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re0.9.1 #8

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Mar 6, 2024
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re0.9.1 #8

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2 changes: 1 addition & 1 deletion examples/01_samples_reads_assembly_bins_mags.yaml
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Expand Up @@ -50,7 +50,7 @@ PAIRED_END_READS:
RELATED_SAMPLE_TITLE: "idx00_main digester sample" # The title of the sample that these reads originate from >>EXAMPLE: "Bioreactor_2_sample"
ADDITIONAL_MANIFEST_FIELDS: # You can add additional fields that will be written to the manifest
ASSEMBLY:
ASSEMBLY_NAME: "idx00_e01_coassembly" # Choose a name, even if your assembly has been uploaded already. Will only be used for naming assembly and bins/MAGs. >>EXAMPLE: "SGMA project mg"
ASSEMBLY_NAME: "idx00_e01_coasm" # Choose a name, even if your assembly has been uploaded already. Will only be used for naming assembly and bins/MAGs. >>EXAMPLE: "SGMA project mg"
ASSEMBLY_SOFTWARE: "MEGAHIT" # Software used to generate the assembly >>EXAMPLE: "MEGAHIT"
ISOLATION_SOURCE: "biogas plant anaerobic digester" # Describe where your sample was taken from >>EXAMPLE: "biogas plant anaerobic digester"
FASTA_FILE: "data/assembly.fasta" # Path to the fasta file >>EXAMPLE: "/mnt/data/assembly.fasta.gz"
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2 changes: 1 addition & 1 deletion examples/02_samples_reads_assembly_bins.yaml
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Expand Up @@ -31,7 +31,7 @@ SINGLE_READS:
RELATED_SAMPLE_TITLE: 'idx00_example02_sample01' # The title of the sample that these reads originate from >>EXAMPLE: "Bioreactor_2_sample"
ADDITIONAL_MANIFEST_FIELDS: # You can add additional fields that will be written to the manifest
ASSEMBLY:
ASSEMBLY_NAME: 'idx00_e02_assembly' # Choose a name, even if your assembly has been uploaded already. Will only be used for naming assembly and bins/MAGs. >>EXAMPLE: "Northern Germany biogas digester metagenome"
ASSEMBLY_NAME: 'idx00_e02_asm' # Choose a name, even if your assembly has been uploaded already. Will only be used for naming assembly and bins/MAGs. >>EXAMPLE: "Northern Germany biogas digester metagenome"
ASSEMBLY_SOFTWARE: 'metaSPAdes' # Software used to generate the assembly >>EXAMPLE: "MEGAHIT"
ISOLATION_SOURCE: 'ant fungus garden' # Describe where your sample was taken from >>EXAMPLE: "biogas plant anaerobic digester"
FASTA_FILE: "data/assembly.fasta" # Path to the fasta file >>EXAMPLE: "/mnt/data/assembly.fasta.gz"
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2 changes: 1 addition & 1 deletion examples/03_samples_reads_assembly.yaml
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Expand Up @@ -68,7 +68,7 @@ PAIRED_END_READS:
RELATED_SAMPLE_TITLE: "idx00_main digester sample" # The title of the sample that these reads originate from >>EXAMPLE: "Bioreactor_2_sample"
ADDITIONAL_MANIFEST_FIELDS: # You can add additional fields that will be written to the manifest
ASSEMBLY:
ASSEMBLY_NAME: "idx00_e01_coassembly" # Choose a name, even if your assembly has been uploaded already. Will only be used for naming assembly and bins/MAGs. >>EXAMPLE: "SGMA project mg"
ASSEMBLY_NAME: "idx00_e03_coasm" # Choose a name, even if your assembly has been uploaded already. Will only be used for naming assembly and bins/MAGs. >>EXAMPLE: "SGMA project mg"
ASSEMBLY_SOFTWARE: "MEGAHIT" # Software used to generate the assembly >>EXAMPLE: "MEGAHIT"
ISOLATION_SOURCE: "biogas plant anaerobic digester" # Describe where your sample was taken from >>EXAMPLE: "biogas plant anaerobic digester"
FASTA_FILE: "data/assembly.fasta" # Path to the fasta file >>EXAMPLE: "/mnt/data/assembly.fasta.gz"
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2 changes: 1 addition & 1 deletion examples/04_reads_assembly_bins_mags.yaml
