Maman-Haddad authored
Remove spaces before and after I and O argments in CleanSam command line (to avoir this ERROR: Invalid argument 'I')
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Celine Noirot authored
In sample.tsv header, replace "name" by "sample_name" (because table dataframe... See merge request !1
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Mathieu Charles authored9758d184
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Sarah Maman-Haddad authored19343e4f
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- Nextflow/template_dev/README.md 0 additions, 44 deletionsNextflow/template_dev/README.md
- Nextflow/template_dev/main.nf 0 additions, 94 deletionsNextflow/template_dev/main.nf
- Nextflow/template_dev/nextflow.config 0 additions, 0 deletionsNextflow/template_dev/nextflow.config
- Nextflow/template_dev/test.sh 0 additions, 0 deletionsNextflow/template_dev/test.sh
- Snakemake/1000GB/scripts/fastq_detect.pl 0 additions, 137 deletionsSnakemake/1000GB/scripts/fastq_detect.pl
- Snakemake/1000RNASeq_chicken/ASE/README.md 23 additions, 12 deletionsSnakemake/1000RNASeq_chicken/ASE/README.md
- Snakemake/1000RNASeq_chicken/ASE/Snakefile 2 additions, 3 deletionsSnakemake/1000RNASeq_chicken/ASE/Snakefile
- Snakemake/1000RNASeq_chicken/ASE/img/full_dryrun.png 0 additions, 0 deletionsSnakemake/1000RNASeq_chicken/ASE/img/full_dryrun.png
- Snakemake/1000RNASeq_chicken/ASE/resources_SLURM.yaml 2 additions, 1 deletionSnakemake/1000RNASeq_chicken/ASE/resources_SLURM.yaml
- Snakemake/1000RNASeq_chicken/ASE/rules/ASE_counter.smk 16 additions, 17 deletionsSnakemake/1000RNASeq_chicken/ASE/rules/ASE_counter.smk
- Snakemake/1000RNASeq_chicken/ASE/script/variantFiltration.py 3 additions, 1 deletionSnakemake/1000RNASeq_chicken/ASE/script/variantFiltration.py
- Snakemake/1000RNASeq_chicken/calling/README.md 1 addition, 1 deletionSnakemake/1000RNASeq_chicken/calling/README.md
- Snakemake/1000RNASeq_chicken/calling/SLURM.sh 3 additions, 3 deletionsSnakemake/1000RNASeq_chicken/calling/SLURM.sh
- Snakemake/1000RNASeq_chicken/calling/Snakefile_calling 2 additions, 19 deletionsSnakemake/1000RNASeq_chicken/calling/Snakefile_calling
- Snakemake/1000RNASeq_chicken/calling/resources_calling_SLURM.yaml 3 additions, 3 deletions...e/1000RNASeq_chicken/calling/resources_calling_SLURM.yaml
- Snakemake/1000RNASeq_chicken_calling_GATK4/README.md 180 additions, 0 deletionsSnakemake/1000RNASeq_chicken_calling_GATK4/README.md
- Snakemake/1000RNASeq_chicken_calling_GATK4/SLURM.sh 53 additions, 0 deletionsSnakemake/1000RNASeq_chicken_calling_GATK4/SLURM.sh
- Snakemake/1000RNASeq_chicken_calling_GATK4/Snakefile_calling 688 additions, 0 deletionsSnakemake/1000RNASeq_chicken_calling_GATK4/Snakefile_calling
- Snakemake/1000RNASeq_chicken_calling_GATK4/config_calling.yaml 45 additions, 0 deletions...make/1000RNASeq_chicken_calling_GATK4/config_calling.yaml
- Snakemake/1000RNASeq_chicken_calling_GATK4/config_calling.yaml.example 44 additions, 0 deletions...0RNASeq_chicken_calling_GATK4/config_calling.yaml.example
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Nextflow/template_dev/main.nf
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Nextflow/template_dev/test.sh
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