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updated qiime2 paths
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@farchaab
farchaab committed Aug 2, 2024
1 parent 709bbc1 commit 8b461f0
Showing 1 changed file with 90 additions and 44 deletions.
134 changes: 90 additions & 44 deletions zamp/rules/5_visualization/QIIME2_import.rules
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Original file line number Diff line number Diff line change
@@ -1,29 +1,29 @@
rule create_biom_from_count_table:
conda:
"../../envs/amplicons_r_utils.yml"
os.path.join(dir.envs, "amplicons_r_utils.yml")
container:
singularity_envs["r_utils"]
input:
count_table="{prefix}/count_table.tsv",
count_table=os.path.join(dir.out.base, "{prefix}", "count_table.tsv"),
output:
biom_count="{prefix}/otu_biom.biom",
biom_count=os.path.join(dir.out.base, "{prefix}", "otu_biom.biom"),
log:
logging_folder + "{prefix}/otu_biom.txt",
os.path.join(dir.logs, "{prefix}", "otu_biom.txt"),
script:
"scripts/create_biom_from_count_table.R"


rule import_count_table_to_QIIME2:
conda:
"../../envs/QIIME2-2020.02.yml"
os.path.join(dir.envs, "QIIME2-2020.02.yml")
container:
singularity_envs["qiime2"]
input:
"{prefix}/otu_biom.biom",
os.path.join(dir.out.base, "{prefix}", "otu_biom.biom"),
output:
"{prefix}/count-table.qza",
os.path.join(dir.out.base, "{prefix}", "count-table.qza"),
log:
logging_folder + "{prefix}/count-table.txt",
os.path.join(dir.logs, "{prefix}", "count-table.txt"),
shell:
"""
qiime tools import \
Expand All @@ -36,15 +36,15 @@ rule import_count_table_to_QIIME2:

rule create_visualize_count_table_QIIME2:
conda:
"../../envs/QIIME2-2020.02.yml"
os.path.join(dir.envs, "QIIME2-2020.02.yml")
container:
singularity_envs["qiime2"]
input:
"{prefix}/count-table.qza",
os.path.join(dir.out.base, "{prefix}", "count-table.qza"),
output:
"{prefix}/count-table.qzv",
os.path.join(dir.out.base, "{prefix}", "count-table.qzv"),
log:
logging_folder + "{prefix}.txt",
os.path.join(dir.logs, "{prefix}.txt"),
shell:
"""
qiime feature-table summarize \
Expand All @@ -55,11 +55,15 @@ rule create_visualize_count_table_QIIME2:

rule force_all_upper_case_rep_seq:
input:
rep_seqs="{denoiser}/{prefix}/dna-sequences.fasta",
rep_seqs=os.path.join(
dir.out.base, "{denoiser}", "{prefix}", "dna-sequences.fasta"
),
output:
rep_seqs="{denoiser}/{prefix}/dna-sequences_all_UPPER.fasta",
rep_seqs=os.path.join(
dir.out.base, "{denoiser}", "{prefix}", "dna-sequences_all_UPPER.fasta"
),
log:
logging_folder + "{denoiser}/{prefix}/dna-sequences_all_UPPER.txt",
os.path.join(dir.logs, "{denoiser}", "{prefix}", "dna-sequences_all_UPPER.txt"),
shell:
"""
awk '/^>/ {{print($0)}}; /^[^>]/ {{print(toupper($0))}}' {input[0]} > {output[0]}
Expand All @@ -68,15 +72,17 @@ rule force_all_upper_case_rep_seq:

rule import_rep_seq_to_QIIME2:
conda:
"../../envs/QIIME2-2020.02.yml"
os.path.join(dir.envs, "QIIME2-2020.02.yml")
container:
singularity_envs["qiime2"]
input:
rep_seqs="{denoiser}/{prefix}/dna-sequences_all_UPPER.fasta",
rep_seqs=os.path.join(
dir.out.base, "{denoiser}", "{prefix}", "dna-sequences_all_UPPER.fasta"
),
output:
"{denoiser}/{prefix}/rep-seqs.qza",
os.path.join(dir.out.base, "{denoiser}", "{prefix}", "rep-seqs.qza"),
log:
logging_folder + "{denoiser}/{prefix}/rep-seqs.txt",
os.path.join(dir.logs, "{denoiser}", "{prefix}", "rep-seqs.txt"),
shell:
"""
qiime tools import \
Expand All @@ -89,18 +95,24 @@ rule import_rep_seq_to_QIIME2:
# Build a new tree based on the filtered sequences
rule create_tree_in_QIIME2:
conda:
"../../envs/QIIME2-2020.02.yml"
os.path.join(dir.envs, "QIIME2-2020.02.yml")
container:
singularity_envs["qiime2"]
input:
"{denoiser}/{prefix}/rep-seqs.qza",
os.path.join(dir.out.base, "{denoiser}", "{prefix}", "rep-seqs.qza"),
output:
aligned="{denoiser}/{prefix}/aligned-rep-seqs.qza",
masked="{denoiser}/{prefix}/masked-aligned-rep-seqs.qza",
unrooted="{denoiser}/{prefix}/unrooted-tree.qza",
rooted="{denoiser}/{prefix}/rooted-tree.qza",
aligned=os.path.join(
dir.out.base, "{denoiser}", "{prefix}", "aligned-rep-seqs.qza"
),
masked=os.path.join(
dir.out.base, "{denoiser}", "{prefix}", "masked-aligned-rep-seqs.qza"
),
unrooted=os.path.join(
dir.out.base, "{denoiser}", "{prefix}", "unrooted-tree.qza"
),
rooted=os.path.join(dir.out.base, "{denoiser}", "{prefix}", "rooted-tree.qza"),
log:
logging_folder + "{denoiser}/{prefix}/rooted-tree.txt",
os.path.join(dir.logs, "{denoiser}", "{prefix}", "rooted-tree.txt"),
threads: 4
shell:
"""
Expand All @@ -116,15 +128,15 @@ rule create_tree_in_QIIME2:

rule export_QIIME2_tree:
conda:
"../../envs/QIIME2-2020.02.yml"
os.path.join(dir.envs, "QIIME2-2020.02.yml")
container:
singularity_envs["qiime2"]
input:
rooted="{denoiser}/{prefix}/rooted-tree.qza",
os.path.join(dir.out.base, "{denoiser}", "{prefix}", "rooted-tree.qza"),
output:
rooted="{denoiser}/{prefix}/tree.nwk",
os.path.join(dir.out.base, "{denoiser}", "{prefix}", "tree.nwk"),
log:
logging_folder + "{denoiser}/{prefix}/tree.txt",
os.path.join(dir.logs, "{denoiser}", "{prefix}", "tree.txt"),
shell:
"""
qiime tools export --input-path {input} --output-path $(dirname {output[0]})
Expand All @@ -133,15 +145,15 @@ rule export_QIIME2_tree:

rule create_visualize_rep_seq_QIIME2:
conda:
"../../envs/QIIME2-2020.02.yml"
os.path.join(dir.envs, "QIIME2-2020.02.yml")
container:
singularity_envs["qiime2"]
input:
"{denoiser}/2_denoised/rep-seqs.qza",
os.path.join(dir.out.base, "{denoiser}", "2_denoised", "rep-seqs.qza"),
output:
"{denoiser}/2_denoised/rep-seqs.qzv",
os.path.join(dir.out.base, "{denoiser}", "2_denoised", "rep-seqs.qzv"),
log:
logging_folder + "{denoiser}/2_denoised/rep-seqs_qzv.txt",
os.path.join(dir.logs, "{denoiser}", "2_denoised", "rep-seqs_qzv.txt"),
shell:
"""
qiime feature-table tabulate-seqs \
Expand All @@ -152,16 +164,33 @@ rule create_visualize_rep_seq_QIIME2:

rule import_taxonomy_to_Qiime2:
conda:
"../../envs/QIIME2-2020.02.yml"
os.path.join(dir.envs, "QIIME2-2020.02.yml")
container:
singularity_envs["qiime2"]
input:
"{denoiser}/3_classified/{classifier}_{tax_DB}/dna-sequences_tax_assignments.txt",
os.path.join(
dir.out.base,
"{denoiser}",
"3_classified",
"{classifier}_{tax_DB}",
"dna-sequences_tax_assignments.txt",
),
output:
"{denoiser}/3_classified/{classifier}_{tax_DB}/dna-sequences_tax_assignments.qza",
os.path.join(
dir.out.base,
"{denoiser}",
"3_classified",
"{classifier}_{tax_DB}",
"dna-sequences_tax_assignments.qza",
),
log:
logging_folder
+ "{denoiser}/3_classified/{classifier}_{tax_DB}/dna-sequences_tax_assignments.txt",
os.path.join(
dir.logs,
"{denoiser}",
"3_classified",
"{classifier}_{tax_DB}",
"dna-sequences_tax_assignments.txt",
),
shell:
"""
qiime tools import \
Expand All @@ -174,16 +203,33 @@ rule import_taxonomy_to_Qiime2:

rule create_visualize_table_QIIME2:
conda:
"../../envs/QIIME2-2020.02.yml"
os.path.join(dir.envs, "QIIME2-2020.02.yml")
container:
singularity_envs["qiime2"]
input:
"{denoiser}/3_classified/{classifier}_{tax_DB}/dna-sequences_tax_assignments.qza",
os.path.join(
dir.out.base,
"{denoiser}",
"3_classified",
"{classifier}_{tax_DB}",
"dna-sequences_tax_assignments.qza",
),
output:
"{denoiser}/3_classified/{classifier}_{tax_DB}/dna-sequences_tax_assignments.qzv",
os.path.join(
dir.out.base,
"{denoiser}",
"3_classified",
"{classifier}_{tax_DB}",
"dna-sequences_tax_assignments.qzv",
),
log:
logging_folder
+ "{denoiser}/3_classified/{classifier}_{tax_DB}/dna-sequences_tax_assignments.txt",
os.path.join(
dir.logs,
"{denoiser}",
"3_classified",
"{classifier}_{tax_DB}",
"dna-sequences_tax_assignments.txt",
),
shell:
"""
qiime metadata tabulate \
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