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Expand Up @@ -21,7 +21,7 @@ SINGLE_READS:
RELATED_SAMPLE_ACCESSION: 'SAMEA113417017' # The accession of the sample that these reads originate from >>EXAMPLE: "ERS15898933"
ADDITIONAL_MANIFEST_FIELDS: # You can add additional fields that will be written to the manifest
ASSEMBLY:
ASSEMBLY_NAME: "idx00_e01_coassembly" # Choose a name, even if your assembly has been uploaded already. Will only be used for naming assembly and bins/MAGs. >>EXAMPLE: "SGMA project mg"
ASSEMBLY_NAME: "idx00_e04_coasm" # Choose a name, even if your assembly has been uploaded already. Will only be used for naming assembly and bins/MAGs. >>EXAMPLE: "SGMA project mg"
ASSEMBLY_SOFTWARE: "MEGAHIT" # Software used to generate the assembly >>EXAMPLE: "MEGAHIT"
ISOLATION_SOURCE: "biogas plant anaerobic digester" # Describe where your sample was taken from >>EXAMPLE: "biogas plant anaerobic digester"
FASTA_FILE: "data/assembly.fasta" # Path to the fasta file >>EXAMPLE: "/mnt/data/assembly.fasta.gz"
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2 changes: 1 addition & 1 deletion examples/05_reads_assembly_bins.yaml
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Expand Up @@ -32,7 +32,7 @@ PAIRED_END_READS:
RELATED_SAMPLE_ACCESSION: 'SAMEA113417018' # The accession of the sample that these reads originate from >>EXAMPLE: "ERS15898933"
ADDITIONAL_MANIFEST_FIELDS: # You can add additional fields that will be written to the manifest
ASSEMBLY:
ASSEMBLY_NAME: "idx00_e01_coassembly" # Choose a name, even if your assembly has been uploaded already. Will only be used for naming assembly and bins/MAGs. >>EXAMPLE: "SGMA project mg"
ASSEMBLY_NAME: "idx00_e05_coasm" # Choose a name, even if your assembly has been uploaded already. Will only be used for naming assembly and bins/MAGs. >>EXAMPLE: "SGMA project mg"
ASSEMBLY_SOFTWARE: "MEGAHIT" # Software used to generate the assembly >>EXAMPLE: "MEGAHIT"
ISOLATION_SOURCE: "biogas plant anaerobic digester" # Describe where your sample was taken from >>EXAMPLE: "biogas plant anaerobic digester"
FASTA_FILE: "data/assembly.fasta" # Path to the fasta file >>EXAMPLE: "/mnt/data/assembly.fasta.gz"
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2 changes: 1 addition & 1 deletion examples/06_reads_assembly.yaml
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Expand Up @@ -30,7 +30,7 @@ PAIRED_END_READS:
RELATED_SAMPLE_ACCESSION: 'SAMEA113417017' # The accession of the sample that these reads originate from >>EXAMPLE: "ERS15898933"
ADDITIONAL_MANIFEST_FIELDS: # You can add additional fields that will be written to the manifest
ASSEMBLY:
ASSEMBLY_NAME: 'idx00_e06_assembly' # Choose a name, even if your assembly has been uploaded already. Will only be used for naming assembly and bins/MAGs. >>EXAMPLE: "Northern Germany biogas digester metagenome"
ASSEMBLY_NAME: 'idx00_e06_asm' # Choose a name, even if your assembly has been uploaded already. Will only be used for naming assembly and bins/MAGs. >>EXAMPLE: "Northern Germany biogas digester metagenome"
ASSEMBLY_SOFTWARE: 'metaSPAdes' # Software used to generate the assembly >>EXAMPLE: "MEGAHIT"
ISOLATION_SOURCE: 'ant fungus garden' # Describe where your sample was taken from >>EXAMPLE: "biogas plant anaerobic digester"
FASTA_FILE: "data/assembly.fasta" # Path to the fasta file >>EXAMPLE: "/mnt/data/assembly.fasta.gz"
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2 changes: 1 addition & 1 deletion examples/07_assembly_bins_mags.yaml
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Expand Up @@ -13,7 +13,7 @@ SEQUENCING_PLATFORMS: ["ILLUMINA"] #
PROJECT_NAME: "idx00_AgRFex 2 Survey" # Name of the project within which the sequencing was organized >>EXAMPLE: "AgRFex 2 Biogas Survey"
SAMPLE_ACCESSIONS: ['SAMEA113417017'] # These samples exist in ENA. Your assembly is based on them. >>EXAMPLE: ["ERS15898933","ERS15898932"]
ASSEMBLY:
ASSEMBLY_NAME: "idx00_ex07_assembly" # Choose a name, even if your assembly has been uploaded already. Will only be used for naming assembly and bins/MAGs. >>EXAMPLE: "Northern Germany biogas digester metagenome"
ASSEMBLY_NAME: "idx00_ex07_asm" # Choose a name, even if your assembly has been uploaded already. Will only be used for naming assembly and bins/MAGs. >>EXAMPLE: "Northern Germany biogas digester metagenome"
ASSEMBLY_SOFTWARE: "MEGAHIT" # Software used to generate the assembly >>EXAMPLE: "MEGAHIT"
ISOLATION_SOURCE: "biogas plant anaerobic digester" # Describe where your sample was taken from >>EXAMPLE: "biogas plant anaerobic digester"
FASTA_FILE: "data/assembly.fasta" # Path to the fasta file >>EXAMPLE: "/mnt/data/assembly.fasta.gz"
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2 changes: 1 addition & 1 deletion examples/08_assembly_bins.yaml
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Expand Up @@ -11,7 +11,7 @@ METAGENOME_TAXID: "718289" #
SEQUENCING_PLATFORMS: ["ILLUMINA"] # One of https://ena-docs.readthedocs.io/en/latest/submit/reads/webin-cli.html#platform >>EXAMPLE: ["ILLUMINA","OXFORD_NANOPORE"]
SAMPLE_ACCESSIONS: ['SAMEA113417017'] # These samples exist in ENA. Your assembly is based on them. >>EXAMPLE: ["ERS15898933","ERS15898932"]
ASSEMBLY:
ASSEMBLY_NAME: "idx00_ex08_assembly" # Choose a name, even if your assembly has been uploaded already. Will only be used for naming assembly and bins/MAGs. >>EXAMPLE: "Northern Germany biogas digester metagenome"
ASSEMBLY_NAME: "idx00_ex08_asm" # Choose a name, even if your assembly has been uploaded already. Will only be used for naming assembly and bins/MAGs. >>EXAMPLE: "Northern Germany biogas digester metagenome"
ASSEMBLY_SOFTWARE: "MEGAHIT" # Software used to generate the assembly >>EXAMPLE: "MEGAHIT"
ISOLATION_SOURCE: "biogas plant anaerobic digester" # Describe where your sample was taken from >>EXAMPLE: "biogas plant anaerobic digester"
FASTA_FILE: "data/assembly.fasta" # Path to the fasta file >>EXAMPLE: "/mnt/data/assembly.fasta.gz"
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2 changes: 1 addition & 1 deletion examples/09_assembly.yaml
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Expand Up @@ -10,7 +10,7 @@ METAGENOME_TAXID: "718289" #
SEQUENCING_PLATFORMS: ["ILLUMINA"] # One of https://ena-docs.readthedocs.io/en/latest/submit/reads/webin-cli.html#platform >>EXAMPLE: ["ILLUMINA","OXFORD_NANOPORE"]
SAMPLE_ACCESSIONS: ['SAMEA113417017','SAMEA113417018'] # These samples exist in ENA. Your assembly is based on them. >>EXAMPLE: ["ERS15898933","ERS15898932"]
ASSEMBLY:
ASSEMBLY_NAME: "idx00_ex09_assembly" # Choose a name, even if your assembly has been uploaded already. Will only be used for naming assembly and bins/MAGs. >>EXAMPLE: "Northern Germany biogas digester metagenome"
ASSEMBLY_NAME: "idx00_ex09_asm" # Choose a name, even if your assembly has been uploaded already. Will only be used for naming assembly and bins/MAGs. >>EXAMPLE: "Northern Germany biogas digester metagenome"
ASSEMBLY_SOFTWARE: "MEGAHIT" # Software used to generate the assembly >>EXAMPLE: "MEGAHIT"
ISOLATION_SOURCE: "biogas plant anaerobic digester" # Describe where your sample was taken from >>EXAMPLE: "biogas plant anaerobic digester"
FASTA_FILE: "data/assembly.fasta" # Path to the fasta file >>EXAMPLE: "/mnt/data/assembly.fasta.gz"
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2 changes: 1 addition & 1 deletion examples/10_bins_mags.yaml
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Expand Up @@ -11,7 +11,7 @@ SEQUENCING_PLATFORMS: ["ILLUMINA"] #
PROJECT_NAME: "Project ex10 idx00" # Name of the project within which the sequencing was organized >>EXAMPLE: "AgRFex 2 Biogas Survey"
SAMPLE_ACCESSIONS: ['SAMEA113417017','SAMEA113417018'] # These samples exist in ENA. Your assembly is based on them. >>EXAMPLE: ["ERS15898933","ERS15898932"]
ASSEMBLY:
ASSEMBLY_NAME: "idx00_ex10_assembly" # Choose a name, even if your assembly has been uploaded already. Will only be used for naming assembly and bins/MAGs. >>EXAMPLE: "Northern Germany biogas digester metagenome"
ASSEMBLY_NAME: "idx00_ex10_asm" # Choose a name, even if your assembly has been uploaded already. Will only be used for naming assembly and bins/MAGs. >>EXAMPLE: "Northern Germany biogas digester metagenome"
EXISTING_ASSEMBLY_ANALYSIS_ACCESSION: # The accession of the assembly analysis that all bins/MAGs originate from >>EXAMPLE: "GCA_012552665"
EXISTING_CO_ASSEMBLY_SAMPLE_ACCESSION: 'SAMEA114745644' # The accession of the virtual sample of the co-assembly which all bins/MAGs originate from >>EXAMPLE: "ERZ21942150"
ASSEMBLY_SOFTWARE: "MEGAHIT" # Software used to generate the assembly >>EXAMPLE: "MEGAHIT"
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2 changes: 1 addition & 1 deletion examples/11_bins.yaml
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Expand Up @@ -11,7 +11,7 @@ SEQUENCING_PLATFORMS: ["ILLUMINA"] #
PROJECT_NAME: "Project ex11 idx00" # Name of the project within which the sequencing was organized >>EXAMPLE: "AgRFex 2 Biogas Survey"
SAMPLE_ACCESSIONS: ["SAMEA113417017"] # These samples exist in ENA. Your assembly is based on them. >>EXAMPLE: ["ERS15898933","ERS15898932"]
ASSEMBLY:
ASSEMBLY_NAME: "idx00_ex11_assembly" # Choose a name, even if your assembly has been uploaded already. Will only be used for naming assembly and bins/MAGs. >>EXAMPLE: "Northern Germany biogas digester metagenome"
ASSEMBLY_NAME: "idx00_ex11_asm" # Choose a name, even if your assembly has been uploaded already. Will only be used for naming assembly and bins/MAGs. >>EXAMPLE: "Northern Germany biogas digester metagenome"
EXISTING_ASSEMBLY_ANALYSIS_ACCESSION: "ERZ21942150" # The accession of the assembly analysis that all bins/MAGs originate from >>EXAMPLE: "GCA_012552665"
EXISTING_CO_ASSEMBLY_SAMPLE_ACCESSION: # The accession of the virtual sample of the co-assembly which all bins/MAGs originate from >>EXAMPLE: "ERZ21942150"
ASSEMBLY_SOFTWARE: "MEGAHIT" # Software used to generate the assembly >>EXAMPLE: "MEGAHIT"
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2 changes: 1 addition & 1 deletion examples/12_mags.yaml
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Expand Up @@ -12,7 +12,7 @@ SEQUENCING_PLATFORMS: ["ILLUMINA"] #
PROJECT_NAME: "idx00_ex12_proj" # Name of the project within which the sequencing was organized >>EXAMPLE: "AgRFex 2 Biogas Survey"
SAMPLE_ACCESSIONS: ['SAMEA113417017','SAMEA113417018'] # These samples exist in ENA. Your assembly is based on them. >>EXAMPLE: ["ERS15898933","ERS15898932"]
ASSEMBLY:
ASSEMBLY_NAME: "idx00_ex12_assembly" # Choose a name, even if your assembly has been uploaded already. Will only be used for naming assembly and bins/MAGs. >>EXAMPLE: "Northern Germany biogas digester metagenome"
ASSEMBLY_NAME: "idx00_ex12_asm" # Choose a name, even if your assembly has been uploaded already. Will only be used for naming assembly and bins/MAGs. >>EXAMPLE: "Northern Germany biogas digester metagenome"
EXISTING_ASSEMBLY_ANALYSIS_ACCESSION: # The accession of the assembly analysis that all bins/MAGs originate from >>EXAMPLE: "GCA_012552665"
EXISTING_CO_ASSEMBLY_SAMPLE_ACCESSION: 'SAMEA114745644' # The accession of the virtual sample of the co-assembly which all bins/MAGs originate from >>EXAMPLE: "ERZ21942150"
ASSEMBLY_SOFTWARE: "MEGAHIT" # Software used to generate the assembly >>EXAMPLE: "MEGAHIT"
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2 changes: 1 addition & 1 deletion setup.py
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Expand Up @@ -10,7 +10,7 @@ def run(self):

setup(
name='synum',
version='0.9.0',
version='0.9.1',
packages=find_packages(),
install_requires=[
'pysam>=0.19.1',
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